News from the BiSciCol team

The BiSciCol project is making great progress and perhaps we nailed down a great way to move forward with assigning globally unique identifiers to digital objects.  Read our latest news update on how we think we can 'GUID'.

Postdoc position available

A 1 year (extendable) Postdoctoral Associate position is available in my lab at the Florida Museum of Natural History, University of Florida starting as soon as possible.  This person will primarily contribute to the BiSciCol project and will work closely with a fantastic group of young developers. We are looking for a highly motivated and creative individual, ideally with experience in UI and RESTful web service development, in addition to Java programming (yes, Java is a must have!).  Please, email me if you wish to have additional information about this opportunity.

Species and Phylogenetic Nomenclature

DISCLAIMER: This post may inflame you if you are not a supporter of phylogenetic nomenclature, so my advise to you before you go on is don't ruin your day and skip reading it.  If you choose to read it, please keep in mind this is not a debate on the validity of the PhyloCode (that's a given to us). However, if you fundamentally share the philosophy at the core of phylogenetic nomenclature, then you may want to know what's going on among us proponents.

Last October, Brent Mishler (University of California, Berkeley), David Baum (University of Wisconsin, Madison) and I submitted a proposal to the International Society for Phylogenetic Nomenclature (ISPN) in order to remove all mention of "species" from the PhyloCode.  We provide justifications for this goal in a supporting paper (Cellinese et al. 2012). The proposal is currently being discussed by the ISPN Committee of Phylogenetic Nomenclature, and given our paper is also in review, this seems to be the right time to stir the pot a little more.

All proponents of phylogenetic nomenclature would agree that the PhyloCode is about naming clades, and removing ranks from nomenclature.  Yet, unfortunately there remain aspects in the current wording of the Code that are not about naming clades and that retain rank considerations.  These aspects all surround the traditional Linnaean rank of species. The PhyloCode currently states that "In this code, the terms "species" and "clade" refer to different kinds of biological entities, not ranks" (note 3.1.1.).  While the concept of species implicitly endorsed by the PhyloCode, that of de Queiroz (2007), does indeed assume that species and clade are distinct entities, this is not universally accepted by any means.  Many different species concepts are currently applied across the different biological domains (Mayden1997).  Some, like de Queiroz (2007) view species as lineages.  Others (e.g. Mishler 1999; Pleijel 1999; Mishler and Theriot 2000 a,b,c; Baum 2009) view species as ranked or unranked clades.  But this disagreement is not relevant to a Code of nomenclature that is (supposedly) rank-agnostic and concerned only with naming clades.  The debate over species concepts does not need to be solved for the purpose of naming clades under the PhyloCode.  Phylogenetic nomenclature can and should remain logically independent from the philosophical debate about species.  Therefore, the PhyloCode need not and should not anoint any particular species concept as the correct one.  By leaving the word “species” out of the entire document it will be clear that the PhyloCode is available to all systematists regardless of their views on the nature of species.

The PhyloCode as currently constructed works under the assumption that species are not clades, yet paradoxically brings species into the naming of clades in a couple of damaging ways.  One is by its current ruling (Article 10.9) that traditional species names should be disallowed for clades.  The current version of the PhyloCode, influenced by Dayrat et al.(2008), effectively applies special rules at the “species” level.  When a clade happens to approximate to a traditional species in content, the PhyloCode now mandates that that clade be given a new name, distinct from the traditional species name.  This is unlike the case when clades approximate in content to genera or families (etc.), in which case the Code strongly encourages the conversion of the traditional name into a clade name.  In this way, the PhyloCode establishes parallel nomenclatural systems for species and species-approximating clades.  We argue that this is illogical; as there are no ranks under the PhyloCode, there should not be an explicit or implicit rank of species.  Phylogenetic nomenclature should accommodate clades whose content is roughly comparable to current species (under whatever species concept).  We propose that the PhyloCode be modified to be neutral about species and thus to accommodate all users, including those who wish to be able to attach appropriate names to clades that approximate taxa at the traditional species level.

Another way in which the current version of the PhyloCode generates problems for itself  is that it allows species to be used as specifiers for clade names (Art. 11), and relegates the governing of species names to the traditional Codes (Art. 21). This means that the PhyloCode is not a freestanding system of nomenclature.  This is unwise; the PhyloCode should be independent and self-contained.  No rules in the PhyloCode should depend on rules in the traditional Codes, including rules for species names.  This is easily solved by requiring that specifiers under the PhyloCode be museum or herbarium specimens (physical reference objects, possibly Linnaean types at the discretion of the taxonomist) at all levels, never Linnaean binomials per se.  Linnaean species binomials are incompatible with phylogenetic taxonomy because they naturally imply the existence of a genus rank, and they are incommensurable with phylogenetic taxa because they are named using only one type (Cellinese et al. 2012).

