26 posts · 15,708 views
I want to make cutting-edge biology research accessible to those who do not have the background, and to attempt to illuminate why it is so important that we spend billions of dollars each year to study how sex is determined in a nematode, how a particular species of tree disperses its seeds, or what changes take place when a yeast cell ages and dies. These studies may not seem relevant — but I will try to convince you, along with myself, that they are, and how they could change the way we live.
Hannah Waters
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- July 19, 2010
- 09:19 AM
- 1,256 views
DMS(P): the amazing story of a pervasive indicator molecule in the marine food web
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
Dimethylsulfide. Does that word mean anything to you? “Why yes,” you organic chemistry nerds may say, “It clearly is a molecule of sulfur with two methyl groups attached.” That’s as far as I could have gotten – until this past week, when I inundated myself with information on dimethylsulfide (DMS) due to a paper published [...]... Read more »
DeBose, J., Lema, S., & Nevitt, G. (2008) Dimethylsulfoniopropionate as a Foraging Cue for Reef Fishes. Science, 319(5868), 1356-1356. DOI: 10.1126/science.1151109
Nevitt, G. (2008) Sensory ecology on the high seas: the odor world of the procellariiform seabirds. Journal of Experimental Biology, 211(11), 1706-1713. DOI: 10.1242/jeb.015412
Seymour, J., Simo, R., Ahmed, T., & Stocker, R. (2010) Chemoattraction to Dimethylsulfoniopropionate Throughout the Marine Microbial Food Web. Science, 329(5989), 342-345. DOI: 10.1126/science.1188418
Simó, R. (2001) Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends in Ecology , 16(6), 287-294. DOI: 10.1016/S0169-5347(01)02152-8
Stefels, J., Steinke, M., Turner, S., Malin, G., & Belviso, S. (2007) Environmental constraints on the production and removal of the climatically active gas dimethylsulphide (DMS) and implications for ecosystem modelling. Biogeochemistry, 83(1-3), 245-275. DOI: 10.1007/s10533-007-9091-5
Van Alstyne, K., Wolfe, G., Freidenburg, T., Neill, A., & Hicken, C. (2001) Activated defense systems in marine macroalgae: evidence for an ecological role for DMSP cleavage. Marine Ecology Progress Series, 53-65. DOI: 10.3354/meps213053
G. V. Wolfe, M. Steinke, & G. O. Kirst. (1997) Grazing-activated chemical defence in a unicellular marine alga. Nature, 894-897. info:/
- April 20, 2010
- 11:21 AM
- 1,000 views
Octopuses doing tricks on the internet and our search for non-human “intelligence”
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
An underwater photographer has his camera stolen by a thieving octopus, who flees with the device, filming along the way. Sure, he was filming his own flesh, but baby’s first movie isn’t too shabby.
