dataesr/scientific-paragraphs-categorization huggingface dataset:
NOW as an ETE Node In 1986, the Evolution of Terrestrial Ecosystems Program (ETE) was established in the Department of Paleobiology at the National Museum of Natural History (Smithsonian). One of its signature early projects was the development of a computer database for the terrestrial fossil record. By 1992, ETE had developed a design and detailed schema for such a relational database  (Damuth et al. , 1997). A chance meeting in the fall of 1992 between Mikael Fortelius and John Damuth (then of ETE) started a conversation about coordination of databases. Fresh from the Reisensburg meeting, Fortelius knew that the kernel of a database of Old World Neogene faunas had taken shape, but the remaining question was the technical issue of how best to turn the data compilation into a database that would have potential for longevity and growth.
ETE offered a general, public structure that could guarantee a degree of generality without sacrificing functionality. Fortunately for NOW, it was also organized as a system of nodes in order to allow participants to work from multiple locations, independently of institutional affiliation. The first version of what we now know as NOW was compiled in the autumn of 1993 by Mikael Fortelius and Suvi Viranta in Paradox for Windows, using the ETE structure. At this point Providence once more smiled upon NOW. In October the same year there was an infrastructure call by the Academy of Finland, to which Fortelius on short notice submitted an application for an HP-UNIX server to host the still embryonic database, with specifications to match those chosen by the ETE for its own database. Against all expectations, the Academy approved this application in December the same year.
Moving NOW to the University of Helsinki's server platform meant that not only the structure, but the user interfaces that ETE had developed could be used seamlessly by NOW. Furthermore, the rise of the Internet made it possible to update and troubleshoot the software applications remotely. Significantly, in the days before the Web, it was nevertheless possible to work directly with the database for research remotely, using the X Windows system in any terminal application that was available at the time in some form or other on all computer platforms. NOW could be served. The user logged in directly to the NOW server in Helsinki, and the interactive graphical user interface appeared on their own computer. This was based on a custom-designed GIS application written for ETE and would later provide the architectural foundation for other databases as well, among them the original Paleobiology Database.
The user was presented with a digital map of the world and could zoom in on any region, specify a timespan, and the localities would appear as points. Their contents could be seen via mouseover, and the map display could be queried for specific taxa or, for that matter, any properties recorded for the localities. Subsets of the data could be created this way and downloaded as delimited text files, or SAS datasets, or other useful formats. Even the map display with localities could be downloaded as a fairly basic PostScript file (this was before PDF). Additional features of the GIS interface included typical ones such as scale bars and measurement of distances. Another graphical interface could be used locally to manage the database. In the summer of 1994, the latest Paradox version of NOW was successfully ported to the new server and over the ensuing months various bugs and implementation issues were worked out.
By 1995, NOW had become a peer-node database in the ETE Consortium, and NOW and ETE were in regular communication. It may be of interest here to record that the Helsinki NOW office was using an early Linux Debian installation on a PC as a NOW terminal during this time, starting from November 1995. The first machine was very nearly installed by Linux creator Linus Torvalds himself, but owing to a mismatch of schedules it was eventually done instead by another early Linux legend, Lars Wirzenius. Linux support in those critical days was most generously supplied by Jussi Sjöström, IT support of Hanken School of Economics, Helsinki (which may or may not have been aware of these goings-on). In time, the ETE Program reset its priorities, and by 2000 it was no longer building and hosting its own database.
Significant subsequent American palaeontology database efforts such as PaleobioDB (https://paleobiodb. org/) and FossilWorks (http://fossilworks. org/) have focused on ambitious national projects to database the entire published fossil record, terrestrial and marine, at first primarily to study patterns of global Phanerozoic diversity. These projects necessarily have a different set of goals and a different relationship with the professional community than does NOW, which was a more focused but also more open-ended and actively maintained database effort. Under these circumstances NOW had little choice but become an independent entity with its own infrastructure and institutional support. This was a time of trial and error, with false starts and temporary fixes of various kinds. But crucially, the NOW community persisted through the crisis and the building of the database continued without any serious disruptions.
An Excursion into the Land of Nod This chapter is the story of how the NOW database came to be and how it grew. There were, of course, all sorts of disappointments, setbacks and failures along the way but rehearsing them at length would serve no useful purpose here. But there is one spectacular failure that may be worth a brief section as it is of some historical interest as well as a great cautionary tale. This is the story of the EEDEN Programme. As the first results of NOW analyses were emerging in the mid-1990's there was considerable enthusiasm and hope that a new and better understanding of deep time ecosystem change might be within reach. The multidisciplinary ambitions of the HOMINET workshops mentioned above also provided a fertile substrate for thinking along such lines. Thus, it came to be that a remarkably ambitious initiative was conceived and proposed to the European Science Foundation as a Scientific Programme.
