[{"content":"WE ARE IN THE MIDST OF A REVOLUTION that is changing our understanding of the natural world. Spurred in part by recent advances in sequencing and computational capabilities, we are poised to fully integrate the deeply rooted principles of evolutionary ecology with the mechanistic approaches of molecular biology. Nowhere have the implications of this union been more pronounced than in the field of microbial ecology (Martiny et al. 2006Martiny et al. (2006). Microbial biogeography: putting microorganisms on the map; Prosser et al. 2007Prosser et al. (2007). The role of ecological theory in microbial ecology). Ongoing work is revealing that taxonomic and metabolic diversity is far greater than previously thought (Hug et al. 2016Hug et al. (2016). A new view of the tree of life). There is also emerging evidence that microbial communities are not random assortments solely recruited from their surroundings; instead they form microbiomes—functionally unified assemblages adapted to specific habitats (Tyson et al. 2004Tyson et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment). The structure of these microbiomes can profoundly affect host biology (McFall-Ngai et al. 2013McFall-Ngai et al. (2013). Animals in a bacterial world, a new imperative for the life sciences) and biogeochemical cycles (Falkowski et al. 2008Falkowski et al. (2008). The microbial engines that drive Earth's biogeochemical cycles). We are only just beginning to grasp the magnitude of this diversity and understand its connection to ecosystem function and evolutionary processes. Microbial ecology as a discipline and philosophy sits at a developmental crossroad.\nOur understanding of the natural world is rooted in humanity’s rich and ancient history of observing and describing biological forms. More than 40,000 years ago people were cataloging natural systems and immortalizing what they saw in exquisite works of art on cave walls (Pike et al. 2012Pike et al. (2012). U-Series dating of paleolithic art in 11 caves in Spain). Over time, sophisticated institutions of natural history developed (Egerton 2002Egerton (2002). A History of the Ecological Sciences, Part 5: Byzantine Natural History), ultimately coalescing into the unified fields of ecology and evolutionary biology (Benson 2000Benson (2000). The emergence of ecology from natural history). There is a logical progression to this development of thought—we observe the natural world, identify the patterns of diversity, discover the processes that give rise to the patterns, and uncover the mechanisms that cause both pattern and process (Anand 1994Anand (1994). Pattern, process and mechanism - the fundamentals of scientific inquiry applied to vegetation science).\nIn contrast, our relationship with microscopic life unfolded quite differently and much more rapidly (see Appendix 1). Almost overnight, an entirely new world opened, one that is both orders of magnitude more diverse and less familiar. Our perception of this world is not based on visible structures and observable phenomena, but on strings of base pair sequences extracted from the environment and put together like an enormous jigsaw puzzle. However, microbial ecology lacks a unified theoretical framework to deal with this sudden accumulation of unfamiliar data (Prosser et al. 2007Prosser et al. (2007). The role of ecological theory in microbial ecology). So, we adopt and adapt established ecological theory and apply it to our microbial puzzle.\nHere’s the kicker: microbes are (mostly) asexual, small, fast growing, and have greater dispersal potential, compared to the majority of plants and animals. Microbial genomes are streamlined—small and densely packed with protein coding genes (Sela et al. 2016Sela et al. (2016). Theory of prokaryotic genome evolution)—and routinely acquire novel traits through horizontal gene transfer (Gogarten \u0026 Townsend 2005Gogarten \u0026 Townsend (2005). Horizontal gene transfer, genome innovation and evolution). Many phenomena—intra- and interspecific interactions, trophic relationships, niche partitioning—that form the basis of ecological theory are poorly understood for microbes (Jessup et al. 2004Jessup et al. (2004). Big questions, small worlds: microbial model systems in ecology). The species concept itself is largely absent and there is debate whether such a concept even exists (Ereshefsky 2010Ereshefsky (2010). Microbiology and the species problem). Thus, it is important to ask whether established ecological theory is applicable to microbes. Where can existing theory be tested to explain microbial diversity, and where do new theoretical constructs need to be developed? The opportunity for discovery and the chance to be a part of a new way of looking at the natural world makes this an amazing time to be a biologist.