People love to talk about octopus “intelligence.” The photographer specifies that the octopus wasn’t attacking him, but just wanted to steal [...]... Read more »
Edelman, D., Baars, B., & Seth, A. (2005) Identifying hallmarks of consciousness in non-mammalian species. Consciousness and Cognition, 14(1), 169-187. DOI: 10.1016/j.concog.2004.09.001
Mather, J. (2008) Cephalopod consciousness: Behavioural evidence. Consciousness and Cognition, 17(1), 37-48. DOI: 10.1016/j.concog.2006.11.006
SETH, A., BAARS, B., & EDELMAN, D. (2005) Criteria for consciousness in humans and other mammals. Consciousness and Cognition, 14(1), 119-139. DOI: 10.1016/j.concog.2004.08.006
- June 18, 2010
- 11:49 AM
- 930 views
Microbe biogeography: the distribution, dispersal and evolution of the littlest organisms
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
In any high school biology class1, we learn that isolation is key to the evolution of species. For example, take Australia, where an array of marsupials such as koalas and kangaroos reproduce like no other animals on the planet. Isolation on a continental island allowed ancestral marsupials to evolve gestation via pouch, a trait which [...]... Read more »
Cermeño, P., de Vargas, C., Abrantes, F., & Falkowski, P. (2010) Phytoplankton Biogeography and Community Stability in the Ocean. PLoS ONE, 5(4). DOI: 10.1371/journal.pone.0010037
Fenchel, T., & Finlay, B. (2004) The Ubiquity of Small Species: Patterns of Local and Global Diversity. BioScience, 54(8), 777. DOI: 10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2
Martiny, J., Bohannan, B., Brown, J., Colwell, R., Fuhrman, J., Green, J., Horner-Devine, M., Kane, M., Krumins, J., Kuske, C.... (2006) Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology, 4(2), 102-112. DOI: 10.1038/nrmicro1341
O'Malley, M. (2007) The nineteenth century roots of 'everything is everywhere'. Nature Reviews Microbiology, 5(8), 647-651. DOI: 10.1038/nrmicro1711
- February 11, 2010
- 06:54 AM
- 754 views
Nature-inspired network design: recent studies in slime mold and leaf veins
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
Nature-inspired design: this phrase makes me think of shark-skin swimsuits, velcro, and an endless assortment of coffee tables using natural knots and tree branches. There is logic behind design reliant upon natural elements. After all, organisms have been undergoing evolution for millions of years for the sake of efficiency. If anyone knows how to [...]... Read more »
Andrew Adamatzky, & Jeff Jones. (2009) Road planning with slime mould: If Physarum built motorways it would route M6/M74 through Newcastle. International Journal of Bifurcation and Chaos. arXiv: 0912.3967v1
Katifori, E., Szöllősi, G., & Magnasco, M. (2010) Damage and Fluctuations Induce Loops in Optimal Transport Networks. Physical Review Letters, 104(4). DOI: 10.1103/PhysRevLett.104.048704
Tero A, Takagi S, Saigusa T, Ito K, Bebber DP, Fricker MD, Yumiki K, Kobayashi R, & Nakagaki T. (2010) Rules for biologically inspired adaptive network design. Science (New York, N.Y.), 327(5964), 439-42. PMID: 20093467
- December 24, 2009
- 12:31 PM
- 744 views
How dirt affects global atmospheric carbon dioxide (Wingate et al. 2009, PNAS)
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
I have a tendency to root for the underdog. I rooted for the Phillies throughout the 90s, when my heroes Lenny Dykstra and Darren Dalton could rarely lead them to a win. It’s a mixture of a desire for upheaval, that the unexpected can happen, as well as pure sympathy for the ones who [...]... Read more »
Wingate, L., Ogee, J., Cuntz, M., Genty, B., Reiter, I., Seibt, U., Yakir, D., Maseyk, K., Pendall, E., Barbour, M.... (2009) The impact of soil microorganisms on the global budget of 18O in atmospheric CO2. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0905210106
- March 2, 2010
- 11:14 PM
- 737 views