Since its purpose is to name clades, any mention of ‘species’ in the PhyloCode should be removed.  We propose to streamline the PhyloCode to focus solely on rational procedures for naming clades with uninomials at any level including the traditional species level.  The rules governing names of clades at and around the traditional species level should follow exactly the same rules and recommendations as at higher levels.  To view the original proposals we submitted to ISPN click here. Also see the posting at Phylonames.

References:

Cellinese, N., Baum D.A., Mishler B.D. 2012. Species and Phylogenetic Nomenclature. Syst. Biol. 61: 885-891.

Baum D. A. 2009. Species as ranked taxa. Syst. Biol. 58:74-86.

Dayrat B., Schander C. , Angielczyk, K. D. 2004. Suggestions for a new species nomenclature. Taxon 53:485–591.

Dayrat B., Cantino P.D., Clarke J.A., de Queiroz K. 2008. Species names in the PhyloCode: the approach adopted by the International Society for Phylogenetic Nomenclature. Syst. Biol. 57:507-514.

de Queiroz K. 2007. Species Concepts and Species Delimitation. Syst. Biol. 56:879-886.

Mayden R.L. 1997. A hierarchy of species concepts: The denouement in the saga of the species problem. In: Claridge M.F., Dawah H.A., Wilson M.R., editors. Species: the units of biodiversity. London: Chapman and Hall, p. 381-424.

Mishler B.D. 1999. Getting rid of species? In: Wilson R., editor.  Species: new interdisciplinary essays. Cambridge: MIT Press, p. 307-315.

Mishler B.D., Theriot E.C. 2000a. The phylogenetic species concept (sensu Mishler and Theriot): monophyly, apomorphy, and phylogenetic species concepts. In: Wheeler Q.D., Meier R., editors. Species concepts and phylogenetic theory.  New York: Columbia University Press, p. 44-54.

Mishler B.D., Theriot E.C. 2000b. A critique from the Mishler and Theriot phylogenetic species concept perspective: monophyly, apomorphy, and phylogenetic species concepts. In: Wheeler Q.D., Meier R., editors. Species concepts and phylogenetic theory.  New York: Columbia University Press, p.  119-132.

Mishler B.D., Theriot E.C. 2000c. A defense of the phylogenetic species concept (sensu Mishler and Theriot): monophyly, apomorphy, and phylogenetic species concepts. In:   In: Wheeler Q.D., Meier R., editors. Species concepts and phylogenetic theory.  New York: Columbia University Press, p.  179-184.

Pleijel F. 1999. Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke (Hesionidae, Polychaeta, Annelida). Syst. Biol. 48:755-789.

TDWG 2011: my post-partum rant

Fresh out of TDWG 2011 I feel the urge to unleash the monster in me.  I think we had a great meeting overall, lots of new ideas, great symposia, good talks, bad presentations, the usual mix we get at any given meeting we go to but with the added bonus from across the pond.

I was heavily invested in the preparation of TDWG 2011.  I take full responsibility for everything that went well and (especially) bad.  I was indeed part of not so great decisions and in many cases I could have done or said something that I chose not to, and therefore I am not removing myself from any equation.  As part of the program committee, I learnt about the million of contraints (some of them ridiculous) that often enough prevent us from doing the right thing.

The Good: Lightening talks!  Having ADD that is indeed my favorite session of any meeting.  As I said it before, for me is just like watching commercials.  I can follow with excitement without losing focus.  Not to mention, some of these projects are so imaginative and inspiring.  However, the session was forced to be placed on Friday morning, last talks session of the meeting :-(  when many had already left or clearly overslept from the previous night's party. Obviously a bad choice and you would want to know why. Why the most creative session, populated by some of the youngest, brightest and most productive has to be relegated to last?
Answer:
a) We had a high number of symposia and contributed papers and pretty much every submitted contribution was accepted.
b) The conflicts with people giving talks in symposia or sessions and also having to participate in parallel interest group meetings was *unbelievable*!!
c) To make b) worse, some people were there from Monday to Wednesday (or Thursday) and all of their activities had to run during those days only. Apparently, everyone had to be accommodated
d) The damn Wednesday excursion!! That really ticks me off, because of all meetings I go to (and I go to way too many) this is the only one where it is believed that people need a rest after 2 days of heavy labor.  Are you kidding me??!!  I'll drop d) now and pick it up later.

