Lead Article: How Many Uses For a Scratchpad?

The Sir Julian Huxley Lecture Joseph Felsenstein Inspirations Davide Pisani: a passion for Life’s Kingdoms

New Journal Biogeography & Systematics

Spotlight Book Reviews Francisco Ayala on Evolution vs. algae and mosses galore Creationism advances in biogeography gene regulatory networks The Systematics Association is Editorial committed to furthering all aspects of Systematic biology. It organises a vigorous programme biogeography, and gene of international conferences on Dear Readers, regulatory networks key themes in Systematics, Issue 30 of our Newsletter We report the imminent including a series of major begins with state-of-the-art launching of a new journal, biennial conferences launched in information technology and Biogeography and 1997. The association also its role in promoting web- Systematics, and draw supports a variety of training based approaches to the attention to a special discount courses in systematics and production, storage, exchange price (for members of the awards grants in support of and update of taxonomica SystAss) for the purchase of systematics research. data. In an elegant, step-by- the Royal Society themed Membership is open to step introduction to web- publication on the evolution amateurs and professionals with based applications, Roberts et of animals. interests in any branch of al guide us through the Finally, the speaker for this fascinating world of year’s Sir Julian Huxley biology, including microbiology Scratchpads. Lecture (2 July, 2008) is and palaeontology. Members are Davide Pisani (Maynooth) is Professor Joe Felsenstein, generally entitled to attend the the author of our Inspirations who will entertain us with the conferences at a reduced column, in which he reveals uncertainties that permeate registration rate, to apply for everything (well, almost phylogenetic reconstruction grants from the Association and everything) about his and novel statistical methods to receive the Associations fascination with the five (or to address them. newsletter, The Systematist and six, or seven) big domains of Sadly, this issue also marks mailings of information. Life. the final editorial effort by The debate on evolution vs. Ron Jenner. Ron’s style and creationism rages on in the spread of scientific and For information on membership, pages of the Spotlight article philosophical knowledge contact the Membership by Francisco Ayala, who remain unsurpassed. We wish Secretary, Dr G. Reid draws attention to the widely him well in all his future ([email protected]), diverging philosophical undertakings and we thank Department of Botany, Natural connotations embedded in him for his outstanding History Museum, Cromwell scientific and religious service to the Systematics Road, London, SW7 5BD, U.K. thinking. Ayala details the Association. content of a pamphlet The Systematist Newsletter of published at the beginning of the Systematics Association. this year by the National Academy of Sciences (USA) with the aim to promote The Editors Editors awareness of evolutionary (in Marcello Ruta particular) and scientific Dept. of Earth Sciences, (more in general) thought, and University of Bristol, Wills to counteract creationists’ Memorial Building, Queen’s argument in favour of the Road, Bristol BS8 1RJ, U.K. introduction of intelligent [email protected] design teaching in US public schools. Ronald A. Jenner We have four wonderful book reviews on subjects as Dept. of Biology and diverse as algae, mosses, Biochemistry, University of Bath, Bath BA2 7AY, U.K. [email protected] Cover illustrations: Joe Felsenstein

The Systematist 2008 No. 30 2 Getting Taxonomy onto the Web

Dave Roberts1, Simon D. Rycroft1, Irina Brake1, Kehan Harman1, Ben Scott2 & Vincent S. Smith1

1Natural History Museum, London; 2Dune Media Ltd. ountless words Encyclopedia of Life, which project EDIT has addressed have been written put information into a this and the result is a product on the desirability standard structure available as called a Scratchpad C of liberating web pages, or by the (http://scratchpads.eu). taxonomy from the provision of basic tools to In a nutshell, vault that is its allow people to create their Scratchpads are an intuitive native habitat, imprisoned on own web sites. This article is web-application, enabling obscure printed pages, and primarily about this second communities of taxonomists freeing it to take part in the approach. The first and most to build, share, manage and glorious information obvious hurdle is the lack of a publish their data on the web revolution (Godfray 2002, web site and, possibly, the (Fig 1). They are available as Wheeler, 2008). Turning this computer skills necessary to a hosted web site containing a desire into reality faces two manage one. In this day and suite of tools for taxonomists major challenges, one age computers and disk space and are a mechanism to technical and the other social. are cheap, so the provision of facilitate collaboration. a fairly substantial server able Scratchpads are easy to use,

Figure 1. The Scratchpad concept. Your data from a variety of sources are uploaded through the import tools and structured onto web pages.

Technical challenges to support many web sites is adaptable to taxonomists’ within the petty-cash range of needs, and provide powerful The technical challenge has most large institutions. On the tools for managing biological been approached in two other hand, software and the information. fundamental ways, either by technical skills needed to Taxonomists are good large collaborative projects manage websites are not to be at organising their data, but like Species2000 and had so easily: the EU-funded commonly lack a

The Systematist 2008 No. 30 3 in either nested columns in a spreadsheet or as a set of explicit parent-child The Sir Julian Huxley Lecture statements that can be directly imported. Alternatively, Professor Joseph Felsenstein classifications can be Department of Genome Sciences and Department of Biology imported via a web service University of Washington, Seattle, USA from ClassificationBank (a service provided by the Not the fly on the wall: Universal Biological Indexer can systematists cope with uncertainty? and Organizer – uBio, see http://www.ubio.org). Once Wednesday, 2 July 2008, 6pm imported, the classification The Linnean Society, Burlington House, Piccadilly, London becomes a menu (Fig 2) through which users can In reconstruction of molecular phylogenies, biologists have largely navigate the site. This shifted their emphasis from inferring a single phylogeny to being classification acts as a comfortable with statistical descriptions of the uncertainty about it, framework to link other data whether by using bootstrapping, jackknifing, or Bayesian posteriors. elements held within or Similar developments for morphological and behavioral characters have been slower in coming, as there have been fewer defensible external to the Scratchpad. statistical models available. The spread of statistical approaches to Additional Information (e.g. the comparative method is changing that. I will describe some new specimen records, images, developments in statistical models for discrete as well as continuous maps) loaded into a site are morphological characters. They can infer correlations of character stored in an underlying change across a phylogeny. However these inferences must database (see ‘The small necessarily be very noisy and uncertain. How will systematists and print’ below) and ‘tagged’ other evolutionary biologists cope with this uncertainty, if they with the appropriate taxon cannot look forward to further molecular sequencing reducing it? names so that they become Can we make use of the information without ignoring its findable. uncertainties or overreacting to them? If we cannot hope for an exact account of actually what happened in evolution, is despair Making it visible inevitable? Information can be explored through a series of ‘views’ straightforward way to link into existing standard content available for each content this information and display structures, such as type or aggregated on a single the results on the web. bibliographies or page for each taxon through a Scratchpads contain tools to classifications, or users can suite of panes (Panels – Fig import data from spreadsheet design their own content types 3). These are windows on the structures, from well- for specific purposes. underlying data, providing a structured text files, XML dynamic view of different output from databases, Getting data in content as the user browsers various image formats and The recommended, and through the taxon pages or as from various reference simplest, way to import more information becomes management packages, like information is to start with the available. The default set of EndNote, BibTeX and classification. panels (Fig 4) can be ProCite. This can be prepared augmented by the Scratchpad The data are imported

The Systematist 2008 No. 30 4

instructional video clips that guide owners through a variety of processes that they will need to customise their site. Each Scratchpad community may need to develop its own customised user help, although as yet few have found it necessary to do so.

The small print Scratchpads are built using a content management system (CMS) called Drupal (http://drupal.org), a popular open source CMS. It operates Figure 2. An imported classification of the Ciliates. The main under the LAMP architecture classification was published in 2002 and has been locally (Linux, Apache, My-SQL, modified. This one contains over 2000 names and took about 3 PHP) on servers at the Natural hours to make a well-formed text file from Dennis Lynn’s web page History Museum, London. (http://www.uoguelph.ca/~ciliates/classification/genera.html) The Scratchpads are backed- that could be imported directly into the Scratchpad up daily on a Tivoli Storage environment to act as a scaffold for further information. Manager. Each Scratchpad owner and the screen layout Making it citable also maintains an internal ‘roll can be adjusted, forming a According to some, “if you back’ facility to recover customised template through can’t cite it, its not science” individual pages without which information about the (http://www.editwebrevisions. disrupting the entire site. selected taxon will be info/content/meeting-report). Drupal contains a core set of displayed. Within panels that To cite a panels page there is functions that are recover multiple items, such a panel called supplemented by modules for as images and bibliographic ‘Authors/sources’ containing a specific purposes. Each citations, Scratchpad editors create citation button. Scratchpad is the can tailor the content by Pressing the button creates an responsibility of a single selecting which items to archived copy of the taxon named individual, a display. For instance, a search page with a permanent web maintainer, who controls for a parasitic taxon will often address pointing to this static access to the site and can recover images of the host version of the dynamic page allocate roles to other that are not the focus of the (Fig 5). When an author uses registered users. By default site. Those images can be this citation, the reader will be the roles are editor, blocked, thus panels provides able to see exactly what the contributor and authenticated an interface that allows users author saw. user. Normally editors can effectively to curate the create new pages, contributors underlying web of Learning how to do it can modify existing pages and information connected to a authenticated users can add page. The system has a collection of comments to pages and the

