Showing posts with label Useful resources. Show all posts
Showing posts with label Useful resources. Show all posts

Friday, October 10, 2014

The Tree of Life

Explore Life on Earth
(or if you need phylogeny help)
Explore Life on Earth
"The affinities of all the beings of the same class have sometimes been represented by a great tree... As buds give rise by growth to fresh buds, and these if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications."
Charles Darwin, 1859

Friday, February 3, 2012

Tidepool App

This looks very cool, and its free!

Make exploring the beach a fun and educational experience and learn about the creatures that inhabit this dynamic and important ecosystem.

It's one thing to find an urchin or a fish.

It's more fun to learn that a red urchin can live for 100 years, or that the fish you've just dicovered is a baby Opaleye that can breathe air when young!

Search a database containing: photos, common and scientific names, taxonomy, description, habitat, eats and eaten by, fun facts, frequently asked questions, and more.

This iPhone app works on an iPad too! And, is a great tool for teachers, naturalists, students, and anyone who is curious about tidepool life on the California coast.

Created by the Channel Islands National Marine Sanctuary, UCSB Marine Science Institute, LiMPETS (Long-term Monitoring Program and Experiential Training for Students), and volunteers from Citrix Systems, Inc. 

The App was also designed to raise awareness about the future Outreach Center for Teaching Ocean Science (OCTOS) which will increase ocean literacy by engaging visitors in scientific discovery (more at octos.ucsb.edu).

Search for Tidepools in the Apple Store and download using a wireless network as it is a fairly large file (186mb).
Screen shots and more info here: http://itunes.apple.com/app/california-tidepools/id497631839?mt=8

Thursday, January 19, 2012

MicrobeWiki

For researching topics and also for some good old fashioned random browsing I recommend MicrobeWiki. For example there was a question about whether the sulfur oxidizing chemoautotrophs I mentioned at the base of hydrothermal food webs were bacteria or achaea - turns out they are both and there is a really nice article at the MicrobeWiki site about Chemotrophy Along Seafloor Hydrothermal Vents.

Thursday, January 20, 2011

How to Learn Stuff

Bruce sent me a cool link on 'How to learn stuff'. Scroll down the page and you'll find some priceless advice.

Monday, November 22, 2010

I don’t know what to believe…

Thanksgiving and Christmas are times where we traditionally meet with family, eat too much and have awkward conversations with relatives we barely know and realize we have very little in common with.

If they find out you are a biologist chances are you'll get asked about topics ranging from global warming to this week's cancer scare. Here's a handy dandy resource for putting people straight about why they shouldn't necessarily believe it when they hear that cell phone towers are killing plants, will cure/cause cancer, or how scientists are all faking global warming. 

Have a safe Thanksgiving.

Wednesday, November 25, 2009

Faculty Research Interests

Faculty in EEMB and MCDB sorted by Research Interests

MCDB
Molecular genetics
Plant molecular biol
Microbial Pathogenesis
Neurobiology (molecular/cellular neuroscience)
Bioengineering 
Quantitative Biology/Omics
Developmental Biology
Biomaterials/Biomimetics
Virology and Immunology
Pharmacology
Cell Cycle/Cell Biology
Stem Cell Biology see also UCSB center for Stem Cell Biology and Engineering
    EEMB
    Biological oceanography
    Freshwater ecology
    Physiology & physiological ecology

      Evolution
      Marine ecology
      Parasitology and Infectious Diseases
      Community Ecology
      Mathematical ecology
      Microbial ecology

      Friday, October 9, 2009

      Writing, Reading, and Reviewing Scientific Articles

      This coming week in the bio colloquium we're reading an article from the primary literature. To provide general background on the elements of a scientific paper we also handed out "guidelines for writing a scientific paper". To help you think about it from the other end (reviewer vs. writer) you may want to see what guidelines the scientific journals provide their reviewers, that is, what helps us decide whether a paper is "publishable" by a given journal. This is useful in writing (and reading) a paper to see what the "critics" are looking for.

      Here is the link for reviewers for the journal, Ecology:
      http://esapubs.org/esapubs/reviewers.htm

      Also informative is the "Reviewers Information Pack" (http://www.nxtbook.com/nxteu/elsevier/reviewersinfopack/) for everything you might want to know about the review process for journal articles. This is provided by Elsevier, which publishes Developmental Biology, and hundreds of other journals (http://www.elsevier.com/wps/find/journal_browse.cws_home)

      Here's their reviewers' home page:
      http://www.elsevier.com/wps/find/reviewershome.reviewers

      Thursday, February 12, 2009

      A World of Possum-bilities II

      I'm reposting this, not just because I like the title, but because it is getting around to that time of year again. The picture to the left is just a very cute opossum, the picture below is the three baby opossums and this was originally posted at the start of April 2008.