Given all of the above, the only available spot for the most exciting session was Friday morning. And if we look into this a little bit more carefully, we clearly prioritized the 'established' efforts vs the new and upcoming. Well, if you left TDWG early I want you to know you missed the best Gumbo!

The Bad: The week-long ordeal. Realistically, this meeting could have ended on Thursday, or even earlier if properly trimmed of some of the unnecessary fat (won't go into details). To make matters worse, we have excursions in the middle of the week apparently because:

e) People get tired after 2 days of meetings (well, perhaps of each other) and they need a distraction (which makes me think I am not the only one with ADD).
f) Excursions are conducive of ideas exchange and foster collaborations (I am convinced that evening excursions to the bar are far more productive that any trip on any river).

Excursions are fun, but they don't need to be mandatory and having them in the middle of the week force people to stay longer even if they do not have any interest in a quick break/vacation (I am here to work, please!). Excursions need to be arranged immediately before or after the meeting and let's have the days to ourselves to work, because that is what I am using my funds for.

Additionally, we still have to find the best balance between contributing papers and group meetings. It's hard, really hard, but these decisions need to be made by a group of people evaluating all options, and not just an appointed person. For example, why not to give space to talks who are 1) providing significant contribution to standards development or their implementation and/or 2) are risky, exciting and promise to impact the current landscape.

The Ugly: The last session in TDWG (aka 'TDWG panel'). Felt more like 'The Last Tango in Paris' but badly directed and with a more glooming ending. I am not too sure about the purpose of this session and don't actually recall how it was conceived.  With no clear goal or focus, as it always happens, people voice their opinions in the absence of any framework. So, it is like asking the floor, 'what do you think we need now?'  Oh, wait! That was exactly what we were asked! The answer is a classic, of course.  We all need money.  We all want money.  We can't operate without money.  And when TDWG had access to a big chunk of money, primarily as I understand it to fix the infrastructure.....I can't finish this sentence, because I truly don't know what happened. What I do know for sure is that we still don't have a viable infrastructure.

I am always surprised to hear people talking about national and international funding opportunities as if we were entitled to receive them. Yet, when I visit the TDWG home page and I click the 'about tdwg' link I see no reason why we should be entitled to anything.  I raised the issues about having a vision because I want to be told why it is better for me to be part of this community.  Why do I need to operate within and not outside.  Makes me think of NESCent, for example, and how it fosters not just collaboration but real, tangible growth. At a *VERY* different scale of course, TDWG could take a similar approach and become the place where young people want to go to be supported, mentored, join existing efforts, contribute and develop their potentials to become the driving force of TDWG 20XX. Yet, how many students do we see at TDWG? We couldn't even establish a student paper prize for lack of young bodies.

This is what I see:

a) a totally dysfunctional infrastructure, but maybe that's not even the core problem.
b) an Executive with exceptional individuals, best intentions, and impressive commitment (and I really mean this!!) but inefficient as a group and without a collective voice.
c) Lack of pure, simple imagination.

I certainly don't pretend to have all the answers, but these are a few ideas/observations:

a) Make investments, no matter how small these are, but make them!  We do have some funds (we don't care how much!). Identify those promising ideas that would clearly benefit from a direct injection from the proof of concept stage to full implementation.  For example, pick from the lightening talks list, choose a couple of exciting projects (I would have a hard time to pick!). They don't have to be big investments.  Support grad students to join an exciting team. Start small but write a story to tell.

b) Identify an impeding bottleneck (as if we didn't have enough around to choose) and launch a challenge a la Rod Page but with a better prize ;-)  Students often enough crave just for the opportunity to be part of an exciting team.  Offer them that opportunity! Foster their growth by bringing projects and students together. For example, develop a contest, offer a little cash and an opportunity for the best to work with, lets' say, the Apple Core or Geomancer teams!

c) Reference implementations are crucial. Limiting TDWG to those projects that only feature TDWG supported standards (that was unfortunately suggested!) would be foolish. Be inclusive and promote adoption by showing the community why it makes a difference.