The Systematist 2008 No. 30 5

Figure 3. A panels page showing images, a text description and a citation. As more data are added to the database they would be exposed in these panels automatically. forum. The maintainer displayed. Users can also http://ww2.bgbm.org/EditDoc controls which pages are download all the data from umentRepository/Taxonomy2 visible to each category of their site as a My-SQL dump 1report.pdf) identified the visitor. should they wish to move it or need for taxonomy to move Scratchpads do not re-use it for another purpose. from an artisanal to an allow non-administrators to industrial process. To achieve install new modules, or to Sociological challenges such a goal taxonomists have write their own, because all to employ industry-style installed modules are Share and enjoy methods typified by the available to all Scratchpads production line (again the The idea of sharing data has and the development team comparison with physics and become commonplace in need to verify that any new molecular biology). There is many fields, such as physics module is compatible with no doubt that the craftsman- and molecular biology, where those already in use. Those built Daimlers of the early data are often generated by with the relevant skills are 20th Century were of far teams and there is a welcome to contact the team, better quality than the model- recognition that the analyses via http://scratchpads.eu/help, T Fords, but how many carried out on large data sets to discuss adding new Daimlers could be built and is far more powerful that functions to the system. Users how many people could those carried out on small do, however, have a great deal afford to use them? The issues sets. The EDIT Future of flexibility over the are volume and fitness for Scoping Group workshop that configuration of their site, its purpose. was held in December 2007 content and the way this is A first step that helped (published here:

The Systematist 2008 No. 30 6 several start-up communities data sets that collectively now be used for further work. has been to work on building form near complete Sharing such snippets through shared taxonomic bibliographies for a given a Scratchpad is a means to bibliographies. This has taxon. Exposing these on a make sure that their effort was already been done for Botany Scratchpad provides a simple not wasted while joining in a through the TL2 project activity that allows users to common goal within a site. It (http://tl2.idcpublishers.info) gain trust in sharing data with is notable that funding for and superseded by an up to their colleagues and builds infrastructure is available, but date list maintained by IPNI confidence in using the not for data generation (e.g. (the International Plant Names Scratchpad system. Similarly, iPlant Collaborative, Ledford, Index, http://www.ipni.org), many taxonomists have data 2008). Scratchpads facilitate but Zoology has not been so fragments that have been the accumulation of small fortunate. Many Scratchpad acquired for some purpose in quantities of data on an users have small bibliographic the past but which will never opportunistic basis.

The Systematics Association Publications Whose site is it anyway? Following the acquisition of CRC Press by Taylor & A key strategy in the project Francis, Systematics Association book production design was that Scratchpads operations have been transferred to the CRC Press are unbranded. Essentially offices in Florida. Members of the Systematics they are blank templates to be Association receive a 25% discount of all imprinted with each Systematics Association volumes published by community’s individual style. Taylor & Francis. Our aim was that Scratchpads would form a focal point All volumes published by Taylor & Francis/CRC where someone with a level Press should now be ordered via either the CRC of computer savvy could build Press offices or the CRC press office in London a site that the community as a (details below). The 25% SA members' discount is whole would own and nurture. claimed by using a promotion code, for details of This was well illustrated by this code please contact Alan Warren, Systematics one of the first Scratchpads Association Editor-in-Chief. that, while being created in London, was discovered by a ORDERING INFORMATION: laboratory in Norway who e- Via Website: mailed the maintainer and www.crcpress.com asked if they could contribute some of their data to the site. CRC Press UK The principal inhibitor 23-25 Blades Court, Deodar Road to people joining these teams London SW15 2NU stems from concern that they United Kingdom will not receive credit or recognition for their work, For more Systematics Association Publications both in terms of personal please visit: effort and arguably more http://www.systass.org/publications/ importantly in terms of measures that are used for career advancement. It is

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developed by Thomson-ISI.

The publication problem It is generally agreed that the publication of alpha taxonomy, especially descriptive taxonomy, is becoming increasingly difficult and, except for a few charismatic organisms, high- impact journals are not an option. Putting descriptions into the public domain on web sites is surely an inevitable end-point of the current trend. It is likely that the Zoological Figure 4. The default set of panels. Those in light grey are panes that Code will be modified to pull content from the web. All panels are configurable and recognise on-line publication other panels can be designed and added by the site manager. at the next review (A. important that we as a environments like the Polaszek, pers. comm). The research community devise a Scratchpads. These need to same issue will be discussed mechanism that measures use- become similar in application at the next Botanical Congress rates for individual’s to citation rates and journal in 2012. If communal web contributions to web-based rankings such as those sites become the new

Figure 5. The current result of pressing the create citation button. The url presented is an archival copy of the page at the time the button was pressed, so went it is used by an author, the reader will see the author saw. This is the first iteration of this routine and the output format is still under development.

The Systematist 2008 No. 30 8 monographs, i.e. the standard The basis for this argument is previously looked at the work for a particular that the debate and conclusion Scratchpads. In February the taxonomic group, for instance are available to everyone with Scratchpads attracted a total The Dipteran Site internet connection in one of 55,772 page-views, (http://www.diptera.org), then place, rather than being reaching a maximum daily there is a real risk that dispersed into increasingly peak of 3,690 on 26 Februari community behaviour will obscure paper journals. Once 2008. outstrip the strictures of the again it is imperative that codes leading to an anarchic those employing taxonomists In the pipeline and unregulated recognise the value of these The EDIT project will be nomenclature. But if there are contributions and they count funded until February 2011. encyclopaedic monographs towards career development. Scratchpad development is that are dynamic and active and on-going under the The small print authoritative exactly how rubric of ‘release early and much of a problem would that Data entered on a Scratchpad release often’, which means be? remain the property of the early adopters can request contributor under a Creative modifications, and influence The peer review problem Commons licence design, during the There is much concern that (http://creativecommons.org). construction phase, rather than web-publication, especially Recovering an individual’s being presented with a though a Scratchpad-type data from a Scratchpad has to finished product on a take-it- environment, can and will be negotiated with the site or-leave it basis. An happen without peer review. It maintainer, who would be immediate priority is the is apposite to observe that able to download the whole provision of an up-to-date very few books and site content and would then help system, which should be monographs are peer- need to separate the available by the time you read reviewed either, but they still individual’s contribution. this. In addition we are trying stand as definitive guides to to work out how to build a many taxa. Where are we now? distance learning package for It is also relevant that The first Scratchpad was a project under such active Wikipedia scored higher than introduced in March 2007. By development. the Encyclopaedia Britannica the end of February 2008 Currently the systems in an accuracy test (Giles, there were 55 Scratchpads work most readily with a 2005). We would argue that (rising) that had attracted 503 single classification that can the taxonomic community is registered users (rising) in be locally modified by best placed to monitor >28 countries, who have addition and deletion of decision-making in a collectively built more than content. An obvious taxonomic domain, so once a 110,000 pages (nodes). requirement is better site becomes a standard Collectively the sites attract management of synonyms, reference work for a particular approximately 200 unique which currently are included, group, that same community visitors per day (rising), who but not part of the taxonomy are best placed to object to each spend an average of 8 proper, making synonymised controversial decisions and minutes (rising) looking at an content less readily accessible. the site forum is the best place average of 8.7 pages(rising) The create citation to argue the pros and cons in each. Of these visitors 54.6% button, discussed above, order to achieve consensus. (falling) have never needs to be extended to

The Systematist 2008 No. 30 9 individual components, so of computer skill. If you are that downloaded components not comfortable with building from a web page take their and maintaining databases, attribution details and licence then it is unlikely that you requirements. will be able to get the best EDIT’s Workpackage from a Scratchpad at this 5 (http://wp5.e-taxonomy.eu) stage and you should wait for are developing a Common additional training material. Data Model that will provide An ideal situation would be powerful data management for someone with computer services. WP5 are also expertise to exist for each working on a bibliographic taxonomic or regional interest services (from Ex LIbris) that group who could take on the will search for web- responsibility for managing availability for cited articles. the site. The data entered into standard Scratchpad structures References could be exposed to data Giles, J. (2005). Internet harvesters like GBIF and EoL, encyclopaedias go provided the data owners head to head. agree. We are currently Nature, Lond 438, writing routines that will 900-901. make such data harvesting an automatic, background task Godfray, H. C. J. (2002). when it is activated by the Challenges for site’s maintainer. taxonomy. Nature, Lond 417, 17-19. Your own, your very own ... Ledford, H. (2008). $50 To apply for a Scratchpad you million simply complete the cyberchallenge for application form plant scientists. (http://scratchpads.eu/apply). Nature, Lond 452, You will need a name and 793. mission statement (200 words Wheeler Q.D. (2008) The that describes your site’s New Taxonomy. scope) and, if you have one, a The Systematic domain name that will point Association to your site. We will provide a Special Volume site to any legitimate group of Series 76. CRC taxonomists or taxonomic Press, Boca Raton. project. Although we are working to make the administration of Scratchpads as easy as possible, there is a requirement for a certain level