\nStudy the past if you would define the future\n-Confucius\nTHE HISTORY OF MICROBIOLOGY is not only an intellectual curiosity but can also guide as we develop a new scientific discipline and help us better understand how microbial processes fit our current models. In some cases, we may have to rethink established paradigms, while in others microbes may shed new light on old mysteries. Either way, it will be an interesting ride. So before we look ahead lets take a look at how we got here in the first place.\nSPECULATION: Two thousand years before humans started growing crops and raising livestock, semi-sedentary foraging communities in Scandinavia were using microorganisms to ferment large quantities of fish for storage and later use (Boethius 2016Boethius (2016). Something rotten in Scandinavia: The world\u0026rsquo;s earliest evidence of fermentation), while artisans in northern China were cultivating microbes to create fermented beverages from a mixture of rice, fruit, and honey (McGovern et al. 2004McGovern et al. (2004). Fermented beverages of pre- and proto-historic China). In fact newer evidence suggests that peoples in the Southern Levant were brewing a cereal-based beer almost 13,000 years ago (Liu et al. 2018Liu et al. (2018). Fermented beverage and food storage in 13,000 y-old stone mortars at Raqefet Cave, Israel: Investigating Natufian ritual feasting), several millennia before the appearance of domesticated cereals in the Near East.\nFermentation is used to detoxify and preserve food, increase nutrient availability, and because many ferments have anesthetic, antimicrobial, and antiseptic properties, they are important medicinal devices (McGovern et al. 2010McGovern et al. (2010). Anticancer activity of botanical compounds in ancient fermented beverages (Review)). Microbial fermentation played an important role in human history, and today vibrant fermentative traditions endure as key cultural elements around the world. It seems that ancient humans were domesticating microbes long before plants and animals, enriching specific microbial assemblages and promoting desired metabolic processes—humanity’s first experimental microbiologists. Remarkably, there is no evidence that ancient peoples were aware that microscopic life was responsible for these chemical transformations.\nOBSERVATION: It would take another eight and a half millennia until, in 1677, a Dutch merchant and amateur glass grinder used his handmade microscope to observe and describe bacteria for the first time (Lane 2015Lane (2015). The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’). Over the next 300 years, more sophisticated and powerful microscopes were developed allowing researchers to study this mysterious world in greater detail. One thing microscopy revealed, especially for bacteria and archaea, was that microbes do not exhibit the same diversity of physical forms as their macro counterparts—not even close. Given our history of using morphology to describe biodiversity, this unsurprisingly led to the premature notion that microbes were simple and minor players in natural systems.\nCULTIVATION: The beginning of modern day microbiology began with the advent of culture-based techniques in the late 1800’s. This allowed scientists to isolate pure cultures of microbes for the first time (Collard 1976Collard (1976). The Development of Microbiology) and delve deeper into their physiological and metabolic properties, giving way to great advancements in biochemistry, genetics, and molecular biology. However, over time many in the field began to suspect that culture-based approaches only recovered a fraction of the microbes they were observing with microscopy, which in turn was limited by the lack of morphological diversity.