A more database-oriented attempt to address this was carried out by a working group at meetings between 1998 and 2001 at the National Center for Ecological Analysis and Synthesis in Santa Barbara (Fig. 2. 7). The results were somewhat disappointing and in retrospect the effort was perhaps premature. But what did emerge was yet another potential paleoclimatic relationship between rainfall, on the one hand, and mean hypsodonty divided by species richness on the other  (Damuth et al. , 2002). A parallel exploration of patterns of hypsodonty and lophedness in fossil data was also in progress at this time (e. g. ,  Fortelius & Hokkanen, 2001; Fortelius, 2003)  but these early efforts were severely hampered by the crude options available for displaying the results. In this intellectual climate, then, it may not be surprising that Fortelius was alert to something that he discovered by chance in 2001 while trying out a new kind of plot offered by a statistics package (incidentally during the Golden Dragon New Year celebrations in a wintery Beijing): the summed pattern of the distribution of molar crown heights in the totality of NOW data showed a striking resemblance to the present-day distribution of rainfall on the Eurasian continent.
NOW Comes of Age Meanwhile, in parallel with the development of ecometric proxies for environmental conditions, a second line of NOW-based research was emerging. Here, the aim was not reconstructing environmental patterns of the past as such, but rather to understand the evolutionary dynamics generating them, through adaptive trait evolution driven ultimately by biotic interactions as well as changing physical conditions. The first to reach publication was  Jernvall and Fortelius (2002) , showing that the changes in spatial hypsodonty patterns in the European Neogene were due mainly to the evolutionary success of herbivores with increased crown height, which became progressively more common relative to herbivores lacking this key feature. The follow-up study of  Jernvall and Fortelius (2004)  delved deeper into the dynamics, looking at the history of the most common lineages in the same dataset.
In retrospect, the most significant finding of the paper was undoubtedly the discovery of what is known today as the hat pattern: the unimodal occupancy history of taxa in the fossil record  (Foote et al. , 2007; Liow & Stenseth, 2007) , currently another subject of vigorous research, still partly involving NOW data. The first explicitly NOW-based publications are from 1996, all but one of them  (Fortelius et al. , 1996a)  being contributions to the Reisensburg Volume  (Bernor et al. , 1996) , described earlier in this narrative. These early papers were strongly focused on the analysis of quantitative patterns of diversity, turnover, biogeography and community structure, but following years saw a broadening of the scope, with a steady stream of papers citing NOW for their data. Some of these papers are cited on the NOW webpage (https:// nowdatabase.
, 1998; Fortelius et al. , 2006b; Puolamäki et al. , 2006; Ukkonen et al. , 2005). Macroevolutionary work also started to emerge at this time  (Liow et al. , 2008; Peláez-Campomanes & Van der Meulen, 2009)  as did paleoclimatology  (Eronen et al. , 2009; Liu et al. , 2009; Micheels et al. , 2009). The research fed by NOW has continued to grow and diversify and many more publications have appeared over the last decade but a description of those developments is beyond our present scope. Figure  2. 9 shows an example of work in progress from 2010, moving towards an ecometric concept of paleobiome space. It is important here to emphasize that NOW has always served two main functions: to provide datasets for quantitative analysis and publication, but equally, if not even more importantly, to function as an online source of information about fossil mammals and localities.
A more detailed search at the Web of Science Core Collection (https://clarivate. com/webof sciencegroup/solutions/web-of-science-core-collection/) provided 1,086 authors for the Web of Science Category "Paleontology" for publications during 2017-2021 with additional 60 keywords, including "Mammalia", "Mammals", "Mammalian" and 57 taxonomic order names listed in NOW database. In this perspective, hundreds of visitors per month is quite a respectable number.
Connecting People (and Disciplines) As is often the case in research, funding opportunities can inspire creative solutions by connecting previously separate disciplines and people. One such opportunity was the 2003 call of Academy of Finland on Systems Biology. Whereas systems biology and fossils did not exhibit any obvious links, Jukka Jernvall, Irma Thesleff, and Mikael Fortelius nevertheless proposed that studying mammalian teeth from evolutionary, ecological, and developmental biology perspectives could in fact be considered systems biology. A key component of the proposal, which ended up being fully funded, was the aim to examine ways to link NOW to datasets ranging from molecular data on developing mouse teeth to digitized, three-dimensional tooth shapes. Here, a key person hired in the project was Gudrun Evans, who developed the database structures to link the different kinds of data.