The Systematist 2008 No. 30 10 interest in zoology after reading King Solomon’s Ring, Inspirations in my early teens. However, my interest in evolutionary biology developed only Davide Pisani to study ethology. It was only during my university years. during my undergraduate Laboratory of Evolutionary Still, to some level, I always Biology, The National University years that I was introduced to wanted to be a scientist, and of Ireland, Maynooth the study of evolution. As part particularly a zoologist. I [email protected] of our General Zoology often ask myself what might course, we were advised to have triggered this interest, read Steve Gould’s Wonderful and sometimes I think it Life (which had just been might have something to do translated into Italian – it was with having watched the TV 1991). It was Gould’s serial “Born Free”, which was Wonderful Life that triggered on air in Italy in the mid to How would you summarize my interest in the study of late seventies. I still remember yourself in the form of a evolutionary biology. I that as one of my favourite title of a scientific paper? completed my studies in childhood shows, but of A chimeric multicellular ethology: my undergraduate course it might well have organism, with a complex life thesis (and my first scientific been that I liked it because it cycle, from a mesophilic article) focused on the was about African wildlife. terrestrial environment of behavioural ecology of the Nature or Nurture? Probably planet Earth. Of course, Italian Ruin Lizard Podarcis both. chimeric here would stress the sicula. For my PhD, I wanted symbiotic nature of the to specialise in evolutionary What are the main goals of eukaryotes, and their dual biology, and particularly in your research, and what is (Archaebacterial and phylogenetics. I thus moved your future ambition? Eubacterial) ancestry. to the University of Bristol, The main goal of my research where I obtained my PhD in is to help uncover the truth Summarize the when and theoretical phylogenetics about the history of life on where of your academic under the supervision of Prof. Earth, and that is also my career Mike Benton and Dr. Mark ambition. It is amazing how I did my undergraduate Wilkinson. I am now a many commonly held studies in Italy, at the lecturer on bioinformatics and concepts about the origin and University of Parma. I chose head of the Evolutionary early evolution of cellular life Parma because at that time, Biology Laboratory at the are questionable if not plain Prof. Danilo Mainardi, Italy’s National University of wrong. Take the Tree of Life most prominent ethologist, Ireland, Maynooth (which is for example. We often refer to was the head of the one of the Dublin-area it as if we were talking of a Department of Biology. My universities). well-supported theory, yet the introduction to biology was data supporting this through the books of Konrad When did you decide to hypothesis are scant at best. Lorentz (particularly King follow the career path you People of the like of Lynn Solomon’s Ring), and when I are on now? Margulis, Jim Lake and Bill enrolled at university I wanted I certainly developed an Martin (for example) would

The Systematist 2008 No. 30 11 say that the “tree of life” is also had involvement in the administration, I work in actually not tree-like because arthropod research for quite a the lab (or I should say in the origin of the eukaryotes while. I proposed the front of my computer). I am coincided with a symbiotic Myriochelata hypothesis, and lucky that most of my event that led to the “fusion” I am still working on this research is computational, so I of an archaebacterium and a group. More generally, current can often set up analyses in eubacterium. The problem is studies in my laboratory focus the evening and let them run that I think they are right. on prokaryote and eukaryote during the day while I am That is, eukaryotes are phylogenetics, the origin of busy teaching and/or carrying chimeric, and the tree of life animal phyla, and arthropod out administrative duties. is actually “a Ring of Life” – interrelationships. to use Jim Lake’s evocative I think all living How many people are there definition. The implications, organisms are interesting, but in your lab? of this, from the phylogenetic I particularly like the Currently I have only one standpoint are huge. extremophilic prokaryotes, PhD student in the lab, Eukaryotes are the only because everything that can however a postdoc and a monophyletic “domain” of grow optimally in boiling second PhD student will start life, while both water intrigues me, and the during the summer. This Archaebacteria and Eubacteria eukaryotes, because of their winter there were five are paraphyletic with dual ancestry and their undergraduate students in the reference to the eukaryotes. I fascinating chimeric nature. lab, while this summer two think all this is just amazing! undergraduate students will How many hours per week join the lab for 10 weeks. What organisms have you do you work? These two students are, worked on, and which are I guess these days I probably respectively, from Japan and your favourites? work an average of 50 to 60 Uruguay and will be in During my academic career I hours per week. It is difficult Ireland to participate in a have been studying a variety to say. I used to work longer Summer School of Molecular of organisms. Of course, hours, but last summer my Evolutionary Research that I having a background in first child (Olmo – which is have organised together with theoretical phylogenetics has the Italian name of the elm my colleague James helped me to become a fairly tree) was born, and of course McInerney (also from flexible phylogeneticist. My my lifestyle has changed quite Maynooth). The school is earliest studies focused mostly drastically. funded by Science Foundation on fossil vertebrates. I am still Ireland, will initially run for involved in the study of What percentage of time do three years, and will admit ten vertebrate palaeontology, but you spend on each of your undergraduate students per these days I engage in fossil- different responsibilities? year (which will join various based research through Since I became a lecturer my research groups in collaborations with administrative and teaching Maynooth). palaeontologists at the duties have increased University of Bristol. I have significantly. This winter most What gives you the most also worked on sponges, of my time was spent teaching satisfaction and frustration caecilian amphibians, or supervising undergraduate in your job? echinoderms, prokaryotes and students. When I am not Satisfaction is the discovery, unicellular eukaryotes. I have teaching, and I am done with finding out something

The Systematist 2008 No. 30 12 unexpected. That is thrilling. Naturalists. Of the three, the Lake’s work taught me about Administration is frustrating. I one that influenced me the versatility. In fact, I think Jim also like to teach quite a lot, most was Gould’s Wonderful Lake is quite an exceptional and I found supervision of life. Note that I disagree with phylogeneticist from this PhD students quite rewarding. most of Gould’s ideas. What I point of view, one who has think is great in Wonderful been able to make significant Do you have any Life is that it is hugely contributions to both international inspirational, no matter theoretical (e.g. Lake’s collaborations? whether you agree with Gould Invariant, Paralinear I have many collaborators and or not. When you read distances, Conditioned I think that today you cannot Wonderful Life, you feel that Reconstruction, Top-Down do science without sense of awe that you get Rooting) and applied (e.g. the collaborators (national and when reading the great Ring of Life hypothesis, the internationals). I think this is novelists, like Twain and his Eocyte hypothesis, the one of the great things in Adventures of Huckleberry Ecdysozoa hypothesis, the science: it is a multinational Finn, or Kerouac and his On Complexity hypothesis) collaborative effort. If I can the Road. After you read those phylogenetics and use a sport metaphor, I would books you almost feel evolutionary biology. Some of say that science is like rugby: compelled to hit the road, his papers, especially those it unites people, even when if when you read Gould you relating to the Ring of Life they are in competition. almost feel compelled to and to the Complexity Currently, my main become an evolutionary hypothesis, are key to most international collaborators are biologist. There are many modern discussions on Mark Wilkinson, from the other scientific (and non- prokaryotic evolution and the NHM in London, Mike scientific) books and papers origin of the eukaryotes. Of Benton from Bristol, and that I found in some way course, the Ecdysozoa Kevin Peterson from inspirational. The work of hypothesis is central to any Dartmouth (USA). authors of the like of Kimura, modern discussion on the Woese, Mayr, Cavalli-Sforza, evolution of animals. Finally I Is there any paper or book Simpson, was certainly think that some strictly that has been very inspirational. However, I think speaking non-scientific influential for your that I should particularly authors also deserve a thinking? mention here two authors mention here, as they strongly It depends what you mean which I particularly like: influenced my thinking. These with “thinking”. I was urged George Estabrook and Jim are (in random order): Cesare to become a biologist after Lake. Pavese, Henry David having read Konrad Lorentz’s Reading George’s Thoureau, John Steinbeck, King Solomon’s Ring, and an papers taught me about Jack London, Pablo Neruda, evolutionary biologist after mathematical rigor. Notable Jack Kerouac, John Stuart having read Steve Gould’s are his early seventies papers Mill, Carlo Rosselli, Gabriel Wonderful Life. So it is clear where, together with Garcia Marquez, Mark Twain that these two books had a McMorris and others, he and Ernest Hemingway. very strong influence on me. defines the concept of A third books that had a very cladistic character within a Who was the most powerful influence on my life purely mathematical important mentor in your was Nico Tinbergen’s Curious framework. Reading Jim career?

The Systematist 2008 No. 30 13 Mark Wilkinson, probably the in our genomes are of can generally help my best mentor you can hope for. eubacterial origin (a- collaborators decide what is proteobacterial), rather than of the best strategy to analyse a How many scientific archaebacterial origin. This of given data set. publications do you have? course is an observation of I published 26 peer reviewed general relevance as it has to What skills do you think a scientific publications since do with the nature of successful researcher in 2002. eukaryotes and therefore with your discipline must the nature of humanity. possess? Could you nominate any of I think the most important your discoveries or papers Is there a particular skill is multidisciplinarity. as the most important one, contribution you generally Today, it is not sufficient to or the one (or several) that bring to collaborative understand the general you personally like best? papers? biology of the organisms you This has to be the 2007 I think it is the ability to deal study, you need to understand Molecular Biology and with data sets that most other molecular biology (as data are Evolution article on the origin researchers would just mostly molecular), you need of the eukaryotes. There are consider to be impossible to skills in computational many reasons why I think that analyse. I can easily handle biology and computer paper was important. First we data sets of hundred of taxa sciences (to analyse the data), performed the largest and thousands of genes. If you and an understanding of the phylogenomic analysis to assume an average gene Earth history (to place your date, analysing almost 6000 length of 100 amino acids, it results in a sensible geological genes for more than 180 means that I can easily deal framework). I think that very organisms. Note that previous with data sets of 200 or more often the limiting factor for phylogenomic studies rarely species and 600,000 systematists is the lack of analysed more then a few characters. Currently, for computational skills. hundred genes. So I think that example, I am working on a Unfortunately, the days of the with this paper (which was data set of 450 eukaryotic menu driven software are co-authored by James species and 3.6 million over. Today, you need to be McInerney and James Cotton) sequences. Performing an all- able to compile software we reset the standards of what versus-all BLAST analysis of (even if you did not write the should be considered a this data set (which is code). You need to learn how phylogenomic analysis. necessary to identify protein to automate processes in a Secondly, this study finally families) took 1600 days UNIX environment (you need and unequivocally showed (CPU-time). That is, if I was to learn Shell scripting), and that the supertree methods (a running this analysis on a quite often, you need to write class of methods I have been desktop PC it would have some code yourself (for working on since I was a PhD taken more then 3 years. Yet, I example in PERL or student) can be extremely completed it in just over a PHYTON) to carry out tasks useful phylogenomic tools. week by using a simple divide for which there is no software Thirdly, and most importantly, and conquer approach and available. we showed that the eukaryotic distributed computing. genomes are chimeric, and Besides, of course, I am a Do you have any tips for that contrary to common theoretical phylogeneticist by students aspiring to a career knowledge, most of the genes training, and that means that I like yours?

