BioLists Taxonomy
    The power of nature's names at your finger-tips.

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BIOLISTS' INNOVATIONS

Species-level ecological field data can only by collected once; repeat samples will contribute novel information. Good quality data will stay useful from now until we get through the sixth mass extinction event (MEE). Meantime, taxonomy is for communicating biodiversity related information and allowing it to be well used.  BioLists is designed to assist this by eliminating ambiguity in the use of formal taxonomic names and to allow Common Names to be used linked to the Scientific names. BioLists promises to speed up all uses of (raw) biodiversity data; the data will be taxonomically classified on collection, it will stay in use, and archived data will stay relevant and be directly usable.

NB:  BioLists "does the taxonomy": the database already contains enough names to quickly let users assemble classified species checklists simply by searching, and, where not internally available, keying names in. No matter what species names are assembled in a checklist, the names of related species will be brought closely together. Users then concentrate on adding species-related information - and analysing it, communicating it, merging it with other lists, and/or archiving it.
To these ends, BioLists is pioneering some new ideas, ones that do not conflict with formal taxonomy:

1.   TAXONOMIC STABILITY
2.   TIME-BANDS
3.   BIOLISTS (checklists)
4.   USING SPECIES' NAMES
5.   COMMON NAMES
6.   THREE-LETTER PROMPTS
7.   BIOLISTS' DEVELOPMENT
8.   BIOLISTS and LINNEAN TAXONOMY
9.   DISCUSSION

1. TAXONOMIC STABILITY
By design, and as an aid to stability, BioLists actions are informal: they do not influence the cutting edge of taxonomic researchTaxonomic stability has long been an ideal. But can it happen? BioLists, as an online database system, offers ways to temporarily stabilise taxonomy for the majority of users - the non-experts; potentially, that is everybody. Where two or more Scientific (Latin) names are in common use for the same species, one is selected pragmatically for use in the BioLists database. Synonyms (alternative "wrong" Latin names) will be available in BioLists in the near future and will be of use in searches for "mainstream" Latin names. Increased use of common names (as in 5 below) will lend stability to taxonomy, as when research-level names are changed, as frequently happens due to advances in understanding, especially of evolutionary theory.

Whereas BioLists is designed to promote an overall standard taxonomy, there is flexibility for users to edit in any new and alternative scientific names:

What you want is what you get, but, for the advantages of keeping your files compatible with all others, stay standard!


2.   TIME-BANDS
BioLists is a database system based on a time series of discrete, taxonomically classified indexes: each index is a total hierarchically classified list and serves as a named Time-band representing a selected mainstream taxonomy for one time period. Each new Time-band is an edited update of the preceding one, which then remains online unaltered
.
 
BioLists inaugural Time-band 2000 (T-b 2000) contains a full classification at Family level (n=8314 Families) and higher (n=1711 ORDERS, etc)(as at March, 2014). We expect that user sourcing of all remaining Genus-level names, and more species and their Vernacular Names will top up T-b 2000. Meanwhile, T-b 2010 will be added to spasmodically for promotional use. But when T-b 2000 is deemed complete, it will be finalised never to be changed. It will be used to produce a definitive T-b 2010 and this will be called T-b 2010+ or T-b 2011. These may be followed by T-b 2015. User demand will dictate future time spacing between updated Time-bands. If feasible, a T-b 2005 will be assembled.

Once a Time-band is effectively complete as a Classified dataset, it will have its never-to-be-changed sequence of coded biodiversity names "closed", and an updated version will be started by editing a copy of it. The last version to be "closed" will then be the "working version". Previous versions will not become redundant; they will continue to support projects using many texts, reports and other publications and notes from their time period. This stable series of Time-bands will permit simple updating, and back-dating, of users files from one T-b to any other.

In an earlier test series using my 1990s SKI-System (SKIS), updating has worked successfully, but with a small proportion of species records sidelined for individual attention.


3.  BIOLISTS (Checklists)
BioLists are taxonomic checklists made of species records taken from a single, dated, Time-band of the BioLists database. Species-related information may be added to any species record; the names and information can be edited at any time. Biolists can be exported as --.CSV files into your spreadsheet program for further editing, e-mailing, etc.