\nREVELATION: Despite the efforts of early 20th century pioneers (reviewed in CollardCollard (1976). The Development of Microbiology (1976); Van NielVan Niel (1949). The “Delft School” and the rise of general microbiology (1949)), microbiology remained rooted in the reductionist belief that microbes were just \u0026ldquo;bags of interesting biochemistry\u0026rdquo; ignoring the implications of ecological and evolutionary processes in the microbial world (Woese \u0026amp; Goldenfeld 2009Woese \u0026amp; Goldenfeld (2009). How the microbial world saved evolution from the Scylla of molecular biology and the Charybdis of the modern synthesis). All that changed beginning in 1977 when Carl Woese and George Fox published a series landmark papers outlining the use of the ribosomal RNA as a universal marker gene (Fox et al. 1977Fox et al. (1977). Classification of methanogenic bacteria by 16S ribosomal RNA characterization; Balch et al. 1977Balch et al. (1977). An ancient divergence among the bacteria). While they were at, it they also described an entirely new branch of life: the archaea (Woese \u0026amp; Fox 1977Woese \u0026amp; Fox (1977). Phylogenetic structure of the prokaryotic domain: The primary kingdoms). To say this work was groundbreaking would be an understatement. Woese \u0026amp; Fox toppled the old paradigms and pulled back the veil, revealing a microbial world far more diverse than most people were ready to accept (Mayr 1998Mayr (1998). Two empires or three?; Morell 1997Morell (1997). Microbial Biology: Microbiology\u0026rsquo;s Scarred Revolutionary). Eventually, the validity of their finding took root and today it is universally agreed that microbes—viruses, bacteria, archaea, and single-celled eukaryotes—are extremely diverse and crucial agents in all planetary systems.\nEXPLORATION: So here we are, some ten thousand years after humans first began harnessing the power of microbes, at the dawning of a new era in biology. Equipped with next (now 2nd) generation sequencing technology (Margulies et al. 2005Margulies et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors) and high-performance computing, we exploring nature anew, in ways that were not possible even fifteen years ago. The most recent estimate of diversity and newest tree of life is simply astonishing: 92 bacterial phyla, 26 archaeal phyla, and 5 Eukaryotic supergroups (Hug et al. 2016Hug et al. (2016). A new view of the tree of life). Continuing advances in portable sequencing technology (e.g., Oxford Nanopore’s MinIon) is helping microbial ecology become a genuine field science and promises to democratize .\nThe history of microbial ecology is a bit like the story Flatland: A Romance of Many Dimensions (1884) by Edwin Abbott Abbott (1838–1926). Flatland is a tale about a two-dimensional world occupied by geometric figures (lines, triangles, squares, pentagons, etc.) who only perceive straight lines and angles—a world devoid of depth. Until one day the protagonist (a square) is given a new perspective by a three-dimensional outsider (a sphere) and must change the way he views the world. Flatland challenges our perspective and so too does microbial world.\nReferences Anand, M. (1994). Pattern, process and mechanism - the fundamentals of scientific inquiry applied to vegetation science. Coenoses, 9(2): 81–92. Balch, W., Magrum, L., Fox, G., Wolfe, R., Woese, C. (1977). An ancient divergence among the bacteria. Journal of Molecular Evolution, 9(4): 305–311. https://doi.org/10.1007/BF01796092 Benson, K. (2000). The emergence of ecology from natural history. Endeavour, 24(2): 59–62. https://doi.org/10.1016/S0160-9327(99)01260-0 Boethius, A. (2016). Something rotten in Scandinavia: The world\u0026#39;s earliest evidence of fermentation. Journal of Archaeological Science, 66: 169–180. https://doi.org/10.1016/j.jas.2016.01.008 Collard, P. (1976). The Development of Microbiology. Egerton, F. (2002). A History of the Ecological Sciences, Part 5: Byzantine Natural History. Bulletin of the Ecological Society of America, 83(1): 89–94. Ereshefsky, M. (2010). Microbiology and the species problem. Biology \u0026amp; Philosophy, 25(4): 553–568. https://doi.org/10.1007/s10539-010-9211-9 Falkowski, P., Fenchel, T., Delong, E. (2008). The microbial engines that drive Earth\u0026#39;s biogeochemical cycles. Science, 320(5879): 1034–1039. https://doi.org/10.1126/science.1153213 Fox, G., Magrum, L., Balch, W., Wolfe, R., Woese, C. (1977). Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proceedings of the National Academy of Sciences, 74(10): 4537–4541. https://doi.org/10.1073/pnas.74.10.4537 Gogarten, J., Townsend, J. (2005). Horizontal gene transfer, genome innovation and evolution. Nature Reviews Microbiology, 3(9): 679–687. https://doi.org/10.1038/nrmicro1204 Hug, L., Baker, B., Anantharaman, K., Brown, C., Probst, A., Castelle, C., Butterfield, C., Hernsdorf, A., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D., Finstad, K., Amundson, R., Thomas, B., Banfield, J. (2016). A new view of the tree of life. Nature Microbiology, 1(5): 16048. https://doi.org/10.1038/nmicrobiol.2016.48 Jessup, C., Kassen, R., Forde, S., Kerr, B., Buckling, A., Rainey, P., Bohannan, B. (2004). Big questions, small worlds: microbial model systems in ecology. Trends in Ecology \u0026amp; Evolution, 19(4): 189–197. https://doi.org/10.1016/j.tree.2004.01.008 Lane, N. (2015). The unseen world: reflections on Leeuwenhoek (1677) ‘Concerning little animals’. Philosophical Transactions of the Royal Society B: Biological Sciences, 370(1666): 20140344. https://doi.org/10.1098/rstb.2014.0344 Liu, L., Wang, J., Rosenberg, D., Zhao, H., Lengyel, G., Nadel, D. (2018). Fermented beverage and food storage in 13,000 y-old stone mortars at Raqefet Cave, Israel: Investigating Natufian ritual feasting. Journal of Archaeological Science: Reports, 21: 783–793. https://doi.org/10.1016/j.jasrep.2018.08.008 Margulies, M., Egholm, M., Altman, W., Attiya, S., Bader, J., Bemben, L., Berka, J., Braverman, M., Chen, Y., Chen, Z., Dewell, S., Du, L., Fierro, J., Gomes, X., Godwin, B., He, W., Helgesen, S., Ho, C., Irzyk, G., Jando, S., Alenquer, M., Jarvie, T., Jirage, K., Kim, J., Knight, J., Lanza, J., Leamon, J., Lefkowitz, S., Lei, M., Li, J., Lohman, K., Lu, H., Makhijani, V., McDade, K., McKenna, M., Myers, E., Nickerson, E., Nobile, J., Plant, R., Puc, B., Ronan, M., Roth, G., Sarkis, G., Simons, J., Simpson, J., Srinivasan, M., Tartaro, K., Tomasz, A., Vogt, K., Volkmer, G., Wang, S., Wang, Y., Weiner, M., Yu, P., Begley, R., Rothberg, J. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437(7057): 376–380. https://doi.org/10.1038/nature03959 Martiny, J., Bohannan, B., Brown, J., Colwell, R., Fuhrman, J., Green, J., Horner-Devine, M., Kane, M., Krumins, J., Kuske, C., Morin, P., Naeem, S., Øvreås, L., Reysenbach, A., Smith, V., Staley, J. (2006). Microbial biogeography: putting microorganisms on the map. Nature Reviews Microbiology, 4(2): 102–112. https://doi.org/10.1038/nrmicro1341 Mayr, E. (1998). Two empires or three?. Proceedings of the National Academy of Sciences, 95(17): 9720–9723. https://doi.org/10.1073/pnas.95.17.9720 McFall-Ngai, M., Hadfield, M., Bosch, T., Carey, H., Domazet-Lošo, T., Douglas, A., Dubilier, N., Eberl, G., Fukami, T., Gilbert, S., Hentschel, U., King, N., Kjelleberg, S., Knoll, A., Kremer, N., Mazmanian, S., Metcalf, J., Nealson, K., Pierce, N., Rawls, J., Reid, A., Ruby, E., Rumpho, M., Sanders, J., Tautz, D., Wernegreen, J. (2013). Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences, 110(9): 3229–3236. https://doi.org/10.1073/pnas.1218525110 McGovern, P., Christofidou-Solomidou, M., Wang, W., Dukes, F., Davidson, T., El-Deiry, W. (2010). Anticancer activity of botanical compounds in ancient fermented beverages (Review). International Journal of Oncology, 37(1): 5–14. https://doi.org/10.3892/ijo_00000647 McGovern, P., Zhang, J., Tang, J., Zhang, Z., Hall, G., Moreau, R., Nuñez, A., Butrym, E., Richards, M., Wang, C., Cheng, G., Zhao, Z., Wang, C. (2004). Fermented beverages of pre- and proto-historic China. Proceedings of the National Academy of Sciences, 101(51): 17593–17598. https://doi.org/10.1073/pnas.0407921102 Morell, V. (1997). Microbial Biology: Microbiology\u0026#39;s Scarred Revolutionary. Science, 276(5313): 699–702. https://doi.org/10.1126/science.276.5313.699 Pike, A., Hoffmann, D., García-Diez, M., Pettitt, P., Alcolea, J., De Balbín, R., González-Sainz, C., De Las Heras, C., Lasheras, J., Montes, R., Zilhão, J. (2012). U-Series dating of paleolithic art in 11 caves in Spain. Science, 336(6087): 1409–1413. https://doi.org/10.1126/science.1219957 Prosser, J., Bohannan, B., Curtis, T., Ellis, R., Firestone, M., Freckleton, R., Green, J., Green, L., Killham, K., Lennon, J., Osborn, A., Solan, M., Gast, C., Young, J. (2007). The role of ecological theory in microbial ecology. Nature Reviews Microbiology, 5(5): 384–392. https://doi.org/10.1038/nrmicro1643 Sela, I., Wolf, Y., Koonin, E. (2016). Theory of prokaryotic genome evolution. Proceedings of the National Academy of Sciences, 113(41): 11399–11407. https://doi.org/10.1073/pnas.1614083113 Tyson, G., Chapman, J., Hugenholtz, P., Allen, E., Ram, R., Richardson, P., Solovyev, V., Rubin, E., Rokhsar, D., Banfield, J. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978): 37–43. https://doi.org/10.1038/nature02340 Van Niel, C. (1949). The “Delft School” and the rise of general microbiology. Bacteriological Reviews, 13(3): 161–174. https://doi.org/10.1128/br.13.3.161-174.1949 Woese, C., Goldenfeld, N. (2009). How the microbial world saved evolution from the Scylla of molecular biology and the Charybdis of the modern synthesis. Microbiology and Molecular Biology Reviews, 73(1): 14–21. https://doi.org/10.1128/MMBR.00002-09 Woese, C., Fox, G. (1977). Phylogenetic structure of the prokaryotic domain: The primary kingdoms. 74(11): 5088–5090. https://doi.org/10.1073/pnas.74.11.5088 ","externalUrl":null,"permalink":"/posts/four-eras/","section":"Posts","summary":"Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean in eleifend justo, vestibulum congue lacus. Quisque est libero, lacinia sed placerat ac, interdum id urna.","title":"A Brief Essay on the History of Microbial Science","type":"posts"},{"content":"I spend a lot of time thinking about color and how I can use color to convey a message. For example, if you use too many colors in a figure you force your reader to continually go back and forth from the chart to the legend. This can be confusing and ultimately may detract from the meaning of the figure (Lipton 2007Lipton (2007). The practical guide to information design; Rolandi et al. 2011Rolandi et al. (2011). A Brief Guide to Designing Effective Figures for the Scientific Paper).\nAnother point to consider is that many of us have different abilities to perceive color and/or detect differences in color (Deeb 2005Deeb (2005). The molecular basis of variation in human color vision). Color blindness, also known as color vision deficiency, is the decreased ability to see color or differences in color. When designing figures, it is important to use a) a relatively small color palette and b) a palette that is friendly to a variety of people. If you want to test yourself for color blindness, search for Ishihara Test\u0026ndash;there are many sites that offer interactive tests.\nFor more information on the topic, I recommend reading Bang Wong’s Nature Methods paper, Points of view: Color blindness. Wong proposes a color-blind friendly color palette that uses contrasting colors that can be distinguished by a range of people (Wong 2011Wong (2011). Points of view: Color blindness). Consider that roughly 8% of people (mostly males) are color blind. So, what do you think? Do you want Keanu Reeves to understand your figures or not? If so, consider a color scheme that is friendly to all vision types\nWong\u0026rsquo;s 8-color palette # Wong’s scheme is conservative\u0026mdash;there are only 8 colors. Limited color palettes like these force us to be more careful when deciding what information to target or how many groups to display.\nPreview Color Name HEX Code RGB Code Black #000000 📋 rgb(0, 0, 0) 📋 Blue #0072B2 📋 rgb(0, 114, 178) 📋 Sky Blue #56B4E9 📋 rgb(0, 114, 178) 📋 Reddish Purple #CC79A7 📋 rgb(204, 121, 167) 📋 Bluish Green #009E73 📋 rgb(0, 158, 115) 📋 Vermillion #D55E00 📋 rgb(213, 94, 0) 📋 Orange #E69F00 📋 rgb(230, 159, 0) 📋 Yellow #F0E442 📋 rgb(240, 228, 66) 📋 📋 Copy All HEX 📋 Copy All RGB Wong\u0026rsquo;s 8-color palette (Krzywinski modified) # In addition to an incredible talent for data visualization, Martin Krzywinski has an excellent post on designing color blind friendly palettes. This post provides an in-depth explanation of on the physics and physiology behind color blindness, plus provides code for several different palette options, including a modified version of Wong\u0026rsquo;s palette.\nPrimary Palette Secondary Palette Preview Color Name HEX Code RGB Code Black #000000 📋 rgb(0, 0, 0) 📋 Sapphire Blue #2271B2 📋 rgb(34, 113, 178) 📋 Cyan #3DB7E9 📋 rgb(61, 183, 233) 📋 Magenta #F748A5 📋 rgb(247, 72, 165) 📋 Sea Green/Viridian #359B73 📋 rgb(53, 155, 115) 📋 Burnt Orange #D55E00 📋 rgb(213, 94, 0) 📋 Marigold #E69F00 📋 rgb(230, 159, 0) 📋 Lemon Yellow #F0E442 📋 rgb(240, 228, 66) 📋 📋 Copy All HEX 📋 Copy All RGB Preview Color Name HEX Code RGB Code Black #000000 📋 rgb(0, 0, 0) 📋 Strong Magenta #AA0DB4 📋 rgb(170, 13, 180) 📋 Violet Pink #FF54ED 📋 rgb(255, 84, 237) 📋 Persian Green #00B19F 📋 rgb(0, 177, 159) 📋 Mexican Pink #EB057A 📋 rgb(235, 5, 122) 📋 ku Crimson #F8071D 📋 rgb(248, 7, 29) 📋 Tangerine #FF8D1A 📋 rgb(255, 141, 26) 📋 French Lime #9EFF37 📋 rgb(158, 255, 55) 📋 📋 Copy All HEX 📋 Copy All RGB Krzywinski\u0026rsquo;s 12-Color Palette # Martin Krzywinski also provides a 12 color palette that offer more options than Wong\u0026rsquo;s palette. Just be careful—-figures with too many colors can inhibit our ability to discern patterns.