One outcome of the collaboration was that it set NOW in motion towards incorporating specimen level data, something that continues to this day. Dental morphology of extant taxa posed its own challenges as the same specimen could be represented by multiple instances in the data. These kinds of cases include tooth wear data obtained from wild animals captured multiple times  (King et al. , 2005) , or time-lapse images of growing teeth on the petri dish  (Harjunmaa et al. , 2012). For these vastly diverse kinds of phenotypic data, Gudrun and Alistair Evans constructed a MorphoBrowser database (http://pantodon. science. helsinki. fi/morphobrowser/) that houses many of the datasets collected in individual studies (e. g. ,  Evans et al. , 2007; King et al. , 2005; Wilson et al. , 2012). Serendipitously, Mor-phoBrowser also became the basis for a new database in the US, thus continuing the transatlantic exchange of ideas that had been part of NOW from the onset.
In 2008, Doug Boyer was working at Stony Brook University with Jernvall when an opportunity arose to re-engineer MorphoBrowser, resulting in the widely used MorphoSource database (https:// www. morphosource. org/), currently coordinated at Duke University by Boyer  (Boyer et al. , 2017). One of the aims of the systems biology collaboration was to develop methods to compare very different, almost incomparable morphologies. To do this, teeth from morphologically diverse taxa were studied using new taxon-free approaches  (Andrews & Hixson, 2014). Initial steps included molar crown types that provide a simple tabulation of number and position of tooth cusps and crests. These ecometrical descriptions were incorporated into NOW and used in some of the early analyses of environmental patterns  (Jernvall & Fortelius, 2002 , 2004).
Crown types were soon followed by more quantitative methods that were developed with Alistair Evans and Gregory Wilson  (Evans et al. , 2007; Wilson et al. , 2012). Unlike work on tooth morphology, tooth genes remained a more protracted challenge. Already by 1998, Irma Thesleff had established a database for genes expressed in developing teeth  (Nieminen et al. , 1998). Whereas this Bite-It database allowed the visual inspection of hundreds of genes expressed in developing teeth, the actual number of genes expressed dynamically in a developing tooth is in the thousands  (Hallikas et al. , 2021). Indeed, new, fast-throughput methods to acquire huge amounts of gene expression data, increasingly at single cell resolution, have transformed the field of developmental genetics to rely on large international data depositories.
Opening the NOW Database up to the World The very first attempt of making NOW open to the world was made by Kari Lintulaakso using the development tools of a private software company where he was working at the time. During 2001-2002 Kari made a proof-of-concept solution of a regular, HTML-based user interface that allowed adding and editing the data. Eventually, the solution proved to be too costly for the essentially volunteer-based NOW, and it was sadly buried without further development. When Gudrun Evans took on the role of technical database coordinator in 2004, the existing UNIX version of NOW still only allowed users to view data remotely, but not to make any changes to it. Gudrun designed the structure for the new Systems Biology database, which linked the NOW database to the new MorphoBrowser and the Gene database (Fig.
2. 10). She rebuilt the NOW database in MySQL, replicating the ETE-based table structure, and strengthening it by enforcing data rules restricting many fields to specific entries at the database level. Significant work was then undertaken to clean the data to meet these rules, and the data was subsequently transferred to the new MySQL database. Evans created a new, user-friendly web interface in Servoy (Java-based, cross-platform software, able to be used by both Mac and Windows users). By downloading the client software, users were then able to directly search and view the database remotely and were also able to log in and enter and edit data directly from anywhere in the world. To maintain the integrity of the data, individual users were granted access to edit only a restricted set of data, which related to their area of expertise, determined either by taxonomy or locality.
Researchers were able to edit records that they themselves had contributed, and regional and taxonomic coordinators were able to edit records related to their field. All changes were logged and could be checked by coordinators. Servoy offered the benefit that the interface could be developed relatively quickly, allowing focus to be directed to how the data should be displayed, and what functionality was required. It also allowed further time to be spent cleaning the data to improve the integrity of the dataset many issues came to light as the data were able to be searched and viewed in more detail, including adequately dealing with diacritical marks in names, locality and taxon synonyms, consistency in usage of 'cf. ', and errors in calculations of fractions of age in time units, errors in latitude and longitude, and of course spelling errors and inconsistencies in taxa, localities and museums.
This is a very time-consuming process, but an essential part of ensuring database integrity, so that a user conducting a search will be able to find all the matching records. Evans created synonym tables and functions for creating synonyms and merging duplicate records to assist with this process. With increasing numbers of users able to edit and enter data remotely, it was also essential to keep track of user permissions, and to create a log of changes that keeps track of who made what changes when and why (by linking these to a reference). It was also important to ensure that the database was being backed up regularly and adequately. As a result of the Systems Biology project described in the previous section, a new Systems Biology database, incorporating NOW, was hosted at the University of Helsinki on a new server called Pantodon.