      Having just utilized the services of the Santa Barbara Wildlife Care Network to find a home for three baby opossums that were left in my yard I thought I would give them a plug here. The woman I spoke to on the phone said that in a few weeks they will be inundated with birds and mammals and can use all the help they can get. If you want to get some volunteer experience working with animals this is a great opportunity. Their new location in the Fairview Center is convenient for campus too. You can complete an application on their website and they can use you even if you can only spare an hour or two a week.

      If you find injured wildlife during the day, you can take it to the Wildlife Care Network located near the OSH store in the Fairview Center in Goleta. After hours, weekends, and holidays, you can take it to the C.A.R.E. Hospital downtown (Garden & Haley) which is conveniently open 24 hours.

      Thursday, February 5, 2009

      UC Museums

      Todays visit to CCBER reminded me to remind me that as CCS students you are also UCSB students (well duh) but you are also UC students. The combined resources of the UC system are tremendous, and are potentially available to you as UC students.

      Berkeley, for example, has a tremendous set of museums and has much of their data online and searchable already.

      In another lifetime I worked on some websites at Berkeley and one of them had a table of all the departments, research groups and museums studying ecology and environmental change in California. This may be useful link to bookmark if you ever need museum data. Although I notice it's already out of date since I think I did most of the work in 2004 or 2005 and since then CCBER has replaced the Museum of Systematics and Ecology at UCSB. There are also pages of links to field sites, field stations, state agencies and much more.

      Remember these are all resources that are available. The use that you put them to is limited only by your imagination.

      Tuesday, January 13, 2009

      A Smörgåsbord of evolution

      A few earlier posts of relevance and a few links of interest.

      Previous Blog postings
      • Web sight - A 2006 Science paper about a fossilized spider web (I knew there was a good pun there somewhere)
      • Tiktaalik - Some links to the fishopod discovery and what we mean by the term 'missing link'.
      • Thirteen year old girls storming the Bastille - Sadly I did not come up with this wonderful imagery. It is from a New Yorker article on human height change and why Europeans are still getting taller but american aren't.
      • Resources - Some links to online places you can read Erasmus Darwin's work. And listen to Charles Darwin's work for free.
      Other links
      • The Berkeley Understanding Evolution webpage.
      • As Biologists you should be so thoroughly familiar with evolution that you know and can refute, as appropriate, the array of attacks against it. Icons of Evolution is a controversial book by the intelligent design advocate Jonathan Wells that focuses on 10 examples used to teach evolution. If you don't want to wade through the book you can read a summary article here. We have, or will, cover most of these examples in class. The National Center for Science Education has a nice paper by Alan Gishlick with the rather confrontational title of ' Why much of what Jonathan Wells writes about evolution is wrong.' Well worth a quick read.

      Tuesday, November 18, 2008

      CCS Biology Colloquium Resources available outside the Biology Departments

      The following is an incomplete list of resources available for research purposes outside of MCDB and EEMB, both on campus and otherwise in Santa Barbara.

      AT UCSB
      Anthropology
      Anthro has a teaching/reference collection of skeletal material of vertebrates that is largely focused to the interpretation of human habitation sites, but the collection and associated courses can be invaluable to students interested in questions of hard-part anatomy of vertebrates.
      • Amy Boddy - evolution, genomics, comparative genomics, human biology, evolutionary medicine, fetal-maternal conflict, life history theory, cancer
      • Michelle Brown - primate behavioral ecology, evolution of social systems, competition and cooperation, evolutionary game theory, behavioral endocrinology
      • Steven Gaulin – Evolutionary psychology
      • Mike Gurven - human social behavior and life history evolution
      • Amber Vanderwarker - Ethnobotany and zooarcheology 

      Biomolecular Science and Engineering (BMSE)
      The Interdepartmental Graduate Program in Biomolecular Science and Engineering epitomizes the highly interdisciplinary approach to research and education that is the hallmark of UC Santa Barbara. In this context BMSE offers a unique mix for graduate training and research at the frontiers of Biochemistry, Molecular Biology, Bioengineering and Biomolecular Materials. The BMSE Program may be for graduates, but an examination of Faculty research pages will lead you to some laboratories working on the forefront of materials and nano-technology where you might find a research option. See particularly:

      The Bren School of Environmental Sciences and Policy
      The Bren School is technically a graduate program. However, there are some good biological folk there, and if you can talk your way in, so much the better:

      Environmental Studies

      Department of Earth Science
      The department has several mass spectrometric facilities focused upon paleoclimatology recorded by isotopes of Carbon, Oxygen, strontium and others. These isotopes can be used to track other things too. The Paleontological Collections. Ostensibly part of the Museum of Systematics and Ecology, but housed in PSB South. Largely focused upon invertebrate fossils, particularly of the last 60 million years of southern California.