\nPrimary Palette Secondary Palette Preview Color Name HEX Code RGB Code Jazzberry Jam #9F0162 📋 rgb(159, 1, 98) 📋 Jungle Green #009F81 📋 rgb(0, 159, 129) 📋 Brilliant Rose #FF5AAF 📋 rgb(255, 90, 175) 📋 Aqua Marine #00FCCF 📋 rgb(0, 252, 207) 📋 Blue Violet #8400CD 📋 rgb(132, 0, 205) 📋 Dodger Blue #008DF9 📋 rgb(0, 141, 249) 📋 Deep Sky Blue #00C2F9 📋 rgb(0, 194, 249) 📋 Plum #FFB2FD 📋 rgb(255, 178, 253) 📋 Scarlett #A40122 📋 rgb(164, 1, 34) 📋 Imperial Red #E20134 📋 rgb(226, 1, 52) 📋 Pinkish Orange #FF6E3A 📋 rgb(255, 110, 58) 📋 Goldenrod #FFC33B 📋 rgb(255, 195, 59) 📋 📋 Copy All HEX 📋 Copy All RGB Preview Color Name HEX Code RGB Code Teal Green #006A5E 📋 rgb(0, 106, 94) 📋 Mexican Pink #ED0D88 📋 rgb(237, 13, 136) 📋 Turquoise #00BDA9 📋 rgb(0, 189, 169) 📋 Pale Crimson #FFC4D4 📋 rgb(255, 196, 212) 📋 Cerulean Blue #0058CC 📋 rgb(0, 88, 204) 📋 Electric Purple #D208FB 📋 rgb(210, 8, 251) 📋 Violet Pink #FF66FD 📋 rgb(255, 102, 253) 📋 Cyan #00EFF9 📋 rgb(0, 239, 249) 📋 Japanese Laurel #156D03 📋 rgb(21, 109, 3) 📋 Islamic Green #009719 📋 rgb(0, 151, 25) 📋 Vivid Malachite #00C61B 📋 rgb(0, 198, 27) 📋 Radioactive Green #00FB1D 📋 rgb(0, 251, 29) 📋 📋 Copy All HEX 📋 Copy All RGB Krzywinski\u0026rsquo;s 15-Color Palette # And finally again from Martin Krzywinski, a 15 color palette.\nPrimary Palette Secondary Palette Preview Color Name HEX Code RGB Code Mulberry #68023F 📋 rgb(104, 2, 63) 📋 Deep Sea #008169 📋 rgb(0, 129, 105) 📋 Persian Rose #EF0096 📋 rgb(239, 0, 150) 📋 Aquamarine #00DCB5 📋 rgb(0, 220, 181) 📋 Azalea #FFCFE2 📋 rgb(255, 207, 226) 📋 Royal Blue #003C86 📋 rgb(0, 60, 134) 📋 Vivid Purple #9400E6 📋 rgb(148, 0, 230) 📋 Azure #009FFA 📋 rgb(0, 159, 250) 📋 Blush Pink #FF71FD 📋 rgb(255, 113, 253) 📋 Electric Blue #7CFFFA 📋 rgb(124, 255, 250) 📋 Burnt Crimson #6A0213 📋 rgb(106, 2, 19) 📋 India Green #008607 📋 rgb(0, 134, 7) 📋 Electric Crimson #F60239 📋 rgb(246, 2, 57) 📋 Radioactive Green #00E307 📋 rgb(0, 227, 7) 📋 Bright Sun #FFDC3D 📋 rgb(255, 220, 61) 📋 📋 Copy All HEX 📋 Copy All RGB Preview Color Name HEX Code RGB Code Aqua Deep #00463C 📋 rgb(0, 70, 60) 📋 Magenta #C00B6F 📋 rgb(192, 11, 111) 📋 Manganese Blue #00A090 📋 rgb(0, 160, 144) 📋 Tickle Me Pink #FF95BA 📋 rgb(255, 149, 186) 📋 Brilliant Turquoise #5FFFDE 📋 rgb(95, 255, 222) 📋 Indigo #590A87 📋 rgb(89, 10, 135) 📋 Cerulean Blue #0063E5 📋 rgb(0, 99, 229) 📋 Fuchsia #ED0DFD 📋 rgb(237, 13, 253) 📋 Deep Sky Blue #00C7F9 📋 rgb(0, 199, 249) 📋 Pale Lavender #FFD5FD 📋 rgb(255, 213, 253) 📋 Bronzetone #3D3C04 📋 rgb(61, 60, 4) 📋 Fire Engine Red #C80B2A 📋 rgb(200, 11, 42) 📋 Islamic Green #00A51C 📋 rgb(0, 165, 28) 📋 Sunshade #FFA035 📋 rgb(255, 160, 53) 📋 Acid Green #9BFF2D 📋 rgb(155, 255, 45) 📋 📋 Copy All HEX 📋 Copy All RGB References Deeb, S. (2005). The molecular basis of variation in human color vision. Clinical Genetics, 67(5): 369–377. https://doi.org/10.1111/j.1399-0004.2004.00343.x Lipton, R. (2007). The practical guide to information design. Rolandi, M., Cheng, K., Pérez‐Kriz, S. (2011). A Brief Guide to Designing Effective Figures for the Scientific Paper. Advanced Materials, 23(38): 4343–4346. https://doi.org/10.1002/adma.201102518 Wong, B. (2011). Points of view: Color blindness. Nature Methods, 8(6): 441–441. https://doi.org/10.1038/nmeth.1618 ","externalUrl":null,"permalink":"/posts/color/","section":"Posts","summary":"High-contrast color palettes that help make figures accessible to all types of people.","title":"Accessible Color Palettes for Data Visualization","type":"posts"},{"content":" Nucleotide Bases # The genetic code is the set of rules used by cells to translate nucleotide sequences into proteins. The code relies on the specific ordering of nitrogen-containing molecules called nucleotide bases. In DNA, these bases comprise Adenine ($\\ce{A}$), Thymine ($\\ce{T}$), Guanine ($\\ce{G}$), and Cytosine ($\\ce{C}$). Adenine and Guanine are both purines (a pyrimidine and an imidazole) while Cytosine and Thymine are both pyrimidines.\nStructure of nucleotide bases Adenine Thymine (DNA) Guanine Cytosine Uracil (RNA) Codons \u0026amp; Amino Acids # Hydrogen bonding between purines and pyrimidines form the standard base pairs $\\ce{A=T}$ (double bond) and $\\ce{G#C}$ (triple bond). During the process of transcription, DNA serves as the template to synthesize messenger RNA (mRNA), where Uracil ($\\ce{U}$) replaces Thymine to pair with Adenine. The linear sequence of these bases is read sequentially by cellular machinery in discrete, non-overlapping triplets known as codons.