The Systematist 2008 No. 30 14 Never give up. The postdoc generally a good idea to think resonate. To the uninitiated, it years in particular can be very about your projects from two can be difficult simply to hard, you will be moving points of view. Think of what disentangle where one from town to town, perhaps you want to do, but think also individual alga ends and from one country to the other, of what the taxpayers might another begins. To the veteran without much certainty about want from you, because of algal sampling, trouble your future. This is very ultimately, they are your might lie in teasing apart frustrating, but the first years employer. So, always ask phenotypic plasticity from after your PhD are essential, yourself: in what way can I species diversity. To experts, so concentrate on the present contribute to the good of the trying to tie various algae and do not worry too much society? This is a key together in stable and natural about the future. You can question that sometime systematic frameworks has always get out of the scientists forget to ask presented problems at nearly academia. Choose your post themselves. If you can come every taxonomic rank. Thus, docs wisely, you need to up with ideas that make your algal enthusiasts at all levels publish as many paper as work of relevenace to society, will find “Unravelling the possible, and in good journals. you will significantly increase Algae” a useful resource, Try to join a group with a your chances of obtaining especially those hoping to high output of published funds, and I guess in the end keep pace with the dizzying papers, and with many you will always feel better changes brought on by the use international collaborators. with yourself. of molecular characters in The latter point is very algal systematics. For most important because through major algal groups, this these collaborators you are Book Reviews volume provides a solid quite likely to be able to find history of systematic your next postdoc. classification, a detailed Unraveling the Algae. The explanation of how recent What do you think are Past, Present, and Future of molecular investigations have currently the greatest Algal Systematics impacted historical views, and impediments to achieving a a thoughtful discussion of the successful career in your Brodie, J. & Lewis, J. (eds.). additional challenges field? CRC Press, Taylor and remaining for researchers in I think funding is our major Francis Group, Boca Raton, the problem. Obtaining funds is FL., field. often very difficult, particularly for young Systematics Association researchers, but I also think Special Volume 75, 402 pp. that this is not necessarily a ISBN: 9780849379895. fault in the system. Scientists Hardcover: £65.99 should be more aware that Euros (or Pounds) are not For anyone who has spent In their introduction, from heaven; they come from time in a diverse intertidal editors Juliet Brodie and Jane the taxpayers’ pockets. community, trying to find and Lewis explain that the book is Accordingly, scientists have identify the individual algae divided into thematic sections; the moral duty to be careful present, the title of this three introductory chapters with this money. It is thus collection certainly should intended to frame the complex

The Systematist 2008 No. 30 15 New Journal Although it does provide a nice discussion of current and Biogeography & Systematics likely future controversies, a New Journal for Taxonomists and Biogeographers such as DNA barcoding, it Under the auspices of the Systematic and Evolutionary Biogeographical also offers the most concise Association (SEBA – http://www.uac.pt/~seba/) a new journal, and eminently readable Biogeography & Systematics, is to be launched later this year; a call for papers has already been announced general overview of the major (http://www.uac.pt/~seba/?q=taxonomy/term/21). The journal is primarily methods that have reshaped a an online production specialising in, but not exclusively, larger good deal of the systematic monographic studies in biogeography and systematics, as well as history, framework covered in the theory, methodology and epistemology. While the journal will consider book. Given that much of the papers that focus solely on a particular taxonomic revision of a group, preference will be given to those contributions that provide a “unravelling” discussed biogeographical analysis of an area or the taxon in question. throughout is based on Biogeography & Systematics will initially have 20 copies of each molecular data, I’d number printed to be deposited in accessible libraries around the world. recommend diving into this Thus, the journal will conform to publication requirements as outlined in chapter first. the International Codes of Zoological and Botanical Nomenclature. The reasons for starting this journal are many but the driving force As for the three formal is the desire to provide a forum for taxonomists whose studies of a introductory chapters, Charles taxonomic group include biogeographic analysis and interpretation and Delwiche does a particularly require a greater page number so that primary data and analyses can be effective job (chapter 2) of included in the body of the paper. Usually, these kinds of studies require summarizing complex issues new taxa to be named and, after biogeographic analysis, the nodes on a cladogram(s) require proper identification. Many systematics print journals related to how plastid will now no longer publish primary data, relegating such details to online endosymbioses have shaped supplementary material. The reasons and consequences of such policies algal diversity, and outlining were outlined in a recent paper by José Padial & Ignacio De La Riva, the remaining areas of situation eloquently captured in their title (‘Taxonomy, the Cinderella of controversy. This chapter science, hidden by its evolutionary stepsister’, Zootaxa 1577: 1—2, 2007). Their concluding sentence runs: “If taxonomies cannot be included in the certainly fulfils the mission main body of phylogenetic or biogeography-oriented papers, they should be intended by the editors. The published elsewhere as full peer-reviewed articles”. That elsewhere is following two chapters might Biogeography & Systematics. be better sampled as dessert than as appetizers. Chapter 3 1 2 3 David M. Williams , Malte C. Ebach & Dalton Amorim by Cavalier-Smith reviews 1 where various algae fit on the Department of Botany, The Natural History Museum, London, UK “major branches of the tree of 2 International Institute for Species Exploration, School of Life Sciences, life.” It is chocked full of Arizona State University, Tempe, AZ, USA details and nomenclature on 3Dalton Amorim, University of São Paulo, São Paulo, Brazil numerous eukaryotic taxa, and issues related to algal systematics) might want to advances some fairly systematics, a 13 chapter walk rearrange the sampling order complicated and often through the various algal just a bit. I would recommend controversial phylogenetic phyla and, finally, two beginning at the end, with scenarios. Many readers will chapters that look to the “Algal molecular systematics: be better able to follow the future. There is no doubt a review of the past and arguments, and come to their some logic to this structure, prospects for the future” own well-reasoned but many readers (certainly (chapter 18) by Medlin, conclusions, once they have any novice in algal Metfies, John and Olsen. absorbed information about

The Systematist 2008 No. 30 16 the diverse algal groups state of algal systematics foreseeable future. contained in the rest of the across all these phyla is that For many algae book. Likewise, in chapter 4 molecular characters have particularly microalgal phyla, David Williams compiles an produced the most satisfying comparably reliable extensive and scholarly results in groups with the ultrastructural characters have algal enthusiasts at all levels will find not been available, and a “Unravelling the Algae” a useful resource, especially number of chapters covering those hoping to keep pace with the dizzying changes these groups come to brought on by the use of molecular characters in somewhat less satisfying or at algal systematics. least definitive conclusions. For example, Robert history of diatom systematics, richest histories of systematics Anderson provides a clear and which makes an excellent based on cellular and thorough review of the companion to the later chapter ultrastructural features. For interplay between structural on diatoms (chapter 13) by example, chapters 7 by and molecular characters in Mann and Evans. However, Pröschold and Leliaert and 8 chrysophyte and synurophyte this history is presented to by Hall and Delwiche algae (chapter 15), and asserts frame a polemic against demonstrate the power of that it is unclear as yet how to paraphyletic groupings in molecular phylogenies when resolve discord between the classification, an argument used to test, reinforce and two. As he puts it, “The readers will more easily digest expand the rigorous eventual resolution of after first acquiring the solid systematic framework conflicts between morphology working knowledge of algal developed from flagellar and molecules will also systematics presented in architecture and patterns of require careful reexamination subsequent chapters. cell division. Likewise, in of the organisms, their Chapters 5 through 16 their discussion of red algal various life forms, and their are devoted to the current systematics, Maggs, sexual reproduction…” Even state of knowledge in nearly Verbruggen and de Clerck well-resolved branching all major groups of algae; the (chapter 6) provide a orders leave a great deal to be only notable exception is the compelling example of how desired, if they do not help to Glaucophyta, for which fairly combining classical systematize and understand little is known in any case. observations on fertilization the underlying biology of the Just about all authors provide development, later algae in question. worthwhile up-to-date reviews ultrastructural investigations In an outstanding of recent developments based of pit-plugs during cell chapter on diatom on molecular phylogenetic division, and finally systematics, Mann and Evans analyses. Of course, molecular phylogenies, led to further describe the problem: systematic classifications at a more robust systematic molecules “have an almost certain key levels and in many framework for Florideophyte metaphysical outworking: the groups remain in flux, so red algae. It is clear that when data they produce are some chapters are more up to such “polyphasic” approaches generally not valued by date than others, and a few are possible, as Pröschold and taxonomists for what they are likely will be somewhat out- Leliaert call them, they have in themselves, only for what of-date in short order. One produced systematics at class they imply about relationships clear theme that emerges after and ordinal levels that are between different organisms.” reading through the current likely to be stable for the They go on to point out that