ORDER Names are coded into a conventional sequence in the BioLists System; as conventions change, with research findings, this sequence will change from one Time-band to the next. Family, Genus and species-level sub-sets may be in either alphabetic or a recognised taxonomic sequences. Currently (2014), when downloaded as a CSV-file, they will be put into alphabetic sequence. In future, taxonomic sequences in the BioList database will be retained, as an option. Starting now, the aim will be to avoid using convenient, but biologically meaningless alphabetic sequences. Computers are good at putting lists into alphabetic sequence, and this format has been increasingly used in recent decades. Within the BioLists database, taxonomic sequencing will be supported by sequence numbers: when files are downloaded, these numbers can be available for data management.

As exported, any two Time-band-compatible biolists can be merged in your spreadsheet by concatenating them into one file and then toggling the resulting file. It will be taxonomically (ie predictably), sequenced as in their Time-band source list. Note: this is a quasi-evolutionary sequence - eg Ferns before Flowering plants, then Worms before Molluscs, then Fishes before Birds. Within such major groups, Families are in alphabetic sequence within ORDERS; Genera are in alphabetic sequence within Families and similarly for species within Genera. Being predictable means that, with practice, you can scan BioLists to locate target species.

Biolists (checklists) are the BioLists System's version of taxonomic checklists consisting of classified annotated species records. The taxonomy for each biolist is derived from a single, dated, Time-band of the BioLists database. The intention is for species-related information to be added in the Notes column; every part of the record can be edited at any time.

Every biolist can be exported as a --.CSV file into your spreadsheet program in taxonomic sequence (in a more refined way than when toggled for within BioLists). Exported BioLists contain numbers representing your input sequence; if appropriate, toggle these to restore compatibility with your source material.


4.  USING SPECIES' NAMES
Striving to be fully scientific (but technically informal), names in the BioLists database are not followed by the names of their authors, or by references to published descriptions that established these taxonomic names. BioLists considers it would not only be wrong (unscientific) to add this information in an informal list, as is commonly seen (eg in online taxonomic lists and databases.
Rather, doing so could be destructive of taxonomic effort by suggesting what is not warranted and liable to lead to synonyms that then need to be dismissed repeatedly in publications. In this way, false accuracy can lead to the loss of taxonomic returns by requiring otherwise unnecessary effort by taxonomists - these being one of the most endangered species of scientist. Attributions belong as the end point in detailed literature searches along with examination of appropriate museum specimens: they should not be copied without this input. BioLists does not use attributions: instead, users accept names as being what they want to use.

Any use of a species' names, as with other taxonomic names, is simply a published opinion of one person at one time. For ORDER, Family Genus and species levels, there are formal guidelines and a general understanding of rules laid down for their use: these are in the various International Codes of Nomenclature - Zoology, Botany, etc. Opinions may seem a shaky base on which to found the single largest edifice in science - systematics, which includes taxonomy. Being just a Human construct, taxonomy's strength must come from the integrity of the overall structure as applied - conformity to a set of simple, basic, time-honoured rules. Currently this edifice is at risk of falling over for a variety of reasons. The proper use of species names is one central feature that is being misused and needs fixing, starting with how to recognise the "correct" name and who contributed to it. But this area of science belongs to research professionals (amateurs tend to increase the need for professional work) and does not involve BioLists. On the other hand BioLists may be of some use to the professionals.

A synonym offers an "opinion" of what was considered to constitute an actual biological species in terms of what previous expert authors had formally reported (in scientific publications). Informal reporting, while adequate for most purposes, is usually taken at face value. A revision recasts formal taxonomy by interpreting the intentions of previous authors in the context of up-to-date information and ideas about such species and evolution and taxonomy in general. (See an example below.) Opinions can differ for many possible reasons at species level, and major advances in biology can lead to major changes of opinion, most usually at higher taxonomic levels.