      Geography
      Extraordinary strengths in remote sensing; both in the use of existing technology and the development of new technologies. Very important for any research involving widespread geographic coverage.
      • Susan Cassels - Epidemiology & Mathematical modeling; social network analysis; infectious disease epidemiology.
      • Timothy DeVries - Interactions between chemical, biological, and physical processes in the marine carbon cycle, and in feedbacks between these processes and the Earth's climate
      • Hugo Loaciaga: Hydrology and Geology
      • Ed Keller: Hydrology and Geology
      • Keith Clarke: Remote Sensing
      • Jennifer King: Biogeochemistry, earth system science, global change, ecosystem ecology  
      • David Lopez-Carr: Human dimensions of global environmental change 
      • Joe McFadden: Land-use and land-cover change, biosphere-atmosphere interaction  
      • Dar Roberts:  Remote sensing of vegetation, geology, ecology, and ecophysiology   
      • David Siegel :  Interdisciplinary oceanography investigating physical, biological, optical and biogeochemical couplings on micro to ocean basin scales.
      • Anna Trugman: Using plant physiology, integrating field measurements with numerical ecosystem models to gain new insight into the biological processes affecting climate-vegetation interactions.
      • Kelly Caylor: Ecology and hydrology of dry lands.
      The Department of Geography hosts a wonderful resource, Spatial@UCSB, dedicated to visualizing and analyzing data in a 3D manner. They offer consultation on your data sets at specific hours.

      Psychology
      The Evolutionary Psychology program has strong ties to the Neurobiology Research Institute. People include:
      Psychology also contains many people who overlap in interests with MCDB:
      The sixteen faculty in the area of Biochemistry center around the common themes of bio-organic and bio-inorganic reaction mechanisms, protein-nucleic acid recognition, nucleic acid structure and dynamics, and membrane transport. They can offer expertise in a number of experimental tools such as Xray diffraction, computer graphics and computational analysis.


        The UCSB Library
        Beyond standard library resources, UCSB hosts the "Map and Imagery Library" (MIL) in the first floor of the SEL wing. This is a national repository, and has both digital and paper images of just about any kind of geographic reference you could want. This includes:
        • Topographic maps
        • Geologic Maps
        • Maps & volumes summarizing vegetation, climate, hydrology, cultural and other features;
        • Aerial photographs from landsat down to old plane-flown photographs.
        • And much more!

        The Marine Science Institute
        The Marine Science Institute (MSI), established at the University of California, Santa Barbara in 1969, is the focus for marine, coastal zone, and freshwater research; marine policy studies; and educational outreach in marine science. MSI administers and supports research projects involving faculty, professional researchers, technical staff, graduate students, and undergraduate students from 14 disciplines. There are a LARGE number of researchers associated with the MSI who are not faculty in one of the biology departments – and many are very student friendly. Some specific faculty to check out include :
        Tom Dudley, Jenny Dugan, Mark Page, Uta Passow, Dan Reed, and Milton Love (See especially Milton Love’s web page – it’s cool!). A complete list of MSI associated faculty can be found here.
        PISCO (Partnership for Interdisciplinary Studies of Coastal Oceans) is a large, long-term, ecosystem research and monitoring program that involves Santa Barbara and three other West Coast campuses (Oregon State, Stanford and UCSC).

        Center for Bioengineering
        The Center for BioEngineering (CBE) is a hub for research and teaching at the interface of biology, engineering and physical sciences. It builds on UC Santa Barbara’s strengths in biophysics, biomaterials, biomolecular discovery, and computational and experimental systems biology, enabling fundamental scientific discoveries to be transitioned to applications in medicine and biotechnology.

        Cheadle Center for the Study of Biodiversity and Ecosystem Restoration (CCBER)
        Located under the south end of the stadium. Used to be the Museum of Systematics and Ecology in EEMB, now independent. Houses the plant and animal collections of the University. Hosts a range of research projects, particularly concerning biodiversity and the reclamation of local ecosystems. Very strong programs in outreach to local school children. Check out their internships.

        National Center for Ecological Analysis and Synthesis (NCEAS)
        An outstanding international think tank on anything ecological and a lot evolutionary. It is a cross road of visiting scientists, in house researchers and periodic work groups who have access to a series of immense computerized databases that allow researchers to seek out explanations for gross patterns in Nature. Many UCSB faculty and graduate students participate, and there are frequent opportunities to work as paid data-collectors or enterers. NCEAS is located on State Street, in the center of the Paseo Nuevo. Note that they have a Thursday lunch seminar that hosts internationally known scholars.