The Systematist 2008 No. 30 17 “for the first time in the chlorarachniophytes? Try timeless. As an instructor in history of systematics, there is looking “In a bright shallow the biology of algae, that beginning to be a significant lagoon of a coral reef, among aspect of book itself is worth divergence between the kinds the bushes of tropical green the sticker price, and of characters we use to seaweed…” or “…among the guarantees that this volume describe and recognize taxa drifting seaweeds, [where] will have a place on my and the characters that are tiny green single-flagellated bookshelf for years to come. most effective for determining plankton swim.” In addition to As with efforts to relationships.” In a many similarly valuable unravel a twisted and knotted compelling review (chapter 5) chapters, the volume contains telephone cord (my apologies on challenges faced in an excellent glossary of both to the cell phone generation cyanobacterial systematics, systematic and phycological …try substituting an electrical Hayes Adel El Semary and terms and provides, up front, wire or garden hose), many Sánchez-Baracaldo, an easy to find list of initial steps lead to further and demonstrate that abbreviations that will be unexpected tangles. For algal morphospecies are not reliable most helpful to almost all systematics, this appears to be but that molecule-based readers. most true for questions related classifications create their Because of the to species delimitation, and own problems, and may dynamic nature of algal those at the broadest ultimately bring us no closer systematics, one of the most taxonomic levels. For to a stable and satisfying insightful decisions made by example, most of the chapters resolution. It is clear from the editors and most of the related to groups with these and other chapters, that authors was to provide a serially-derived red algal the ultimate unravelling of thorough and scholarly plastids are framed within the much of microalgal historical context for the working hypotheses of the systematics will require new recent developments in each Chromalveolata. Recently, the and innovative approaches to respective group. That is, they chromalveolate model has escape what, at present, may explain how the specific algal come into increasing conflict be unresolvable conundrums. taxon was organized with both plastid and nuclear In a brief review, such classically and how characters and its future is as this, it is not possible to systematics may have uncertain, at least in its discuss all the chapters changed during earlier current incarnation. In this, individually, but each has revolutions based on and numerous other cases, something worthwhile to cytological, ultrastructural or there is likely to be further offer. For example, although biochemical data. This kind of unravelling of new tangles one of the shortest, chapter 9 information can be difficult to that emerged from initial on the chlorarachniophytes by locate for many algal groups; molecular systematic studies. Ishida, Yabuki and Ota, prior to this publication, I Far from a weakness, compiles new and exciting don’t think it could be found however, delineating current genetic and genomic results, for the algae as a whole in a uncertainties is perhaps the many of which have yet to single and handy source. greatest strength of this make their ways into Thus, regardless of further compilation. The editors’ textbooks. Parenthetically, this changes brought about by stated goal is “…to inspire the chapter is worth the read just current and emerging next generation of scientists to for its quality of writing. technologies, this valuable study the Wondering where to find historical perspective will be taxonomy/systematics of

The Systematist 2008 No. 30 18 algae.” In laying out both the regulation of gene expression development. Not advances and the difficult relates to the development of surprisingly, the paper has challenges that have emerged animal form. earned a certain amount of from molecular studies, they A few years ago notoriety in the field, have made the best choices Davidson and his lab attracting 213 citations at the possible. When I first was managed to provide the first date of this writing. Refining attracted to the field of detailed elucidation of a and elaborating his thinking to phycology, it was because genomic regulatory network book length, Davidson there were really big and involved in development published Genomic regulatory exciting questions to be based on many years of systems: development and addressed. Many of those evolution in 2001. The last same questions, in one form chapter of that book presented or another, keep me interested a provocative and tantalizing to this day. That so many of discussion of what the important issues remain structure of genomic unresolved, from what defines regulatory systems could a species for most algae, to teach us about animal body how major groups originated ingenuous and elegant plan evolution. However, from heterotrophic ancestors, embryological experiments: when the time came to update is perhaps the best bait to the endomesoderm the book for a second edition entice the brightest and most specification network in the a few years later, “everything free-thinking young sea urchin Strongylocentrotus seemed to have been researchers to join the ranks purpuratus (Davidson et al. transformed to another of algal systematists. I suspect 2002). landscape” Davidson writes in that this book will be a This work becomes of the preface of his new book. valuable asset in helping to outstanding interest to So The regulatory achieve that goal. systematists when placed in genome is built upon a an evolutionary context, and stronger empirical foundation The Regulatory Genome. this has long been an than the previous work, Gene Regulatory Networks overarching goal of Davidson incorporating many new in Development and who has produced some of the insights about the nature of Evolution most provocative and developmental gene imaginative ideas about regulatory networks. This Davidson, E. (2006). animal evolution of the last stronger foundation in the Academic Press, U.S.A. ISBN several decades. For example, genetic underpinning of 13: 978-0-12-088563-3; ISBN a 1995 Science paper led by development is then mined in 10: 0-12-088563-8. Davidson was titled “Origin the final chapter of the book Hardcover: £43.99 of bilaterian body plans: for new insights about the evolution of developmental evolution of animal form. Eric Davidson is no regulatory mechanisms.” This This final chapter by itself household name in paper explicitly rooted the fully justifies buying this systematics. He is an explanation of the Cambrian book. embryologist at the California radiation of animal body plans The first four chapters Institute of Technology, and in the structure of genetic of the book provide a detailed he specializes in regulatory mechanisms that overview of the nature and understanding how the underpin embryonic functional significance of the

The Systematist 2008 No. 30 19 regulatory apparatus that is proteins in muscle cells, they influence each other’s encoded in the genome. The pigment in skin cells). transcriptional activity, that core components of genomic The final chapter their coordinated activity is regulatory architecture are the explores the implications of uniquely employed in the cis-regulatory sequences of the architecture of GRNs for development of a certain body genes. These DNA regions the evolution of morphology. part, and that interference regulate the pattern of Here the architecture of GRNs with the expression of any transcriptional activity of is used as a guide to the one kernel gene destroys genes in space and time. likelihood of the occurrence kernel function, preventing The cis-regulatory of viable mutations (i.e. those proper development of the regions consist of modules in that allow the organisms to affected body part. Since which transcription factors survive and reproduce), and changes in the expression of can bind, and these regions the expected magnitude of kernel genes are likely to lead achieve the regulation of gene activity by functioning as I strongly recommend [the book] to everybody information processing units who is interested in the reconstruction of that integrate the various phylogenetic relationships based on morphological inputs they receive from and molecular data irrespective of the nature of the combinations of organisms he or she is working on. transcriptional activators and repressors. The architecture of phenotypic changes. The most to developmental catastrophe, gene regulatory networks striking of these arguments evolution of the dependent (GRNs) is defined by the are summarized in Davidson body parts may be severely functional relationships & Erwin (2006). At one constrained. This is proposed between transcription factor extreme, at the periphery of as a mechanistic explanation encoding genes, and between GRNs, changes in of the existence and these and genes encoding differentiation genes (either in evolutionary inertia of animal signalling molecules. The their coding or regulatory body plans characters. The functional relationships sequences) are expected to be relative evolutionary volatility between these genes consist both frequent and relatively of body parts may then in of the interactions of the minor in effect. Because these large part be due to transcription factors that these changes have no downstream differences in the regulatory genes encode and their cis- consequences for the architecture that underpins regulatory regions. The regulation of gene expression, their development. ultimate output of and thus development, these This is of course developmental GRNs is the changes are the stuff of where GRNs become very regulation of the expression of adaptive evolution, often interesting to us systematists. genes that do not encode characterizing differences Davidson in effect proposes transcription or signalling between related species that the phenotypic factors. These genes are (integument colour). The consequences of changes in therefore located at the other extreme are changes in different parts of GRN periphery of the GRNs, and components of GRNs that architecture roughly correlate consist of the protein coding Davidson & Erwin (2006) call with the Linnaean hierarchy. differentiation genes that ‘kernels.’ Kernels are circuits Changes in differentiation actually built parts of the of interacting regulatory genes genes can occur frequently, phenotype (contractile with the defining criteria that and these produce differences