d) Do we have a well documented set of use cases developed within TDWG that support the need for all these standards? How do we keep track of progress besides telling each other what have we been doing in the past 12 months? Most of all, how effectively do we communicate needs, progress, successful implementations to downstream consumers? How do we make them care? There is a clear disconnect between consumers and developers. Funding agencies are very sensitive to that connection. A potential solution would be for each task group to develop and document use cases (at least one!) to justify their existence, not only for our own sake, but for the community sake. Preliminary data and prototypes should be then used to seek external funds to support the goals of the group. In other words, no use cases, no task groups (aka let's cut some of the crap).

e) It's not just about TDWG seeking funding. What about the people who make up the TDWG community.  If we think about it, we are actually pretty damn well funded individually or by project, but it doesn't trickle down enough to the task groups per-se. Maybe, next time we write a proposal we should stress and rethink of TDWG as the venue where at least some of our activities and project development will take place.

f) Promote Open Source! The suggestion was made this year (not by me) to have one (only one!) session featuring only open source projects but that was flatly rejected.  Why?!

g) Mini-hackathon are fun and worth the investment, especially when students are involved. They can be small, not expensive, and have an easy target (as in doable in 2-3 days). Task groups should generate ideas based on well defined goals (remember those use cases?) and help supporting this activities as much as they can.

The point I am trying to make is that TDWG is an umbrella organization and it is true that ideally injection needs to come mainly from the community. However, I see a community-organization co-dependency here as in a vicious cycle.  The community would be more supportive if TDWG were more relevant, more significant, made a larger impact. It's about what we can do for each other. It's the 'help me to help you' approach that I think needs to be more emphasized. Small investments can go a long way and set a different stage, build incentives, plant ideas and foster their growth. I think we can do way better and we should just stop whining about lack of funds. We do have funds. Many projects that are relevant to TDWG are funded indeed (do I have to name you a list?). Let's just be more creative on how we use them. Let's rework on the core TDWG activities, clarify the focus of these interest and task groups. And let's hear TDWG's voice. I am listening.

I am a member of TDWG and stubborn enough to stay one.

Postdoc in phyloinformatics available

A postdoc position in phyloinformatics is available at the Florida Museum of Natural History, University of Florida, to work on the integration of database developments and analytical workflows.  Experience with phylogenetic and workflow software (RaXML, MrBayes, Galaxy, Kepler etc.) and a background in data management is highly desirable. The successful candidate must have a PhD in biology, computer science, computational biology or related fields. Additionally, Java will most likely be your everyday cup of coffee.  The position is available for at least 2 years. Please contact me for additional details.

Lab openings

I have openings in my lab to work on the evolution, systematics and biogeography of preferably Campanulaceae and Melastomataceae (but I am open to other groups too).  If you are interested, contact me directly and apply to UF by the 31st of December, 2011.

Call For Participation: Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard

Synopsis

Many phylogenetic analysis results are published in ways that present serious barriers to their reuse in numerous research applications that would stand to benefit from them. While some of these barriers are well understood, such as issues with adherence to standard exchange formats, those centering on the associated metadata necessary for researchers to evaluate or reuse a published phylogeny have only recently begun to be articulated. One of the critical next steps towards formalizing these metadata requirements as a minimum reporting standard is to convene meetings of key stakeholder communities with the goal to identify information attributes  necessary and desirable for facilitating reuse, and to build consensus on their priority. To this end, we are holding a workshop at the 2011 Biodiversity Information Standards (TDWG) Conference to determine how a future reporting standard for phylogenetic analyses can best serve biodiversity science and related research applications.  We invite all interested colleagues to participate.

Background

The workshop of the Biodiversity Information Standards (TDWG) Phylogenetics Standards Interest Group held at the 2010 TDWG conference included a project focused on how to publish re-usable trees that can be linked into an emerging global web of data.  Through follow-up work, this led to the following tangible results:

1. An online draft report of the 2010 TDWG workshop [1], and a corresponding manuscript on best practices for publishing phylogenetic trees (Stoltzfus et al. in preparation);
2. An 2011 iEvoBio presentation on “Publishing re-usable phylogenetic trees, in theory and in practice” [2];
3. A lighting talk presentation and Birds-of-a-Feather gathering at 2011 iEvoBio, and
4. A survey group that explored barriers to re-use and developed plans for a survey

These activities have considerably clarified our understanding of the theory and practice of publishing re-usable phylogenetic trees: how many phylogenies are published each year, the (low) frequency of archiving, what archives and tools are available, what policies are in force, etc.  We have identified a number of barriers to re-use involving such aspects as technology, standards, culture, and access.  