        The UC Natural Reserve System.
        The UC System is unusual (not quite unique) in owning its own set of natural reserves dedicated to instruction and research. Each reserve is selected as representative of an important ecosystem in California. Most are managed by resident scientists. All are available for visitation or research with proper initial approval (signing of waiver forms indicating respect of the property, etc. ). Each Reserve has its own web site, and most list past research conducted on the Reserve. A good way to see who is doing what.

        UCSB has one on campus (Coal Oil Point Note particularly here that Cristina Sandoval (director of Coal Oil Point) is an active researcher who interacts with undergrads) and two nearby (Sedgwick Reserve & Carpinteria Salt Marsh). We also manage the Santa Cruz Island Reserve, the Kenneth S. Norris Rancho Marino Reserve near Cambria, the Sierra Nevada Aquatic Research Lab in Bishop, and the Valentine Camp on the eastern face of the High Sierra.

        OFF CAMPUS

        Channel Islands National Park (And the Channel Islands National Marine Sanctuary)
        The National Park Service manages several of the Channel Islands, and is interested in supporting research on them. Most of their voucher specimens come to Museum of Natural History

        Lotusland Botanic Garden
        Located in Montecito, Lotusland occupies 38 acres, much planted with exotic plant species in striking array. Lotusland has the world's third largest collection of cycads, and outstanding collections of Agave, Aloe and cool-tolerant palms. The garden is looking to become increasingly involved in research.

        Santa Barbara Botanic Garden
        Nearly a century old, the garden focuses upon native Californian plants. It has an outstanding living collection arranged by habitats, and a good library and herbarium focused in native flora. The Garden has a long-standing reputation for research into native Californian plants, and the biogeography of the Channel Islands. Research students interested in botany would do well to explore this. The Garden has a long-standing reputation for research into native Californian plants,
        ( and https://www.sbbg.org/conservation-research/black-holes-blog) and the biogeography of the Channel Islands.

        Santa Barbara Museum of Natural History and Sea Center.
        The Museum of Natural History is likewise nearly a century old, and has an established research reputation. It has internationally-recognized collections of living Mollusca and bird egg shells, and a very strong collection of marine invertebrates of the Santa Barbara Channel. Other collections include an excellent collection of mammals, particularly marine mammals, of southern California, a wide range of fossil whale material, a decent insect collection, and collections of particularly Pleistocene fossil marine and terrestrial organisms. It hosts active researchers working on -
        Marine Mammals - Krista A. Fahy, Michelle L. Berman
        Marine octopods - F. G. Hochberg
        Marine gastropods - Henry Chaney
        Marine Mollusca - Paul Valentich Scott
        Ethnobotany - Jan Timbrook,
        Vertebrate Biology - Paul Collins, Patricia Sadeghian
        Vertebrate Paleontology - Jonathan Hoffman
        Invertebrate zoology (gastropods) - Daniel Geiger

        Santa Barbara Zoological Gardens

        The Zoo is mostly dedicated to the culture and reproduction of living, endangered, taxa. However, while they might not take kindly to dissecting a living animal, they certainly offer opportunities to examine behavior, and who knows what else might be worked out.

        USC Wrigley Marine Science Center, Catalina Island
        For those of you with marine interests, a local (SoCal) resource is the Wrigley Marine Science Center on Catalina island, run by USC. It offers research opportunities and summer courses.

        Thursday, November 6, 2008

        REU site

        A couple of the students on Wednesday mentioned the National Science Foundation's Research Experience for Undergraduates program. NSF maintains an extensive website where you can find details of what the REU program is all about and allows you to list the sites by subject or state. The list of sites in the Biological Sciences is impressive. Many (most?) of the REU programs run over the summer so this is early notice of something you may want to consider for next summer.

        Thursday, February 14, 2008

        UC

        Todays visit to CCBER reminded me to remind me that as CCS students you are also UCSB students (well duh) but you are also UC students. The combined resources of the UC system are tremendous, and are potentially available to you as UC students.

        Berkeley, for example, has a tremendous set of museums and has much of their data online and searchable already.

        In another lifetime I worked on some websites at Berkeley and one of them had a table of all the departments, research groups and museums studying ecology and environmental change in California. This may be useful link to bookmark if you ever need museum data. Although I notice it's already out of date since I think I did most of the work in 2004 or 2005 and since then CCBER has replaced the Museum of Systematics and Ecology at UCSB. There are also pages of links to field sites, field stations, state agencies and much more.