At any time several leading taxonomists may hold different opinions about the relationships of any particular species to all others; usually these differences result from various details of the interpretation of the possible pathways of evolution leading to the species in contention, or of wider issues. So the use of species names can be a minefield of trouble, especially when amateurs and parataxonomists get too deeply involved. (Their mistakes need fixing, usually slowing down the work of professionals.)

Conducting a revision of a group involves a group expert using new evidence to reinterpret published scientific descriptions and to re-evaluate the taxonomic merits of characters that have been found to be useful in describing such species in earlier research. Usually this will involve examination of relevant museum specimens and related scientific publications.

The taxonomy of Biodiversity is the fundamental basis of much of science, including Ecology and its many sub-categories, which, to be realistic including Agriculture and Medicine. Yet taxonomy is an unstable, delicate, evolving process. That just means it is alive, as it should be.

BioLists does not provide, or call for the naming of species authors or of formal synonyies: it does not approve of informal or un-researched attributions. Synonyms? Yes, these will be available in BioLists later.

Linking attributions to a species name in a scientific publication is a core function of research taxonomists. Doing so is often laborious because this should follow inspection of museum specimens as well as analysis and interpretation of associated taxonomic information.  All published taxonomic opinions and related data remain in contention for further assessment at any time in the future; all published taxonomic work may make important contributions to future revisions.

BioLists does not provide, or call for attributions because they are only valid if freshly researched and formally published in an appropriate scientific journal so as to be peer reviewed: such peer review would need to involve hands-on research. Otherwise the many existing errors in species recognition will continue to be propagated. Taxonomy is a formal legal system, so, unlike in other sciences, loose errors can be disruptive and need to be formally put right: usually this is done by posting new interpretations as freshly researched attributions linked to taxonomic names.

5.  COMMON NAMES
BioLists has identified Common Names as being underused and undervalued, yet with huge potential for assisting the aims of conservation, biodiversity education, ecology and natural history.  BioLists recognise four types of Common Names (two newly contrived), each with unique properties. These categories are:


 

SCIENTIFIC (LATIN) NAMES:           - 1.  SPECIES Names            "Genus + trivial"  combination = a "Binomen": 
                                                                                                   (= 'Genus + species epithet')       Binomena (Pl.)

COMMON NAMES: 
                        --  Commom Names  (informal)                    -  Common Names in a "loose sense" (s.l.)
                                                         - 2.  VERNACULAR Names - - - Any and all Language-based Common Names.

                        --  BioLists' Contrived (formal) Names          -  Common Names in a "strict (defined) sense" (s.s.).
                                                         - 3.  UTILITY Names  - - - Each a unique, Genus-based Common Name.

                                                         - 4.  TAG Names  - - - - - - Each a unique, specially selected Vernacular Name.

 

UTILTIY names and TAG names are species-level names supplied from the BioList database to your BioLists. Where you have keyed in additional species names, the Utility and Tag columns will be blank. These names cannot be entered by editing records into a BioList. After downloading a BioList, you can give your species unique Utility and Tag names.

UTILITY names are contrived by adding one or more leading letters of the trivial speices name to the Genus name, with an underscore between. One, two or three leading letteres may be needed to keep all names unique, but In large Genera within the full database, more than three characters can be needed. But instead of adding a fourth letter, etc, the system changes to using two letters followed by a numerical range.  Where this is needed, but not supplied in your BioLists, we suggest you define the numbers. As BioLists grows, we will to include all species for all possible Genera rather than having some Genera with just a proportion of its species.

TAG names are selected from the range of available Vernacular names. If missing in a BioList (because the species name was keyed in), users should improvise personal Tag names in place of the missing ones. Again, this problem will reduce as the database fills. Alternatively, in place of a missing Tag name, use the corresponding Utility name.

Vernacular names, in many and diverse languages, are part of Taxonomy, but usually with low and undefined status. Ideally, each common name should be used so as to mean the same as the scientific name of its species. But where the Latin names are not stable this is not possible. On the other hand common names can add stability as Scientific names change. BioLists adds a new category of contrived common name, the Utility Common Name (UCN); one unique UCN is created for each species. Another BioLists class of common name is the "Species name" - this puts on screen in one column the full species binomial name - the combined Genus and species couplet.

