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Archive for November 2011

The eternal value of Natural History and the dazzling molecular promise

nescent imageThe advent of highly efficient and low cost sequencing techniques along with increased computing power have been important catalysts for the massive generation of genomic data (Davey et al., 2011). In parallel have come studies of gene expression and regulation, each of which has earned its own field such as "trancriptomics," "proteomics," "metabolomics," etc. (Zhou et al., 2011). In addition, the combination of these disciplines with ideas associated with graph theory has produced a new area of study called Systems Biology (Saito and Matsuda, 2010). Certainly in the last 30 years we have learned more than we ever imagined and unexpected avenues of research have opened. Every day the dream of deciphering the genetic identity of every living organism becomes more and more possible.

However, in the middle of the Post-Genomic Era it has become clear that we have forgotten something. That "something" is what has been fundamental to biology since its inception: Natural History. The great technical complexity, versatility and explanatory power of molecular studies have produced a shadow on the more “traditional” approaches. Some argue that the age of exploration to remote areas and the discovery of new species and detailed monographs with morphological descriptions are part of a distant and romantic past. However, we have described about 1.8 million species and there are calculations that estimate a total of 10 million without considering those present in the fossil record. Is the exercise of the natural history really an anachronistic activity?

The lack of knowledge of the species with which we share our planet is only the tip of the iceberg, because in many cases the knowledge of the biology of those already described is even more precarious. Walking through the shelves of various libraries I have found that most new books address issues associated with genetics and molecular biology, while most of those which are about anatomy or taxonomy are written in brown paper and illustrated in ink. At some point I thought the latter would look good in a museum, but now I have another opinion. Who is capable of replicating that knowledge today? How many students are being instructed in these areas today? To my relief a few names do come to mind, but it’s is a very small number.

Faced with this "molecularization" of biology, those old natural history books take a new value as the sole repository of a discipline that in many cases has not been practiced for years. So those faded pages are the only remnant we have of that knowledge. Not only are the data and descriptions in these books important, but the hypotheses and speculations have enormous value, because they are the products of an integration that emerged from someone who had an extensive knowledge of biodiversity. So despite the lack of molecular understanding these ideas have elements that only someone who has spent years in the field or amongst museum specimens is able to see.

The lack of support for the study of natural history is a critical problem that if left alone will likely reach a tipping point from which recovery would be difficult if not impossible. The lack of master-apprentice continuity in the study of a group of organisms can be fatal, because much of the taxonomic and technical knowledge is simply lost. What is the cause of this trend?

As was the case with positivism, when it was stressed that all of the sciences be quantifiable and models, today molecular biology shines with its own splendor. This glow was won by the large amount of data and the results that have been produced from it. However, it has also shaded the importance of non-molecular studies.

This can be seen not only in major research programs, but also in the training of future biologists. More than once I came to know a great deal of metabolic and genomic data for a particular organism, but had no idea how big it was. Similarly, on several occasions I have seen how the tree of life is reduced to a phylogeny of only "model organisms."

Although the molecular approach can reveal a lot of secrets, there are other secrets that molecular approaches simply cannot reveal. The over-emphasis of techniques, can reduce or even stop the investment of resources in non-molecular studies and close funding opportunities and job positions. In an extreme case, this could make taxonomists swell the lists of endangered species that only they are able to recognize.

The dazzling molecular promise is that by reducing everything to its scale, it would allow an understanding of most biological phenomena. This initially generated great enthusiasm, but it also prohibits considering the existence of unique properties at different levels of organization that are not possible to study from a simple decomposition of the whole into numerous small parts. Molecular tools have opened vast windows in understanding the phenomenon of life, but like all tools, are not able to open them all. It is important to overcome the excitement of a novelty itself and be able to assess the limitations of these powerful techniques.

The eternal value of natural history, on the other hand, relates to the fact that the questions like "What is this?," "Where does it come from?," "What does it eat?" never become outdated. The human capacity to identify and recognize the components of the natural world is the foundation of all our biological knowledge. For hundreds of years the tools of natural history have remained unchanged, and the data produced by these tools is critical for the future as well. Either deep in the forest or collecting along the coast line, whenever the naturalist finds a new organism he/she always returns to the same eternal questions ….

Darko Cotoras Ph.D.(c)
Department of Integrative Biology
University of California, Berkeley

This text will be presented in the blog contest sponsored by National Evolutionary Synthesis Center (NESCent). It is based on: “El eterno valor de la historia natural y la encandilante promesa molecular” uploaded by the author to on 08/04/2011.

Literature cited

Davey J.W., P.A. Hohenlohe, P.D. Etter, J.Q. Boone, J.M. Catchen, and M.L. Blaxter. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12:499-510.

Saito K., and F. Matsuda. 2010. Metabolomics for functional genomics, systems biology, and biotechnology. Annual Review of Plant Biology 61:463–89.