The Systematist 2008 No. 30 20 commonly observed between Erwin (2006) claim, no new part based on the papers closely related species. origins of phylum-level body presented at a symposium Qualitatively different parts since the Cambrian titled ‘What is changes in less peripheral because of the constraints Biogeography?’ held in parts of GRNs will result in imposed by GRN kernels? Cardiff in August 2005 as part larger phenotypic effects, such These fundamental of the Fifth Biennial Meeting as those that roughly separate issues are always worth of the Systematics different families, orders, or discussing, and they deserve Association. According to the classes. Such changes tend to our dedicated attention. editors of the book, occur less frequently because However, as Davidson biogeography is suffering of the greater likelihood of himself candidly admits, there from something like an downstream pleiotropic is now a more pressing need identity crisis, being closely effects that can disrupt for more empirical data. connected to and partly development. These claims History shows that personal dependent on other biological put up for discussion a lot of conviction and intuition are disciplines (such as ecology, fundamental issues that have insufficient to resolve these evolution, taxonomy or already started to be debated issues. Let us hope that the molecular systematics) but (once again in most cases) in next decade will shed new also struggling to maintain a the recent literature. Is empirical light on these position as an independent macroevolution just fascinating fundamentals of discipline with a core of microevolution writ large, or systematics. accepted knowledge and are they underpinned by qualitatively different kinds of References genetic change? Are there Davidson, E. H. et al. 2002. A marked discontinuities in genomic regulatory network evolutionary step sizes based for development. Science 295: on where the regulatory 1669-1678. genome is changed by a Davidson, E. H. and Erwin, mutation, and might these D. H. 2006. Gene regulatory correlate with observed networks and the evolution of methodological principles that differences in the amount of animal body plans. Science guide research. Contributors intraspecific phenotypic 311: 796-800. to the book are current variation and the step size of leading proponents of morphological Biogeography in a Changing differing methods in transformations at different World biogeography and the aim of times in a clade’s history? Is, the book was to produce a in contrast to what all good Ebach, M. C. & Tangney, R. broad-based perspective on neo-Darwinians should assert, S. (eds). (2007). Systematics the nature of biogeography homology perhaps more than Association Special Volume offering both historical just historical residue? What 74, U.K. ISBN 10: 0-8493- perspectives and are the relative contributions 8038-3; methodological advances as of external selection pressures ISBN 13: 978-0-8493-8038-9. well as a foresight as to what and internal constraints in Hardcover: £47.49 the future might hold for the determining the direction of discipline. Rather worryingly, evolutionary change? Have The book ‘Biogeography in a Adams’ foreword and his there been, as Davidson & Changing World’ is in large animation of an expanding

The Systematist 2008 No. 30 21 earth featured However, if such concepts are the ‘conflicts of intellect’ uncompromisingly on the not without controversy even between Haeckel and Agassiz. cover and McCarthy’s final amongst biogeographers The conclusion of the chapter, chapter, seem at odds with the themselves, that should come well in line with Ebach’s declared pluralistic approach as no surprise! In our opinion opening, again seems to call of the book, and leave the – as fortunately Riddle & for the need for reader with the feeling that Hafner manage to convey in biogeographers to ‘stick’ to perhaps here current Chapter 7 – genetic tools have classification of areas, and geological understanding is the potential to ‘solve’ or at refrain from using methods being unhinged with the least circumvent many aimed at ‘discovering wrong tools. controversies in biogeography, ancestry’, which – more than Given the many by discovering patterns (e.g. three decades after definitions in the book for revealing cryptic species) and Dobzhansky’s famous subdisciplines of at the same time uncovering statement – sounds puzzling biogeography, e.g. historical, processes (e.g. direction of to say the least. cladistic, or phylogenetic gene flow) or to provide a In the second chapter, biogeography, it is obvious historical biogeography for Parenti warns against the that there is no easy answer to one (or several species) that philosophy that one aim of the question ‘what is may include episodes of historical biogeography is to biogeography?’. It is also vicariance followed by range generate an explanation as obvious that biogeography as expansion and dispersal. well as to discover a pattern. a discipline is severely The first chapter by She also warns against a divided with authors stressing Williams is aimed at rejection of biogeographic the importance of finding providing an historical patterns using estimates of shared patterns of distribution grounding for the book, by divergence times based on and others focussing on focusing on the ‘threefold molecular data (because identifying causes of patterns, parallelism’ between calibrations rely for a large some stressing the importance ontogeny, phylogeny and part on fossils). She unjustly of vicariance, and others of paleontology – championed in blames the application of dispersal. We find it a pity particular by Ernst Haeckel at molecular tools to that Ebach’s introductory the end of the 19th century – biogeography for reviving pages put more effort in and discussing its importance untestable hypotheses of carving a deep fracture in the development of modern center of origin, recognition between disciplines – biogeographical thinking. of ancestors, and dismissal of ultimately pinpointing at the Whilst we believe that an the importance of Earth alleged ‘faults’ of historical perspective is history at all levels. However, phylogenetics – rather than crucial to understand the rise she admits that molecular data preparing a constructive (and fall) of scientific ideas, also have great potential to framework for a subsequent we also felt that if this chapter unravel fine scale patterns of synthesis. We could not help had been 60% shorter, it relationships among endemic but sometimes feeling would have provided a much areas, especially throughout ‘attacked’ by some authors for more focused ‘rooting’ for the the marine realm where they being phylogeographers and subsequent essays. Instead, it have not been expected. She failing to use terms, concepts, offers a huge amount of also calls for a reclassification methods and philosophies that interesting, yet largely of global biogeographic are central to biogeography. irrelevant, information about regions, which should include

The Systematist 2008 No. 30 22 both terrestrial and marine they cannot be delimited if those distributions over time. components. dispersal occurred. Secondly, She reviews recent In chapter three, another prediction of the methodological developments Grehan starts with yet another vicariance model is tested, that are event-based and have stern attack of molecular namely that closely related led to an extraordinary methods (a section entitled species originate on different revolution in biogeographic ‘Molecular Mithology’!) and sides of an emerging barrier. studies. She convincingly the defence of systematic Their case studies indicated shows that including all ‘biogeographic maps’, fully that speciation modes other biogeographic processes into independent from a Darwinian than vicariance were frequent the analysis is the way approach, as fundamental or that the imprint of forward for biogeography. She units of biogeography. He vicariance on the ranges was clearly explains and compares then goes on in the attempt to often obscured by extensive two event-based methods, deconstruct a long-distance postspeciational dispersal, dispersal-vicariance analysis dispersal model developed for regional extinction or and parsimony-based tree a genus of daisies. Data from sympatric speciation. The fitting, and offers practical other taxa with similar methods described in this tips as to when to use which disjunct distributions are chapter can help to identify method. She dismisses a invoked to support a ‘fit-for- those taxa and areas that are common critique against all’ vicariance model possibly most promising for further event-based methods (that if consistent with an expanding analysis of vicariance events. the models are wrong, the Earth. Despite the lack of Chapter 5, by Stuessy, biogeographic inference details provided, a number of is a clear and useful synopsis would be wrong) by citing aspects remain unclarified, on the different processes Ronquist’s (2003) argument in and a great extent of the affecting species and genetic favour of model-based evidence provided could be diversity during the four methods in phylogenetic interpreted in more that one successive phases in the analysis (such as Maximum way. ontogeny of island Likelihood and Bayesian The fourth chapter by biogeography. Shifting from inference) ‘ignoring process Hausdorf & Hennig deals the classical McArthur & in the formulation of a with biotic element analysis Wilson’s model, the author method does not make it more and vicariance biogeography. stresses that diversity never objective; the method’s These authors provide a clear really reaches an equilibrium, performance is still argument that it should be and that island-island and/or determined by the nature of tested first whether the island-continent comparisons the evolutionary processes clustering of ranges is of biological diversity should being studied’. stronger than expected by always take into account the The excellent chapter chance (thus vicariance ‘ontogenetic phase’ of the 7, by Riddle & Hafner, is the should not be predisposed) biotas considered. only chapter that attempts to and describe how this should According to bring historical biogeography be done with some clear Sanmartín in chapter 6 and phylogeography closer examples. The appropriate historical biogeography aims together. The authors identify units for this are biotic to infer the distribution two promising areas of elements, i.e. groups of taxa history of biotas and to growth likely to bridge the with similar ranges, and not identify the causal factors or gap between phylogeographic areas of endemism because processes that have shaped and area-based biogeography:

The Systematist 2008 No. 30 23 statistical phylogeography and not adopt a rigorous scientific sound framework to uphold comparative phylogeography. approach for his paper, what essentially are plain Indeed, as neatly synthesized especially for scientists that speculations and grave in Figure 7.4, the latter are unfamiliar with the assumptions’. (defined as the geographical expanding Earth theory. He In our opinion, comparison of evolutionary lists his arguments leaving biogeography cannot survive subdivision across multiple little room for the without embracing genetic co-distributed species or consideration of alternative tools, a bit like systematics species complexes; Arbogast possibilities, even though the has done before. This book & Kenagy 2001) can generate explanation provided (the was certainly an the hypothesis than can be expanding Earth) is by far the unconventional read to us and subsequently tested by the least parsimonious. Not only sparked some ideas about former. The authors also – as noted by Briggs (2004) – focussing more on species present a case study can the expanding Earth with shared distribution illustrating the application of theory not explain the patterns in a comparative a five-step approach to Precambrian to Paleozoic framework. Yet, we are still interactively and successfully fossil record of marine life, unsure as to the real purpose employ phylogeographic and which provides evidence of of the book: if its main intent biogeographic analyses in the extensive oceans, but more was to bridge different study of the warm desert biota importantly, the very approaches and philosophies of western North America. geological and physical currently contributing to As much as chapter 7 disciplines that he invokes as biogeographic analysis, and to seemed to finally come to a support for the theory have pave the way for their fruitful synthesis, we were left long dismissed the expanding synthesis and integration, we bemused by McCarthy’s Earth as pseudoscience, on the believe the objectives have closing contribution. As early grounds of its disagreement not been met, as only one as in the abstract, and all the with paleomagnetic estimates chapter (7) seems to possess way to the final summary, the of the Earth radius such synthetic characteristics. author seems to follow a (McElhinney et al., 1978) and If the goal was instead to personal agenda to use some its moment of inertia simply showcase the current selected biogeographic (Williams, 2000). Perhaps methods in biogeography and evidence that would uphold even more gravely, expanding forecast its potential future the expanding Earth theory. Earth assumptions are in developments, the picture McCarthy argues that for a contrast with overwhelming obtained is still that of a field number of relatively closely evidence of subduction and characterised by a deep related taxa found on both the basic principles of fracture, across which the sides of the Pacific Ocean, Einstein’s theory of General ‘dispersal’ of novel ideas for dispersal interpretations do Relativity, and the Standard scientific integration appears not fit, whilst a vicariance Model of particle physics. strongly hindered. interpretation of an expanding McCarthy’s final Earth, featuring a spectacular summary should have References opening and expansion of the probably included a fourth Pacific beginning in the point, stating: ‘no researcher Arbogast, B. S. and Kenagy, Triassic, would explain all supporting the expanding G. J. 2001. Comparative disjunct distributions. Earth theory has hitherto phylogeography as an Unfortunately, McCarthy does provided any scientifically integrative approach to