\n1 DNA to RNA (Transcription) RNA polymerase reads a specific gene on the DNA strand and builds a matching single-stranded copy called messenger RNA (mRNA). During this step, the RNA base uracil (U) replaces the DNA base thymine (T). The mRNA then leaves the nucleus and goes into the cytoplasm. 2 RNA to Amino Acids (Translation) The ribosome reads the mRNA code in groups of three bases called codons. Another molecule called transfer RNA (tRNA) brings the matching amino acids to the ribosome one by one. Each codon matches a specific amino acid. 3 Amino Acids to Proteins (Folding) The ribosome joins the amino acids together with peptide bonds into a long chain called a polypeptide. Once the chain is complete, it twists and folds into a complex, three-dimensional shape based on the traits of its amino acids. This finished shape becomes a working, functional protein. Example sequence showing messenger RNA (mRNA) codons translated to amino acids. Replication: DNA makes exact copies of itself so cells can divide and pass instructions to new cells.Transcription: The cell copies a section of DNA into a messenger RNA (mRNA) molecule inside the nucleus. Translation: Ribosomes read the mRNA code to link amino acids together and build a functional protein.\nBecause there are four distinct bases ($\\ce{A}$, $\\ce{T}$, $\\ce{G}$, and $\\ce{C}$), three-base combinations yield $4^3 = 64$ possible codons, where specific codons code for particular amino acids (or one of three stop codons). Since there are only $20$ amino acids1, we say there is redundancy, or degeneracy, in the genetic code. In other words, multiple codons can map to a single amino acid.\nFor example, Glutamine (Gln) is coded by $\\ce{CAG}$ and $\\ce{CAA}$ while Histidine (His) is coded by $\\ce{CAC}$ and $\\ce{CAU}$. In fact only methionine and tryptophan are specified by a single codon. The remaining amino acids are coded by at least two, and up to six, codons. Below is a lookup table that describes the relationship between codons and amino acids.\nUse this → link for more detailed information about each amino acid. Standard codon table used to translate a three-letter mRNA sequence (codon) into a specific amino acid or a stop signal. NOTE. Methonine (Met) is the start codon. Second base First base U C A G Third base U Phe (F) Ser (S) Tyr (Y) Cys (C) U C Leu (L) Stop Stop A Stop Trp (W) G C Leu (L) Pro (P) His (H) Arg (R) U C Gln (Q) A G A Ile (I) Thr (T) Asn (N) Ser (S) U C Lys (K) Arg (R) A Met (M) G G Val (V) Ala (A) Asp (D) Gly (G) U C Glu (E) A G Note Though the genetic code is degenerate (i.e., multiple codons may map to a single amino acid) the code is not ambiguous. In other words, a given codon always maps to exactly one amino acid\nDegeneracy \u0026amp; Nucleotide Ambiguity Codes # To represent nucleotide degeneracy, or positions with more than one possible base in a codon, the IUPAC (International Union of Pure \u0026amp; Applied Chemistry) defines single-letter nucleic acid ambiguity codes. Below is the complete list of the IUPAC nucleic acid ambiguity codes.\nIUPAC Nucleic Acid Ambiguity Codes ------------------------------------ R (Purines): A or G Y (Pyrimidines): C or T/U M (Amino): A or C K (Keto): G or T/U S (Strong): G or C W (Weak): A or T/U ------------------------------------ H (not G): A, C, or T/U B (not A): C, G, or T/U V (not T/U): A, C, or G D (not C): A, G, or T/U ------------------------------------ N (Any base): A, C, G, or T/U Don\u0026rsquo;t get confused here. The single letter nucleic acid ambiguity codes are not the same as single letter abbreviations for amino acids. Returning to the examples above, Glutamine (Gln) is coded by $\\ce{CAG}$ and $\\ce{CAA}$. Note that the third position of both codons is a purine ($\\ce{G}$ or $\\ce{A}$). Looking at the nucleic acid ambiguity table above we see that the code for purines is $\\ce{R}$. So we can say the Glutamine is coded by $\\ce{CAR}$. Similarly, Histidine (His), which is coded by $\\ce{CAC}$ and $\\ce{CAU}$, can be rewritten as $\\ce{CAY}$, where $\\ce{Y}$ is a pyrimidine. If instead we reference the codon lookup table we see that Serine (Ser) is coded for by 6 different codons: $\\ce{UCA}$, $\\ce{UCG}$, $\\ce{UCC}$, $\\ce{UCU}$, $\\ce{AGU}$, and $\\ce{AGC}$. Applying the ambiguity codes, we say that Serine (Ser) is coded by $\\ce{UCN}$ and $\\ce{AGY}$, where $\\ce{N}$ stands for any base and $\\ce{Y}$ corresponds to pyrimidine.