Invasive species corrupt DNA, not just ecosystems (Fitzpatrick et al., PNAS 2010)
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
I rarely think about how invasive species affect genetics. It’s always in terms of ecosystems or species: invasive brown tree snakes gobbling up birds and lizards in Guam, or zebra mussels overwhelming and altering the environment of the Great Lakes. How one species outcompetes and replaces another, changing the natural system. This is partly [...]... Read more »
Fitzpatrick, B., Johnson, J., Kump, D., Smith, J., Voss, S., & Shaffer, H. (2010) Rapid spread of invasive genes into a threatened native species. Proceedings of the National Academy of Sciences, 107(8), 3606-3610. DOI: 10.1073/pnas.0911802107
- February 5, 2010
- 03:29 PM
- 676 views
How to measure the progress of science (Rosvall and Bergstrom, PLoS 2010)
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
No one can deny that the field of science is undergoing explosive growth. The “technological age” has treated it kindly, giving it both access to new equipment and techniques, as well as creating a larger scientific community with more connections between labs around the world. We are bombarded with information in general: hundreds of papers [...]... Read more »
Rosvall, M., & Bergstrom, C. (2010) Mapping Change in Large Networks. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008694
- June 25, 2010
- 11:28 AM
- 650 views
How did they get there? The colonization of a hydrothermal vent after volcanic eruption
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
To some people, a volcanic eruption means “Ahh! Run! Hot Lava!” But to others, it means “SCIENCE!” To those studying hydrothermal vent communities, that is (and a wide berth of geologists). Hydrothermal vents are cracks in the seafloor formed when tectonic plates spread apart, which spew out hot, mineral-rich water from the interior of the [...]... Read more »
Mullineaux, L., Adams, D., Mills, S., & Beaulieu, S. (2010) Larvae from afar colonize deep-sea hydrothermal vents after a catastrophic eruption. Proceedings of the National Academy of Sciences, 107(17), 7829-7834. DOI: 10.1073/pnas.0913187107
- April 7, 2010
- 05:36 PM
- 640 views
Animals without oxygen and their implications for the evolution of life
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
It’s been a slow few weeks around here at Culturing Science. It’s due to a little bit of writer’s block, but mainly it’s just the beautiful weather keeping me outdoors and away from the computer. Hopefully you’ve been outside so much that you haven’t noticed.
But today my dream article was published: microorganisms, extreme environments, evolution, [...]... Read more »
Danovaro, R., Dell'Anno, A., Pusceddu, A., Gambi, C., Heiner, I., & Kristensen, R. (2010) The first metazoa living in permanently anoxic conditions. BMC Biology, 8(1), 30. DOI: 10.1186/1741-7007-8-30
- May 25, 2010
- 10:13 AM
- 623 views
Molecular biology and globsters: dashing cryptozoologists’ dreams
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
On July 29th 2008, the day I turned 21 years, I received the best thing I could ask for: a birthday gift from Poseidon. I was living in Newport, OR at the time. After a long morning of observing nesting seabirds through a telescope, I returned home for what I presumed to be a long [...]... Read more »
Carr, S., Marshall, H., Johnstone, K., Pynn, L., & Stenson, G. (2002) How to Tell a Sea Monster: Molecular Discrimination of Large Marine Animals of the North Atlantic. Biological Bulletin, 202(1), 1. DOI: 10.2307/1543217
Pierce, S., Massey, S., Curtis, N., Smith, G., Olavarria, C., & Maugel, T. (2004) Microscopic, Biochemical, and Molecular Characteristics of the Chilean Blob and a Comparison with the Remains of Other Sea Monsters: Nothing but Whales. Biological Bulletin, 206(3), 125. DOI: 10.2307/1543636
- June 22, 2010
- 04:05 PM
- 617 views
Inevitability and Oil, Pt. 1: the inherent risk for accidents in complex technology