The Systematist 2008 No. 30 24 historical biogeography Pleurocarpous mosses are the the pleurocarpous mosses Journal of Biogeography, 23: largest group of mosses, based on molecular data but 269-277. comprising around 6,000 of without neglecting the the overall assumed 10,000 morphology, as unfortunately Briggs, J.C. 2004. The species. By far the largest happens so often in the recent ultimate expanding earth group of pleurocarps, the molecular era. In contrast, the hypothesis. Journal of Hypnales underwent a rapid morphological characters are Biogeography, 31:855-857. radiation and is re-evaluated in the light of morphologically highly molecular results and much McElhinney, M. W., Taylor, S. plastic, which in the past interesting congruence is R., and Stevenson, D. J. made it a very difficult task to found even though there are (1978). Limits to the reconstruct the phylogeny many remaining questions. expansion of Earth, Moon, solely based on morphology The first chapter is Mars, and Mercury and to and intuition. dedicated to the history of changes in the gravitational In its history the pleurocarp classification, constant. Nature, 271: 316- classification of the pointing out the problem that 321. pleurocarpous mosses has the usefulness of been subject to great changes morphological characters of Ronquist, F. 2003. Parsimony mainly due to changes in the gametophyte and sporophyte analysis of coevolving species evaluation and interpretation has been assessed very associations. In: Cospeciation of morphological characters. differently in history, leading (ed. by Page, R. D. M.) pp. At one time sporophyte to periodic and quite drastic 22-64. Chicago University characters were believed to changes in the classification Press, Chigaco. provide the most useful of this group. Several aspects information for systematics; of this problem are addressed Williams, G.E. (2000). later, gametophyte characters in the following chapters. Geological constraints on the were accepted as the most The next chapters Precambrian history of the important. These points of throw light on the Earth’s rotation and the view alternated until relationships of the earliest- moon’s orbit. Reviews of diverging lineages of mosses Geophysics 38(1): 37-59. in which pleurocarpous morphology appeared using Pleurocarpous Mosses both molecular and Systematics and Evolution morphological data, followed Newton A. E. & Tangney, by chapters about other basal R.S. (Eds.) (2007) CRC Press, pleurocarpous groups, Taylor & Francis Group. comprising reconstruction of ISBN9780849338564 molecular methods were their phylogeny and re- (hardcover) available. Only then, when evaluation of morphological 82£, 149.95$, 104.99€ more reliable phylogenies characters. were available for the first Chapters 6 – 10 focus The book is the product of a time, could morphological on the relationships within the symposium on pleurocarpous characters be (re)evaluated. Hypnales, the most derived mosses held at the National The book gives an and by far the largest order of Museum of Wales, Cardiff in overview of the recent pleurocarps, primarily based 2004. knowledge of relationships of on analyses of molecular data

The Systematist 2008 No. 30 25 but never neglecting morphological character in the text. In order to be able morphology. The main evolution and the other on to use the molecular datasets a emphasis is put on the geographic distribution copy of an alignment editor is relationships within certain patterns of pleurocarpous included. One folder families but valuable insights mosses in the Australasian obviously contains into the backbone phylogeny region in comparison with photographs of the of the whole pleurocarps are patterns known for symposium and an excursion also gained. The strength of angiosperms. that took place in its context these chapters is the use and A very extensive and helpful but there is no other discussion of many different index closes the book. information about their analytical techniques, like The technical quality contents than the file-names. alignment optimization or the of the book is also very good. Thus, these photos will use of secondary structure to It is printed on high quality unfortunately be of use for the name only two. paper. participants of the symposium In contrast to the Drawings and only. A simple text-file with previous chapters the photographs are mostly of some information about the following five (11 – 15) deal high quality although some of photos would have been mainly with morphology. the black and white helpful. The CD contains Morphological characters and photographs could benefit useful data but one cannot their use in pleurocarpous from somewhat higher help thinking that it was moss systematics are contrast. However, most of assembled in a hurry. reviewed. Many characters are the photographs can be found To summarize, the critically evaluated or re- as better full-color versions on book covers the current evaluated regarding the attached CD. knowledge about the homology/homoplasy leading The book comes with phylogeny of the pleurocarps to a new understanding of a CD-ROM. It provides as well as the ongoing certain structures. For datasets corresponding to research. It furthermore points example, stem structures like some of the chapters of the at the open questions and pseudoparaphyllia are book, so that the interested discusses possibilities for their examined, and the branching reader can for example run solution in the future. A wide architecture of whole plants analyses with his own range of methods for which is necessary to define programs and/or personal phylogeny reconstruction is pleurocarpy s.str. and for settings as well as use the critically discussed. It is not understanding relationships datasets as a basis for further just one of the many books within pleurocarps. research without having to about molecular phylogeny of The two following download the data from a certain group of organisms. chapters explore the origins of GenBank. It would be perfect Its strength is that the focus pleurocarpous mosses, the to have data for all chapters moves from molecular data to first one by utilizing fossil but that’s unfortunately not other aspects of biology, data and the second by the case. Other contents of the showing that molecular and calculations based on CD are full-color versions of morphological data for molecular data. many of the B/W-photographs example can complement In the final two appearing in the book as each other leading to a better chapters, evolutionary already mentioned earlier and understanding of the questions are analyzed, one additional drawings as well as organisms’ evolution. This “is focusing on reconstruction of other information referred to a rare type of book for any

The Systematist 2008 No. 30 26 group of plants” as already Brent Mishler pointed out in the foreword to the book. Spotlight Looking on the composition of authors it is noticeable that many names appear several times in different Francisco Ayala combinations demonstrating an extensive network of Department of Ecology and Evolutionary Biology, cooperating researchers, a fact University of California, Irvine, USA [email protected] that is surely contributing to March 2005, 76% would not the high quality of the book’s “be upset if public schools in content. The Missing Link: [their] community taught The book is a ‘must Science Literacy creationism,” but only 63% have’ for all bryologists but I would not “be upset if the strongly recommend it to Scientists and science schools taught evolution.” everybody who is interested educators have a lot to Only 22% would be upset if in the reconstruction of account for. The lack of creationism would be taught, phylogenetic relationships scientific education, even of while 34% would be upset if based on morphological and the most basic kind, in the evolution would be taught. molecular data irrespective of United States is appalling; or Other polls yield similar the nature of the organisms he dreadful if we take into statistics. There can be no or she is working on. account that our world is doubt that a crucial link is Unfortunately, the high becoming increasingly missing in the US educational price will discourage many technological and that system: scientific literacy. potential readers from buying economic prosperity and jobs On January 4, 2008, the book. This is in so far a depend on a scientifically the National Academy of pity as especially interested literate citizenry. According to Sciences (NAS) published students and young scientists a Gallup poll of 1,016 US Science, Evolution, and would benefit from its adults, taken in November Creationism, which was contents 2004, 45% of those surveyed favored the statement that prepared by a committee of “God created human beings in the NAS, as an effort to their present form within the counteract the widening Memorable Quotes last 10,000 years. (38% exertions of antievolutionists favored that “Man developed seeking to eliminate from “ We must remember the over millions of years, but public schools the teaching of distinction between the cart God guided the process,” and evolution, or at least, to – the explanation – and the 13% that “Man developed “balance” it by also teaching horse – the data. And where over millions of years from creationism and intelligent models are introduced in less advanced life forms.”) design. Science, Evolution, phylogenetic reconstruction, The and Creationism is the third we should prefer models evolution/creationism divide edition of Science and dictated by features of the is no less scary. In a Creationism, published in data to models derived from CNN/USA Today Gallup poll 1984, but sufficiently explanatory theories. ” of 1,001 adults conducted in modified to deserve a new (Colin Patterson 1994) title. A second edition of