Zhou Z., J. Gu, Y. Du, Y. Li, and Y. Wang. 2011. The -omics era — toward a systems-level understanding of Streptomyces. Current Genomics 12:404-416.

Cal Day 2011 Highlights!

Interested in learning more about fossils and what they can tell us about the history of life and how they inform our understanding of biodiversity and climate change?  Well you're in luck!  Just join us for Cal Day!  Every April the UCMP and the entire campus is open to the public to engage with UC Berkeley's ongoing research. Check out the events during the 2011 Cal Day in the video below and be inspired to join us next year, April 21, 2012!


UCMP at the Bay Area Science Festival

UCMP joined the other Berkeley Natural History Museums, the Space Science Lab, Departments of Physics and Chemistry, SynBERG, nanotechnology experts, and a host of other science units as part of the campus-wide participation in the first annual Bay Area Science Festival – a 10 day celebration of science extending from San Jose to Santa Rosa!

Dave Lindberg gave a great talk on The History of Kelp Forests: Global and Local Surprises at the November East Bay Science Café and Rosemary Romero and Jenna Judge intrigued the huge crowds at the "fossil booth" at the culminating festival event at AT&T Park last Sunday! At last, it was revealed who lived there before the San Francisco Giants!

Under the umbrella of Science@Cal these were just two of numerous activities to engage the public of all ages and to share the value of science research at Cal. Read more on the Science@Cal site.

Science@Cal efforts were also a little outside of the box including science at local farmers' markets and in local art studios – see Art in Science.

And for more on the festival, visit Bay Area Science!

UCMP at the 71st Annual Meeting of the Society of Vertebrate Paleontology

Las Vegas SVP logoThe 71st Annual Meeting of the Society of Vertebrate Paleontology took place November 2-5 in the Paris Las Vegas Hotel on the dazzling Vegas strip, and UCMP's usual presence was as strong as ever. At least 18 Berkeley faculty, staff, graduate students, and undergraduates presented talks or contributed to posters highlighting the range of work UCMP and affiliates accomplish, from bird development to biogeography, ecosystem conservation to dinosaur histology. In case you missed out on all the fun, check out the talk/poster titles and abstracts below.

ATTERHOLT, J. 2011. Phylogenetic mapping of the avian altricial-precocial spectrum and its implications for inferring early avialan life history. Journal of Vertebrate Paleontology 31(3, suppl.):64-65A. Abstract

CARRASCO, M. 2011. Comparing extant mammalian species diversity to paleospecies richness: Problems and solutions. Journal of Vertebrate Paleontology 31(3, suppl.):85A. Abstract / download the Powerpoint presentation

Carroll, N., A. POUST, and D. Varricchio. 2011. A third azhdarchid pterosaur from the Two Medicine Formation (Campanian) of Montana. Journal of Vertebrate Paleontology 31(3, suppl.). Abstract

FERRER, E.A., and N.J. MATZKE. 2011. Are raw taxic counts really reflecting shifts in diversity dynamics? A case study in canids. Journal of Vertebrate Paleontology 31(3, suppl.). Abstract

GOODWIN, M., K. Stanton, J.R. Horner, and S.J. Carlson. 2011. Oxygen isotopic variability and preservation in Tyrannosaurus rex, modern ratites and crocodylians: Revisiting the thermophysiology of T. rex using Δ18O. Journal of Vertebrate Paleontology 31(3, suppl.):117-118A. Abstract / Select slides from the presentation

HUYNH, T., S. Cam, A. Kwong, H. Mehrabani, K. Tse and D. Evangelista. 2011. Aerodynamic characteristics of feathered dinosaur shapes measured using physical models: a comparative study of maneuvering. Journal of Vertebrate Paleontology 31(3, suppl.). Abstract

LINDSEY, E.L. 2011. A sloth-dominated late-Quaternary asphalt seep from Santa Elena, Ecuador. Journal of Vertebrate Paleontology 31(3, suppl.). Abstract

LIPPS, J.H. 2011. PaleoParks: Preservation and conservation of fossil sites worldwide. Abstract

Matzke, N., and K. MAGUIRE. 2011. Inclusion of fossil species range data in dispersal-extinction-cladogenesis (DEC) analyses aorrects low estimates of extinction rate and improves estimates of historical biogeography. Journal of Vertebrate Paleontology 31(3, suppl.):154A. Abstract

Morris, Z., and E.A. FERRER. 2011. Ontogenetic variation in epiplastral shape among Eocene testudinoid turtles (Echmatemys) of western North America. Journal of Vertebrate Paleontology 31(3, suppl.). Abstract

PADIAN, K. 2011. Phylogenetic distribution of ecological traits in the origin of bats. Journal of Vertebrate Paleontology 31(3, suppl.):170A. Abstract / Nature news blog

STEGNER, A., and M. HOLMES. 2011. Using paleontological databases to assess spatial and temporal conservation of mammalian community structure as an aid to conservation planning. Journal of Vertebrate Paleontology 31(3, suppl.):199A. Abstract