A design feature of BioLists is that it should interest children of about 12-years-old and up by being immediately useful. The prominence of common names should help, and the 3-letter prompt (see 6. below) should mean that spelling is not an obstacle. A new feature, already pioneered in my SKI-System will encourage anyone to invent and use common names - meaningful, fanciful or otherwise.

A single, fixed common name for a species is unworkable and even undesirable since common names can have their own useful properties. For example, when, as routinely happens, a scientific name is changed, for a surprising range of possible reasons, often its common names need not change, in which case they help maintain taxonomic stability. Maori language names have served this function in New Zealand (thanks due to Anthony Harris, Entomologist, Otago Museum, New Zealand).

Well known species typically have multiple common names, possibly in a number of languages and dialects. Whatever names people use count as common names and should be available to be used. Alternatively, some common names refer to different species in different places, or to many similar overlapping species. It's a taxonomic quagmire - so BioLists sorts these out in a range of options.

BioLists' initiates a new category of unique common name based on what gardeners often do: they apply a Genus name to some of its popular species. The BioLists' take on this is the "Utility Common Name" (UCN). It's an experiment to give every species (even ones only known to science) its own common name. Most UCNs will take the form "Genus_c", where "c" is one or more (as necessary) characters from the species/trivial name. Eg Viola riviniana, the Common Dog Violet can now be called Viola-r in an international context. But the form "Hawthorne_cun" for Crataegus cuneatus, the Japanese Hawthorn, might also be acceptable in some cases. I'm hoping UCNs will find general approval and utility. Some catalogues of standardised vernacular names used in industry (eg in fisheries) may be acceptable as UCNs. (This is being investigated; your comments please.)

Every species in BioLists has a "scientific" common name: the Genus + species names combined (Binomena). That is, lists of full Latin names appear in one column rather than two.

Where a suitable range of common names is present in the BioLists database, users may not need to select or refer to any Latin names while assembling a BioList - that's right, do your taxonomy without Latin names!

With BioLists, users can always key in their preferred common names, maybe so as to follow names they know well from a well-worn text. In schools, students can make up fanciful names...

Finally, common names from any one or two availablr Languages can be brought into any biolist (set these as the file is created).  By getting two, effectively you have a means of translating the names form one language to the other.

In all such ways, BioLists aims to make multiple common names easily available and usable - each linked to its scientific name.


6.  THREE-LETTER PROMPTS
Currently, 3-letter prompts are being used in searching for taxonomic names in the BioLists database.  As the database grows, various conventions will be used to maintain this 3-letter feature, but at some point 4-letter, or 5-letter prompts may be needed as standard.


With the ability to make use of common name, BioLists overcomes the "Latin language barrier" in searching its database. More so, it overcomes the total "language barrier" with the ease and simplicity of using 3-letter prompts for searching. These features should help to make BioLists easily usable in schools for pupils aged about 12 and over, and similarly wherever else local, hands-on, species-level natural history, ecology and conservation are being pursued.

Three-letter prompts are surprisingly effective, such that 4-letter or 5-letter prompts will not add efficiency proportionately, so a variety of strategies will be used to keep the searching of the BioLists database simple.


7.  BIOLISTS' DEVELOPMENT
Dissemination of biolists will be easy over the Web starting with edited biolists being exported as --.CSV files. By maintaining compatibility (as before editing), two or more exported --.CSV files will  be able to be merged and the taxonomic sequence
of their Time-band will be retained. With the basics workable, BioLists is well able to develop a range of ancillary functions; the main task will be to select and develop only the most useful ones.

In addition to dissemination of individual biolists by email, word about them may spread functionally. For example, if one city such as Dunedin, my home base in New Zealand, gets a 5000-species biolist representing its best known biodiversity, someone could simply edit it to start a new biolist relevant to a neighbouring city.