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
When I read updates on blogs or the news about the BP oil spill, my expression is generally very serious: furrowed brow, pursed lips which I’m probably chewing in alternation with gnawing a nail. But last week I laughed out loud, a true LOL, a brash guffaw. (“What?!” my labmates inquired.) I had read this [...]... Read more »
Gephart, R. (2004) Normal Risk: Technology, Sense Making, and Environmental Disasters. Organization , 17(1), 20-26. DOI: 10.1177/1086026603262030
Leveson, N., Dulac, N., Marais, K., & Carroll, J. (2009) Moving Beyond Normal Accidents and High Reliability Organizations: A Systems Approach to Safety in Complex Systems. Organization Studies, 30(2-3), 227-249. DOI: 10.1177/0170840608101478
Weick, K. (2004) Normal Accident Theory As Frame, Link, and Provocation. Organization , 17(1), 27-31. DOI: 10.1177/1086026603262031
- January 12, 2010
- 12:26 AM
- 600 views
Why research articles should be publicly accessible (Shulenburger 2009, PLoS Biology)
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
I cannot even count the number of times when I have been denied access to a journal article I needed. Oftentimes, it was while I was working on a paper in college and couldn’t read the paper that all the other scholars cited, or the paper that supported an argument I was trying to make. [...]... Read more »
Shulenburger, D. (2009) University Public-Access Mandates Are Good for Science. PLoS Biology, 7(11). DOI: 10.1371/journal.pbio.1000237
- December 15, 2009
- 08:55 AM
- 581 views
Apoptosis, or programmed cell death, is regulated by the protein RanBPM (Atabakhsh et al. 2009, Molecular Cancer Research)
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
I have been fearful of molecular biology for most of my life. This is partially because I so clearly defined myself as an ecologist that I partitioned molecules into “little biology” and out of my range. But mostly it was a fear of what I considered unnatural. Scientists who play around with chemicals and [...]... Read more »
Atabakhsh, E., Bryce, D., Lefebvre, K., & Schild-Poulter, C. (2009) RanBPM Has Proapoptotic Activities That Regulate Cell Death Pathways in Response to DNA Damage. Molecular Cancer Research. DOI: 10.1158/1541-7786.MCR-09-0098
- February 8, 2011
- 10:20 PM
- 541 views
The many relationships of leaf-cutter ants
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
Trying to capture the movement of a colony of leaf-cutter ants in a single photo is nearly impossible in my (amateur) experience. The queues of ants follow a worn-down trail in the ground that they themselves made with the impact of their little ant feet. There are ants moving in both directions, between the food [...]... Read more »
Currie, C., Scott, J., Summerbell, R., & Malloch, D. (1999) Fungus-growing ants use antibiotic-producing bacteria to control garden parasites. Nature, 398(6729), 701-704. DOI: 10.1038/19519
Schoenian, I., Spiteller, M., Ghaste, M., Wirth, R., Herz, H., & Spiteller, D. (2011) Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants. Proceedings of the National Academy of Sciences, 108(5), 1955-1960. DOI: 10.1073/pnas.1008441108
- July 28, 2010
- 09:12 AM
- 531 views
Forest canopy height: why do we care?
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
If you’ve been on the internet at all in the past week, you’ve probably seen these lovely images from NASA, visualizing the height of tree canopies around the world. They’ve been on science sites along with art ones. In a sense, that alone is useful: using beautiful visuals to make people think about the world [...]... Read more »
Cohen, W., Harmon, M., Wallin, D., & Fiorella, M. (1996) Two Decades of Carbon Flux from Forests of the Pacific Northwest. BioScience, 46(11), 836. DOI: 10.2307/1312969