The Systematist 2008 No. 30 27 Science and Creationism was remove the teaching of District of Pennsylvania, published in 1999. evolution, by reviving the old issued a 130-page-long Science and “argument from design,” decision (Kitzmiller v. Dover Creationism was prepared in under the moniker of Area School District) response to statutes passed by Intelligent Design Theory declaring that “The the legislatures of the states of (ID). The argument from overwhelming evidence at Arkansas, first, and Louisiana, design for the existence of trial established that ID is a shortly thereafter, that God, based on the complex religious view, a mere re- required that “creation organization of living things, labeling of creationism, and science” be taught in the was elaborated by English not a scientific theory … ID is public schools together with clergyman William Paley in not supported by any peer- evolution. The Louisiana his Natural Theology, reviewed research, data, or “Creation Act” was appealed published in 1802. Paley’s publications.” all the way to the United argument from design is two- Science, Evolution, States Supreme Court, which tined. The first prong asserts and Creationism consists of in 1987 (Edwards v. Aguilard) that humans, as well as all three main chapters. The first concluded that the Act’s sorts of organisms, in their chapter briefly describes the “primary purpose was to wholes, in their parts, and in process of evolution and the change the public school their relations to one another nature of science in contrast science curriculum to provide and to their environment, to other forms of knowledge. persuasive advantage to a cannot have come about by The second chapter surveys particular religious doctrine chance, but rather manifest to the scientific evidence that that rejects the factual basis of have been designed for supports evolution from evolution in its entirety. Thus, serving certain functions and diverse disciplines that the Act is designed either to for certain ways of life. The include astronomy, promote the theory of creation second prong of the argument paleontology, comparative science that embodies a is that only an omnipotent anatomy, biogeography, particular religious tenet or to Creator could account for the molecular biology, genetics, prohibit the teaching of a perfection and functional and anthropology. The third scientific theory disfavored by design of organisms. The new chapter examines intelligent certain religious sects. In advocates of ID modified the design and other creationist either case, the Act violates second prong of the argument perspectives so as to point out the First Amendment.” by referring to an unspecified the scientific and legal Science and Creationism was “intelligent designer,” thus reasons against teaching made part of an “amicus avoiding explicit reference to creationism in public school brief” submitted to the God, so that the argument science classes. The text Supreme Court in Edwards v. from design would not concludes with a selection of Aguilard by the NAS, with necessarily have religious frequently asked questions the endorsement of the connotations, and thus could and additional readings. American Association for the be taught in the public schools Much has happened in Advancement of Science and as an alternative to evolution. evolutionary biology since the other organizations. This hypocritical subterfuge release of the first two In the 1990s, several amounts to nothing else than a editions of Science and authors schemed a new tactic charade. On December 20, Creationism. The new edition to introduce creationism in the 2005, John E. Jones III, provides important updates schools, or alternatively to Federal Judge for the Middle about these developments.

The Systematist 2008 No. 30 28 Fossil discoveries have paleontology and the older asserted that “Nothing makes continued to produce new and disciplines continues to sense in biology except in the compelling evidence about accumulate, such as the light of evolution.” Evolution evolutionary history. New discovery published in 2006 provides a scientific information and and described in Science, explanation for why there are understanding about the Evolution, and Creationism, so many different kinds of molecules that make up of Tiktaalik, a fish that lived organisms on Earth and gives organisms has emerged, in shallow freshwater streams an account of their similarities including the complete DNA and swamps about 380 and differences sequence of humans. DNA million years ago. Tiktaalik is (morphological, physiological, sequencing has become a a nearly precise intermediate and genetic). It accounts for the appearance of humans on ...many people of faith have questions about Earth and reveals our species’ biological evolution, because they have been told biological connections with that the scientific understanding of evolution is other living things. It provides incorrect or at least doubtful, and that accepting an understanding of the evolution is not compatible with their religious constantly evolving bacteria beliefs and viruses, and enables the powerful tool for establishing between typical fish and the development of effective new genetic relationships among first known four-legged ways to protect ourselves species. DNA evidence has animals, from which would against the diseases they both confirmed fossil evolve all animals that live on cause. Evolution has made evidence and allowed studies the land, from frogs to possible improvements in of evolution where the fossil reptiles, to birds and to agriculture and medicine, and record is still incomplete. An mammals, including humans. has been applied in many entirely new field, No intermediate fossils fields outside biology, evolutionary developmental between humans and apes including forensics and biology, enables scientists to were known in Darwin’s time. software engineering; it has study how the genetic changes Now, thousands of remains stimulated chemists, for that have occurred throughout are known that belong to the example, to use the principles history have shaped the forms human lineage after it of natural selection for and functions of organisms. separated from the lineage developing new molecules The study of biological that goes to the apes. with specific functions. evolution constitutes one of Biological evolution is Biological evolution is the most active and far- the central organizing part of a compelling historical reaching endeavors in all of principle of modern biology. narrative that scientists have modern science. The lack of scientific education, even of the Evolutionists are no most basic kind, in the United States is appaling; or longer concerned with dreadful if we take into account that our world is obtaining evidence to support becoming increasingly technological and the the fact of evolution. Rather, economic prosperity and jobs depend on a evolutionary research scientifically literate citizenry nowadays seeks to understand further and in more detail how In 1973, the eminent constructed over the last few the process of evolution evolutionist Theodosius centuries. The narrative occurs. Yet the evidence from Dobzhansky famously begins with the formation of

The Systematist 2008 No. 30 29 the universe, the solar system, the contrary, the evidence experience. Scientific and the Earth, where supporting the evolution of explanations are based on conditions occur suitable for organisms is both evidence drawn from life to evolve. There are overwhelming and examining the natural world theories that seek to account compelling. In the century and and rely exclusively on for how life originated on a half since Darwin, scientists natural processes to account Earth, but none of them has have uncovered exquisite for natural phenomena. gathered enough supporting details about many of the Scientific explanations are evidence to be generally mechanisms that underlie subject to empirical tests by accepted by scientists. But biological variation, means of observation and natural selection, discovered inheritance, and natural experimentation, and are by Darwin, has been selection, and they have subject to the possibility of convincingly demonstrated as shown how these mechanisms modification and rejection. the process that accounts for lead to biological change over Religious faith, in contrast, the adaptive configuration and time. Because of this immense does not depend on empirical function of organisms, for body of evidence, scientists tests, nor is it subject to the their “design.” Darwin is treat the occurrence of possibility of rejection based often credited with providing evolution as one of the most on empirical evidence. compelling evidence that securely established of Nevertheless, many evolution has occurred, but scientific facts. Indeed, people of faith have questions Darwin’s greatest contribution critical thinking demands that about biological evolution, to science is not that he ID and other creationist because they have been told accumulated evidence proposals be kept out of the that the scientific demonstrating the evolution science curriculum, because understanding of evolution is of life, but that he discovered they lack scientific content: incorrect or at least doubtful, natural selection, the process they are not scientific theories and that accepting evolution is that accounts for the design of nor are they supported by any not compatible with their organisms, their wonderful scientific evidence. religious beliefs. Science, adaptations to survive and Religious authors, and Evolution, and Creationism reproduce in the environments scientists as well, have written speaks to these questions. It is where they live: wings for eloquently about their awe written to serve as a source of flying, legs for running, eyes and wonder at the history of information and as a resource to see, and kidneys that the universe and of life on this for people who find regulate the composition of planet, explaining that they themselves embroiled in the blood. see no conflict between the debates about evolution. It A strategy of ID evidence for evolution and should be helpful to “school proponents and other their belief in God. board members, science creationists is to argue that Authorities of diverse teachers and other education science teachers should teach religious denominations have leaders, policy makers, legal “critical thinking” and thus issued statements affirming scholars, and others in the that they should present the the compatibility between the community who are controversies surrounding tenets of their faith and the committed to providing evolution. But there is no acceptance of biological students with quality science controversy in the scientific evolution. Science and education.” Moreover, as community about whether religion concern different stated in the Preface, Science, evolution has occurred. On aspects of the human Evolution, and Creationism

The Systematist 2008 No. 30 30 Evolution of the Animals – a Linnean Tercentary Celebration Please find additional information on this Royal Societythematic publication at: http://publishing.royalsociety.org/linnean

A specially discounted price is available to SystAss members by contacting Debbie Vaughan at the Royal Society direct ([email protected]) or by contacting Portland Customer Services (quoting reference TB 1496) using the contact details on the attached pdf or via the Portland Press website.

The Systematist 2008 No. 30 31 “is also directed to the Linnean Society, London 10th Young Systematists’ broader audience of high- Forum, Flett Lecture school and college students as 2-4 July 2008 Theatre, The Natural well as adults who wish to 10th Symposium of the History Museum, London, become more familiar with International Organization UK the many strands of evidence of Plant Biosystematists supporting evolution and to Evolution of Plants in 3 December 2008 understand why evolution is Mountainous and Alpine Annual General Meeting both a fact and a process that Habitats and Lecture accounts for the diversity of Visoke’ Ttatry, Slovakia life on Earth.” Our 11-14 August 2009 educational system and July 29-August 1r 2008 7th Biennial Meeting society as a whole are best Saltation: Macroevolution National Herbarium of the served when we teach science, by Profound Phenotypic Netherlands, Leiden, and not religious faith, in science Change Across a Single National Museum of classrooms. That is but one Generation Natural History, Leiden. step in the efforts to fill in the Euro Evo Devo 2 For more information see missing link of science Ghent, Belgium www.systass.org literacy. Organizers: Richard Science, Evolution, Bateman (Kew), Jan and Creationism is beautifully Deutsch (Paris) Details of the SA produced and illustrated in research grants, color and only 70 pages long. 1-3 September 2008 conference bursaries and An eight-page brochure, Climate Change and funding for the adapted from the full-length Systematics book, and also beautifully organisation of meetings Organizers: can be found at: produced in color, is also Trinity College Dublin, on www.systass.org available from the NAS. The behalf of Systematics brochure and the full-length Association and Linnean document are available for Society free download and ordering at http://www.nap.edu/catalog.ph 3 October 2008 p?record_id=11876 Beyond Cladistics – A Festschrift for Chris Humphries Organizers: Calendar David Williams ([email protected]), Paula Rudall 2 July 2008 The Sir Julian Huxley 19-24 October 2008 Lecture 4th International Rubiaceae Prof. Joe Felsenstein (Gentianales) Conference, Talk: Not the Fly on the Jalapa, Veracruz, Mexico Wall: Can Systematists Cope With Uncertainty? 2 December 2008

The Systematist 2008 No. 30 32 The Systematist 2003 No. 22