Evans was helped by database technician Joonas Kauhanen, who set up this server and created back-up routines, and also a website traffic monitoring feature so that we could keep track of the number of visitors to the site. Kauhanen continued his association with the project for a number of years, and his expertise was invaluable in trouble shooting many issues as the database and interface were developed. The Servoy user database interface went live in April 2005. Over time the limitations of using Servoy became apparent: many users experienced problems using the client software, the server software required updating frequently, which inevitably led to necessary fixes in the interface, and there was an annual license fee that was unsustainable in the long term. Therefore, in 2007, Evans commenced building a new user interface in PHP, replicating the look and functionality of the Servoy interface, still connecting to the MySQL database and using an Apache server (Fig.
2. 11). This eliminated all the problems with Servoy, but it was more complicated to develop and took longer to create because everything had to be coded manually. Evans designed and created much of this interface herself, but was helped by a few database technicians, each of whom brought invaluable expertise to the project. Veli-Pekka Kestilä helped check the new interface for potential security flaws before it was released, and also helped move the database from the aging Pantodon server to a new server called Mutikka, hosted by the Finnish Museum of Natural History,   Although NOW at the time of writing enjoys a comfortable and hopefully long-lasting relationship with the Finnish Museum of Natural History, the first attempt to place the database within the museum was not successful. In 2010, the database moved servers again, this time to a server called Mormyrus, hosted by the Institute of Biotechnology, part of the University of Helsinki.
Atro Tossavainen provided a lot of assistance moving the database, and getting it functioning correctly on the new server. Evans continued her association with NOW from Australia for some years, communicating with Jouni Vepsäläinen and Atro Tossavainen as the database continued to be developed, working with Susanna Sova who was preparing the Harvard Siwaliks dataset for entry, and, together with Alistair Evans, on preparing the North American dataset for upload: the latter were uploaded in 2011, as described below.
Across the Vastness of Asia Inevitably, and as has already been testified, the history of the NOW database was always intertwined with the individual histories of its participants. A case in point concerns its expansion from the original scope of central Europe versus the eastern Mediterranean to cover the entire Eurasian continent. While the NOW database was being born, Fortelius was shifting his field project from western to eastern Asia. This was a very deliberate move, motivated partly by the decline of the Sinap Project in Turkey  (Sen, 2003:14)  and partly by a (retrospectively remarkably naïve) hypothesis arising from the first analyses of the initial NOW data: that the faunal developments seen in western Asia (e. g. ,  Fortelius et al. , 1996b ) might be mirrored on the eastern half of the continent.
The first field season was a challenging one, not least because Fortelius broke his leg just before it and therefore arrived in China three weeks late and on crutches. He was met in pouring rain by a dispirited field party, which had endured exceptional heat and very meagre findings in the previous weeks. Despite further challenges of similar kind, the field season was not only completed but became the beginning of a successful collaboration that still continues at the time of writing. From the very beginning, the project was set up with the dual purpose of data compilation as well as field work, and it naturally became the task of Zhang and Liu to help with the practical aspects of the database part as well, joining the NOW the advisory board along with a few more senior colleagues. The data compilation progressed well in the early years of the project and had by the turn of the millennium reached a sufficient stage of completeness to provide a first inkling of continental-scale patterns, as related above.
After the International Congress BiochroM'97 in Montpellier in 1997, Innessa A. Vislobokova (PIN) joined the NOW team as a Coordinator, and later Alexey Tesakov (GIN) also took part in this work. It was not an easy task to convert many faunas from this huge territory to NOW standards, because some old localities were tied only to the regional stratigraphical schemes, and their place in the NOW database was uncertain. Vislobokova and Tesakov subsequently continued in charge of these questions and with the updating of mammal lists from the localities of this territory. In 2000, Diana Pushkina joined the work on the NOW database, mainly searching for the interglacial Eemian faunas on the former USSR territories, while completing her PhD under Mikael Fortelius' supervision. Yet another NOW-story merits brief mention here.
Into the New World In the mid-1980s, Christine Janis (Fig. 2. 13) hatched the idea of compiling a book on North American Tertiary mammals (i. e. , Paleogene and Neogene mammals, the term "Tertiary" is now obsolete): the Pleistocene was excluded because of the existing compilation of Pleistocene North American mammals by  Kurtén and Anderson (1980) , and additionally the fact that including this time period would have vastly expanded the nature of the project. The notion was to encompass a who's who for each family that also included information on taxonomy, higher level systematics, ecomorphology (including a molar measurement for body size estimates), evolutionary patterns, standardized phylogenies and figures showing range times for each genus, and perhaps most importantly in terms of future utility for databases such as NOWa link for each species to a specific fossil locality.