Lefsky, M., Cohen, W., Harding, D., Parker, G., Acker, S., & Gower, S. (2002) Lidar remote sensing of above-ground biomass in three biomes. Global Ecology and Biogeography, 11(5), 393-399. DOI: 10.1046/j.1466-822x.2002.00303.x
Lefsky, M., Harding, D., Keller, M., Cohen, W., Carabajal, C., Del Bom Espirito-Santo, F., Hunter, M., & de Oliveira, R. (2005) Estimates of forest canopy height and aboveground biomass using ICESat. Geophysical Research Letters, 32(22). DOI: 10.1029/2005GL023971
Running, S. (1999) A Global Terrestrial Monitoring Network Integrating Tower Fluxes, Flask Sampling, Ecosystem Modeling and EOS Satellite Data. Remote Sensing of Environment, 70(1), 108-127. DOI: 10.1016/S0034-4257(99)00061-9
Silva, L., Anand, M., & Leithead, M. (2010) Recent Widespread Tree Growth Decline Despite Increasing Atmospheric CO2. PLoS ONE, 5(7). DOI: 10.1371/journal.pone.0011543
- January 21, 2010
- 12:16 AM
- 528 views
Photosynthetic Evolution: how 2 organisms gained or lost the ability to eat sunshine
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
Biologists and taxonomists love to put organisms into categories to help us organize the complicated living world. I grew up on the 5 kingdom system of classification: plants, animals, fungi, bacteria and protists. The first four categories seemed simple enough, but the term “protists” always confused me. This kingdom seemed to be a dumping ground [...]... Read more »
de Castro, F., Gaedke, U., & Boenigk, J. (2009) Reverse Evolution: Driving Forces Behind the Loss of Acquired Photosynthetic Traits. PLoS ONE, 4(12). DOI: 10.1371/journal.pone.0008465
Rumpho, M., Worful, J., Lee, J., Kannan, K., Tyler, M., Bhattacharya, D., Moustafa, A., & Manhart, J. (2008) Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proceedings of the National Academy of Sciences, 105(46), 17867-17871. DOI: 10.1073/pnas.0804968105
- August 19, 2010
- 12:33 PM
- 510 views
Marine Snow: dead organisms and poop as manna in the ocean
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
“When I think of the floor of the deep sea…I see always the steady, unremitting, downward drift of materials from above, flake upon flake, layer upon layer…the most stupendous “snowfall” the earth has ever seen.” -Rachel Carson, The Sea Around … Continue reading →... Read more »
Bochdansky, A., van Aken, H., & Herndl, G. (2010) Role of macroscopic particles in deep-sea oxygen consumption. Proceedings of the National Academy of Sciences, 107(18), 8287-8291. DOI: 10.1073/pnas.0913744107
Boyce, D., Lewis, M., & Worm, B. (2010) Global phytoplankton decline over the past century. Nature, 466(7306), 591-596. DOI: 10.1038/nature09268
Fowler, S., Buat-Menard, P., Yokoyama, Y., Ballestra, S., Holm, E., & Nguyen, H. (1987) Rapid removal of Chernobyl fallout from Mediterranean surface waters by biological activity. Nature, 329(6134), 56-58. DOI: 10.1038/329056a0
Goldthwait, S., Carlson, C., Henderson, G., & Alldredge, A. (2005) Effects of physical fragmentation on remineralization of marine snow. Marine Ecology Progress Series, 59-65. DOI: 10.3354/meps305059
Iseki, K. (1981) Particulate Organic Matter Transport to the Deep Sea by Salp Fecal Pellets. Marine Ecology Progress Series, 55-60. DOI: 10.3354/meps005055
Lampitt, R., Hillier, W., & Challenor, P. (1993) Seasonal and diel variation in the open ocean concentration of marine snow aggregates. Nature, 362(6422), 737-739. DOI: 10.1038/362737a0
SILVER, M., SHANKS, A., & TRENT, J. (1978) Marine Snow: Microplankton Habitat and Source of Small-Scale Patchiness in Pelagic Populations. Science, 201(4353), 371-373. DOI: 10.1126/science.201.4353.371
Turner, J. (2002) Zooplankton fecal pellets, marine snow and sinking phytoplankton blooms. Aquatic Microbial Ecology, 57-102. DOI: 10.3354/ame027057
WOTTON, R., & MALMQVIST, B. (2001) Feces in Aquatic Ecosystems. BioScience, 51(7), 537. DOI: 10.1641/0006-3568(2001)051[0537:FIAE]2.0.CO;2
- May 5, 2011
- 12:15 AM
- 504 views
Swarms of tasty cicadas don’t help the birds — what gives?