City biolists would be of use in local schools, libraries, for city planning and might be of interest in Sister City relationships. This could be one avenue for BioLists to go viral. In anticipation of that at some early stage (as a threat to its management), plans are needed as to how BioLists will develop - a gradual evolution prioritising only the most useful routes will be best.

At present, the most useful advance seem to be to solicit crowd data collection starting with Genus names for most remaining Animals, then Lower Plants and Fungi, then Micro-organisms. Next could come representative species from every Genus, these to be ones with common names that represent the Genus.

So far, possible new functions include involving synonyms (some are already entered in the database). Rather than seek new functions, I suggest making sure that computer programmers are never allowed free reign with the software: they must only do work pre-arranged with an in-touch taxonomist. Why? Computer programmers and software experts seem to act impulsively to fix anything and everything that they notice on screen: thinking does not seem to happen. BioLists works the way it does despite the best efforts of a highly competent software operator to move it towards "industry standards"; not doing so was difficult for him. Biologists should do their own programming: I wish I had bothered early on with SKIS.


8.  BIOLISTS and LINNEAN TAXONOMY
The BioLists system (possibly with my SKI-System added as a "front end") has the potential to restore a basic Linnean system of taxonomy and then evolve with it, but only if its active destruction is soon halted.


The Linnean system of taxonomy came under threat in the 1980s when the London Natural History Museum was swept with a vicious broom with shades of Thatcherism. The Management Board, which had followed its inaugural guidelines till then, was replaced with a smaller leaner, meaner Board of Governors who were almost entirely unacquainted with the aims and functions of any sort of museum, more especially a natural history museum. Having business ethics and money skills, but they lacked a foundation for comprehending the value and needs of a world-leading research facility and a source of fundamental information. Well, very few people have ever developed such skills. The result, soon half of the professional taxonomists were ousted from the world stage to become some sort of street-corner consultants.

At about the same time on the other side of the World, here in Dunedin, New Zealand, Otago Museum  which was once a world renowned Natural History Museum did the same - except here the destruction was taken to the limit, now possibly being reviewed. Destruction? Yes! No paid biological staff; no proper oversight of the the Natural history collections; no library, but soon it got a nice cafe and a cheery atmosphere.

Taxonomy remains in trouble on a widespread scale. I'll just refer to two deceitful policies - both promoted by academic taxonomists. One is a plan to put images online of each and every specimen from all significant natural history collections from around the world. The idea will seem acceptable to most people who are lacking a knowledge of history, natural history and collection skills - use online computer images instead of specimens for future taxonomic research. Good theory, but in practise, with the photographs being taken by people who lack the ability to handle taxonomic material without causing irreparable damage, and with scant knowledge of what images to take of specific identification features that would be of use to taxonomists, the specimen collections will be in serious risk of being rubbished to no advantage.

Secondly, a cry has gone out worldwide to name the last undescribed species. Again a seemingly good idea. But it is not - for the simple reason that it is impossible to do and will not achieve any worthwhile result. Estimations show that the task would take 300 years using as many taxonomists as are now working, and with today's biggest computers.

While science is fundamentally about communications of what we know, taxonomy is the key to opening the scientific literature about everything that we know about life and with all of the important clues about the future of life on Earth.


9. DISCUSSION
BioLists is a taxonomy-based system for managing environmental information. All necessary taxonomy (Nomenclature and Classification) is present in the system. Following that, it's not a computer system that uses complex and mysterious ways to makes biodiversity names look sexy while doing everything else that unfocused users might want. It operates very simply, based on a 4-digit code. Being taxonomically classified, all biolists conform to one overall taxonomic sequence. This will simplify using its biolists for biodiversity data collection and initial management of that information
.