        For those who enjoy very slight coincidences (everyone, right?). I just finished reading 'Anthrax: The Investigation of a Deadly Outbreak' about the Sverdlovsk anthrax leak, an incident where spores of anthrax were accidentally released from a military facility in the city of Sverdlovsk in the former Soviet Union in 1979. The ensuing outbreak of the disease resulted in 94 people becoming infected, 64 of whom died over a period of six weeks. The outbreak was denied by the Soviet Union for decades. Prior to communist rule Sverdlovsk was known as Yekaterinburg. In fact it has reverted to this name again today. Having gone my whole life without ever hearing of this town it seemed a coincidence to hear that was where Katherine Essau was from.

        Tuesday, February 12, 2008

        Deep Green

        Page from Darwin's notebooks around July 1837 showing his first known sketch of an evolutionary tree.

        There are a number of useful resources on the web to help you understand the relationship between the different plant groups and explore their diversity.

        The Tree of Life is a collaborative project that provides information about the diversity of organisms on Earth, their evolutionary history and their characteristics. The link above takes you to the main page or you can skip directly to the green plants.

        The Green Plant Phylogeny Research Group (Deep Green) is a group that coordinates research into the phylogeny of the green plants. Their website contains a useful hyperbolic tree. Hyperbolic trees are one way to display complex trees clearly. I posted a link to the hyperbolic trees earlier when we talked about phylogenies.

        The Green Tree of Life aims to resolve the primary pattern of evolutionary diversification among green plants. An overview of the results to date can be seen in this poster.

        Tuesday, January 15, 2008

        Resources

        You can find Erasmus Darwin's work at the Internet Archive Open-Access Text Archive - a wonderful resource with over 200,000 items, most of them out of copyright or otherwise in the public domain.

        Here are links to the Temple of Nature, and Zoonomia. Select the format you want to download from the panel on the left.

        You can also find Erasmus at Project Gutenberg, the first producer of free electronic books. They have Zoonomia and the Botanic Garden. They also have most of Charles Darwin's books, including the more obscure ones.

        Whilst I'm pointing out resources I should also mention Librivox, which provides free audiobooks of books that are in the public domain. This includes a nice reading of Darwin's Origin of Species. (Full title:
        On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.)

        Monday, January 14, 2008

        Read widely

        One of the best pieces of advice to a young scientist is to read, and read widely. The internet has made this whole lot easier and there are numerous sites out there that will direct you to papers worth reading in whatever areas your interest takes you. Over the next few weeks we will be covering a number of topics in evolution. Two blogs that are worth checking out for some clear writing and interesting links on these topics are:

        PZ Meyers Pharyngula blog - self-described as 'Evolution, development and random biological ejaculations from a godless liberal'. That seems to describe it fairly well. PZ Myers is a biologist and associate professor at the University of Minnesota (and the pharyngula period is a stage in the embryonic development of vertebrates).

        Speaking of the godless, and I mean that quite genuinely, Richard Dawkins has two websites/blogs that are well worth checking out. The official Richard Dawkins website self-described as 'A Clear-Thinking Oasis' and the Richard Dawkins Foundation for Reason and Science (another Clear-Thinking Oasis'). Richard Dawkins holds the Charles Simonyi Chair for the Public Understanding of Science at Oxford University. He came to prominence through his 'Selfish Gene' book in 1976, a book that all Biology undergraduates at my University were recommended to read a decade after its publication - a recommendation I am happy to pass on thirty years after its publication (that makes me 43 if you are curious, I know I look much younger....). Lately Richard Dawkins has been rather prominently involved in the debate between creationism and evolution and is often described, usually by others, as an 'outspoken atheist'. His latest book, 'The God Delusion', combines his work on evolutionary biology and his passionate atheism to ask why, if there is no god, a belief in one so widespread and prominent as to be almost universal? In the hands of an evolutionary biologist this turns out to be quite an interesting question.

        Friday, January 11, 2008

        Interactive Tree of Life

        I've never had enough time to investigate it fully but the Interactive Tree of Life looks like an amazing tool that provides a whole suite of ways to represent, manipulate, and display phylogenetic trees. One of my interests is in the graphical representation of data (see Edward Tufte's forum/blog for some superb discussions on this) and the Interactive Tree of Life website combines both this and biology. Presenting such complex data in a way that people can understand is not easy so it's great to be able to see a whole bunch of different attempts at this - you can scroll through several on the right hand side of the webpage. A related way of presenting the complexity of a tree of life is the hyperbolic tree approach at the Deep Green website. Notice how you can pick up nodes and move through the tree.