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
Every thirteen years they come. After over a decade underground, they build burrows to the earth’s surface and emerge in synchrony, clawing and crawling up through the soil, rip their skins down the back and are reborn as adults. And after a month, they will be dead, whether consumed by the animals awaiting their arrival [...]... Read more »
Wheeler, G., Williams, K., & Smith, K. (1992) Role of periodical cicadas (Homoptera: Cicadidae: Magicicada) in forest nutrient cycles. Forest Ecology and Management, 51(4), 339-346. DOI: 10.1016/0378-1127(92)90333-5
Pray, C., Nowlin, W., & Vanni, M. (2009) Deposition and decomposition of periodical cicadas (Homoptera: Cicadidae: ) in woodland aquatic ecosystems . Journal of the North American Benthological Society, 28(1), 181-195. DOI: 10.1899/08-038.1
Yang, L. (2004) Periodical Cicadas as Resource Pulses in North American Forests. Science, 306(5701), 1565-1567. DOI: 10.1126/science.1103114
Yang, L. (2005) Interactions between a detrital resource pulse and a detritivore community. Oecologia, 147(3), 522-532. DOI: 10.1007/s00442-005-0276-0
Speer, J., Clay, K., Bishop, G., & Creech, M. (2010) The Effect of Periodical Cicadas on Growth of Five Tree Species in Midwestern Deciduous Forests. The American Midland Naturalist, 164(2), 173-186. DOI: 10.1674/0003-0031-164.2.173
Koenig, W., & Liebhold, A. (2003) Regional impacts of periodical cicadas on oak radial increment. Canadian Journal of Forest Research, 33(6), 1084-1089. DOI: 10.1139/X03-037
Yang, L. (2008) PULSES OF DEAD PERIODICAL CICADAS INCREASE HERBIVORY OF AMERICAN BELLFLOWERS. Ecology, 89(6), 1497-1502. DOI: 10.1890/07-1853.1
Krohne, D., Couillard, T., & Riddle, J. (1991) Population Responses of Peromyscus leucopus and Blarina brevicauda to Emergence of Periodical Cicadas. American Midland Naturalist, 126(2), 317. DOI: 10.2307/2426107
Koenig, W., & Liebhold, A. (2005) EFFECTS OF PERIODICAL CICADA EMERGENCES ON ABUNDANCE AND SYNCHRONY OF AVIAN POPULATIONS. Ecology, 86(7), 1873-1882. DOI: 10.1890/04-1175
Koenig, W., Ries, L., Olsen, V., & Liebhold, A. (2011) Avian predators are less abundant during periodical cicada emergences, but why?. Ecology, 92(3), 784-790. DOI: 10.1890/10-1583.1
Lehmann-Ziebarth, N., Heideman, P., Shapiro, R., Stoddart, S., Hsiao, C., Stephenson, G., Milewski, P., & Ives, A. (2005) EVOLUTION OF PERIODICITY IN PERIODICAL CICADAS. Ecology, 86(12), 3200-3211. DOI: 10.1890/04-1615
- September 17, 2010
- 10:33 AM
- 462 views
Can seabirds overfish a resource? The case of cormorants in Estonia
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
“Overfishing” is a term associated with resource depletion, extinction, and human greed. While the definition of overfishing is technically a subjective measure (How much fishing is too much?), it has been widely accepted to mean catching more of an aquatic … Continue reading →... Read more »
Dulvy, N., Sadovy, Y., & Reynolds, J. (2003) Extinction vulnerability in marine populations. Fish and Fisheries, 4(1), 25-64. DOI: 10.1046/j.1467-2979.2003.00105.x
Vetemaa, M., Eschbaum, R., Albert, A., Saks, L., Verliin, A., Jurgens, K., Kesler, M., Hubel, K., Hannesson, R., & Saat, T. (2010) Changes in fish stocks in an Estonian estuary: overfishing by cormorants?. ICES Journal of Marine Science. DOI: 10.1093/icesjms/fsq113
- September 29, 2010
- 08:52 AM
- 449 views
The evolution of the eukaryotes and our human story
by Hannah Waters in Culturing Science – biology as relevant to us earthly beings
“Taxonomy and classification are funny,” my father joked recently, “because the organisms being classified really don’t care what they are. We’re the only ones who care!” Well, at least I thought it was a good joke. And it speaks to … Continue reading →... Read more »
Cotton, J., & McInerney, J. (2010) Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1000265107
Gribaldo S, Poole AM, Daubin V, Forterre P, & Brochier-Armanet C. (2010) The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?. Nature reviews. Microbiology, 8(10), 743-52. PMID: 20844558
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