The BioLists "Operating System", is as unusual as it is simple - it's a four-digit code, but capable of extension. The starting point was finding that computer systems cannot  handle complex hierarchical structures (well, not in 1982), or so I inferred at an early stage in my design of  the SKI-System (SKIS, a precursor of BioLists). My assumption was confirmed as correct when the Encyclopedia of Life project set out in the 1990s to put taxonomy online.  After some false starts the scheme settled on producing protocols to unite a range of existing online taxonomic databases; they had no useful results for years. The EoL end product, gives a good, but false appearance of a unified taxonomic system, but it acknowledges using over 50 independent databases. Despite a great appearance, its handling of the basics may be weak; maybe it is sufficiently flawed to have only a limited potential to assist taxonomy. A major question hangs over the scene - why has the international taxonomic community developed several fundamentally similar, but independent systems of Classification and Nomenclature. The result is confusion.

For BioLists, four-digit ORDER numbers have been allocated manually for Time-band (Year-version) 2000. For successive Time-bands, occasional number changes may be forced by parts of the Classification growing disproportionately as taxonomy evolves and new species get named, but nothing is critical.

The basic rule of Linnean Taxonomy is that scientifically published opinions are the basis of taxonomy including classification (and nomenclature). I still assume that no formula-based numerical code can replace the simplicity of the BioLists numerical code, and then evolve along with taxonomic innovations. So, the operational format of both SKIS and BioLists respect the need for taxonomic nomenclature and its word-based hierarchical structure to be superior to any contrived parallel structure such as a numerical listing. On the other hand, computer whiz kids can do anything - maybe. While BioLists is working: hands off. Stick to data syndication; genomic integration, grid computing, bioinformatics applications, and distributed sequence ontologies for people in white coats - hands off anything that's working for ecology and conservation. Please go and help molecular ecology and keep computer modeling in the laboratory.

From the standpoint of having researched and then implemented (as yet without their promotion) both the SKI-System and BioLists, I see some theoretical merit in some of the attempted alternative classification systems for Life - cladistics through to evolutionary genetics and chemo-taxonomy, etc, but I am convinced that these systems do not offer an alternative to the Linnean System in terms of being able to cope with data management for ecology and conservation, and they offer no permanent way of coping with future information management in real life including schools and local environmental groups in whose hands the future health of ecosystems lie. The alternatives may be theoretically interesting, but are otherwise unlikely to be of significant use in maintaining our civilisation in a healthy environment. Rather, they threaten to dis-inherit our civilisation from the basic scientific understanding of Life, and thus threaten our survival in civilised communities. More so, without us using new-found, ecology-based conservation scientifically, Human effort will find it impossible to reverse the ongoing ecosystem collapse - the one ecologists are calling the sixth mass extinction event (MEE) - the sixth in the long evolutionary history of Life. Without help, invasive species, farming and climate change will continue contributing to the present acceleration of species extinctions and thus ecosystem collapse.

I offer BioLists as a system capable of repairing the Linnean System, of being robust enough to evolve with coming changes in taxonomy, and to be usable by anyone interested in knowing what species is what, about what is known of them (c/o the scientific and related literature), and especially about the relationships between species. I believe that Linnean taxonomy will be particularly important in assisting expert taxonomists to assist parataxonomists and members of the general public working locally to amass the necessary field information to promote species-level ecology. This ecology will then form the basis of research and management strategies to be able to promote similarly detailed conservation efforts.

Species-level ecology, in the services of species-level conservation, is needed to adequately inform the public (especially the "educated public"), to inform people globally of the total reliance that our species has on fully functional ecosystems, that is, on multiple other species, to understand and fight against further degradation of ecosystems, and in the final analysis (if our species is to survive as "civilised" beings for more than a few more Human generations), to be able to repair ecosystems from existing species losses and the ongoing losses being wrought by invasive species, climate change as well as farming practices, both traditional and industrial. The latter is equivalent to mining our living resources.

Such repairs to ecosystems, even without any major attempts to reduce Human numbers, but usually involving massive reductions in cattle numbers and aggressive re-afforestation, might well be efforts that might seem to return Earth to pre-climate change conditions. But this measure alone is unlikely to lead to a return to pre-climate change climates, so even deeper ecological understanding will be called for - this being the only form of technical fix that might be reasonably safe, mostly by being much less destructive than the changes wrought as "progress", and by being somewhat ecologically reversible - if based on sound taxonomy.

 

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