Many of these barriers can be interpreted as a consequence of the lack of a community-agreed standard for what constitutes a well documented phylogenetic record.  In the absence of such a standard, trees are often archived as image files rather than in appropriate data exchange formats, and lack important accompanying information (metadata), such as externally meaningful identifiers, that would be needed to make them useful to others. The idea of a Minimum Information About a Phylogenetic Analysis (MIAPA) standard has been suggested [3], but so far there has not been a deliberate process to develop and disseminate a community standard.  Meanwhile, a number of systematics and evolution journals have begun to require archiving of the data underlying published research findings [4].  The emerging cultural shift in data archiving and sharing promoted by this policy change offers a unique window of opportunity to move ahead with the development and actual specification of a MIAPA standard.

Similar to other minimum reporting standards [5], the primary focus of a future MIAPA standard would be on defining a “checklist” of metadata information attributes that, at a minimum, needs to accompany an archived phylogenetic analysis, and to which standards values for these attributes would need to adhere. The key step in developing community consensus on these elements of the standard is to convene a series of meetings that collectively involve participants from all major groups of stakeholders who would be affected by such a standard, such as users, producers, publishers, or archivists of phylogenetic analyses.  To aid this process, the Phylogenetics Standards Interest Group is holding a workshop at the 2011 TDWG conference, with the goal to obtain consensus requirements and priorities for a MIAPA checklist for the purposes of biodiversity science, taxonomy, museum collections, and related research applications.

Goals and deliverables

The main goal of the workshop is to develop a shared understanding of the role that a MIAPA standard could play in facilitating re-use of phylogenetic analyses for the biodiversity science and related communities, and what the standard would need to specify in order to  best fill that role. Possible deliverables include

1. A draft set of information attributes that should or could be included in a provisional MIAPA checklist, with a level of consensus for each of them.
2. A database with use-cases based on exemplifying publications, that report phylogenies to elucidate a broad spectrum of questions relating to biodiversity science.
3. A refined MIAPA survey to be informed by biodiversity science cases for reuse.
4. A plan for further community engagement and consensus-building among biodiversity science stakeholders.

Workshop format

The workshop will start with a few presentations focused on (i) introducing MIAPA and its potential in facilitating reuse (J. Leebens-Mack); (ii) summarizing recent developments and current status of MIAPA-related efforts (A. Stoltzfus); and (iii) past experiences and resulting best practice recommendations on developing a minimum reporting checklist standard (D. Field). The rest of the workshop will be hands-on.  Participants in the workshop will break out into groups to address separate issues according to the anticipated deliverables and best practice recommendations.

The workshop will be 1.5 days in duration, and be held during the 2011 Biodiversity Information Standards (TDWG) conference, to take place Oct 17 to 21, 2011 in New Orleans, USA. (http://www.tdwg.org/conference2011/).  The workshop will start in the afternoon of Monday, Oct 17, and end on Tuesday. Oct 18.

How to participate

Participation in the workshop is open to everyone interested. However, space is limited, and we therefore ask that, if you are interested in attending, to please communicate your interest through the MIAPA discussion group [6]. This will also allow us to include you in pre-workshop planning. Since the workshop is part of the TDWG conference, participants will need to register either for the full conference, or for the days of the workshop.  

The organizers will provide an electronic venue for participants to share ideas and develop plans in advance of the workshop.  After the initial presentations, participants will self-organize into task groups.  

Organizers

1. Nico Celinese, University of Florida
2. Hilmar Lapp, NESCent  
3. Jim Leebens-Mack, University of Georgia
4. Enrico Pontelli, New Mexico State University
5. Arlin Stoltzfus, NIST & University of Maryland

References

[1] Whitacre et al. (2010). Current Best Practices for Publishing Trees Electronically. http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010

[2] O’Meara et al. (2011). Publishing re-usable phylogenetic trees, in theory and practice. Available from Nature Precedings<http://dx.doi.org/10.1038/npre.2011.6048.1>

[3] Leebens-Mack, J., T. Vision, et al. (2006). "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)." Omics 10(2): 231-7.

[4] Whitlock, M., M. McPeek, M. Rausher, L. Rieseberg, and A. Moore (2010). Data Archiving (Editorial). The American Naturalist 175(2): 145.

[5] Taylor, C.F., D. Field, S. Sansone, J. Aerts, R. Apweiler, M. Ashburner, C.A. Ball, et al. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology 26(8): 889-96. doi:10.1038/nbt.1411

[6] MIAPA discussion group: http://groups.google.com/group/miapa-discuss