\nMapping Codons to Amino Acids # In addition to codon tables, other methods have been developed to show the mapping between codons and their cooresponding amino acids. Memorizing codon to amino acid assignments is not a mandatory skill but it can significantly speed up data analysis, enable quick error detection in sequences, and generally deepen your understanding of sequence analysis, all without constantly relying on reference charts or tables.\nBelow are a few examples of different tools to show the relationship between codons and amino acids. The codon wheel for example is a circular chart where the inner ring is the first base of the three-letter codon. The middle ring is the second base, and the outer ring in the third base. The codon chart works similarly but also overlays additional information like amino acid properties (e.g., acidic, basic, etc.) and chemical structures.\nPopular methods to map codons to amino acids Codon table Codon wheel Codon chart Codon 3D A Better Map? # ✕ flowchart LR A(Cytosine) --\u003e B(Adenine) %% 1. Subgraph Layout with Markdown Titles subgraph 1st_base [\"`**1st base**`\"] A(\"`**C** Cytosine`\") end subgraph 2nd_base [\"`**2nd base**`\"] B(\"`**A** Adenine`\") end subgraph 3rd_base [\"`**3rd base**`\"] C(Guanine) D(Adenine) E(Cytosine) F(Uracil) end B --\u003e C(\"`**G** Guanine`\") B --\u003e D(\"`**A** Adenine`\") B --\u003e E(\"`**C** Cytosine`\") B --\u003e F(\"`**U** Uracil`\") subgraph Amino_Acids [\"`**Amino Acids**`\"] C -- \"`**R**`\" --\u003e G(((\"`**Gln** Glutamine`\"))) D -- \"`**R**`\" --\u003e G E -- \"`**Y**`\" --\u003e H(((\"`**His** Histidine`\"))) F -- \"`**Y**`\" --\u003e H end %% ========================================== %% NODE STYLING (REUSABLE CLASSES) %% ========================================== classDef largeFont font-size:22px; classDef mediumFont font-size:16px; class A,B,G,H largeFont; class C,D,E,F mediumFont; %% ========================================== %% SUBGRAPH BOX STYLING %% ========================================== %% Syntax: style [subgraph_id] CSS_properties style 1st_base fill:currentColor,fill-opacity:0.07,stroke:currentColor,stroke-opacity:0.3,stroke-width:1px; style 2nd_base fill:currentColor,fill-opacity:0.07,stroke:currentColor,stroke-opacity:0.3,stroke-width:1px; style 3rd_base fill:none,stroke:none; style Amino_Acids fill:currentColor,fill-opacity:0.12,stroke:currentColor,stroke-opacity:0.5,stroke-width:2px; %% ========================================== %% LINK \u0026 ARROW TEXT STYLING %% ========================================== %% Edges are numbered sequentially (0, 1, 2...) in order of code appearance. %% Edges 0 through 4 handle the top layout branching rules. %% Edges 5 through 8 map the R and L paths inside Amino Acids. linkStyle 5 font-size:24px,font-weight:bold,fill:none; linkStyle 6 font-size:24px,font-weight:bold,fill:none; linkStyle 7 font-size:24px,font-weight:bold,fill:none; linkStyle 8 font-size:24px,font-weight:bold,fill:none; I tried forever to memorize codon assignments using the tools described above with little luck\u0026ndash;it just wouldn\u0026rsquo;t stick. If you are more of a visual learner like me, then tables are pretty useless. I tried the various wheel and chart representations but those didn\u0026rsquo;t help either.\nConventional methods to map codons to amino acids Codon Tree 5\u0026rsquo; G Codon Tree 5\u0026rsquo; C Codon Tree 5\u0026rsquo; A Codon Tree 5\u0026rsquo; U In this artcile I discuss the standard genetic code but it is important to note that there are several variant translation systems used in certain organelles and microbes. Alternative genetic codes are variant translation systems where specific codons are reassigned to encode different amino acids or stop signals.\u0026#160;\u0026#x21a9;\u0026#xfe0e;\n","externalUrl":null,"permalink":"/posts/codons/","section":"Posts","summary":"Which codons specify particular amino acids? To help memorize the codon to amino acid assignment, I created a new way of visualizing these relationships.","title":"Codon Map","type":"posts"},{"content":"Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.\nAppointments # Research Associate Smithsonian Tropical Research Institute 2022 - 2026 STRI/Moore Foundation Postdoctoral Fellow Smithsonian Tropical Research Institute 2017 - 2022 Bocas del Toro Panama Grant title: Divergence of Marine Symbiosis After the Rise of the Isthmus of Panama\nI created a website for the project which you can view here\nPostdoctoral Research Associate Bigelow Laboratory for Ocean Sciences 2012 - 2017 East Boothbay ME, USA Wisconsin Distinguished Graduate Fellow University of Wisconsin 2010 - 2011 Madison WI, USA Smithsonian Institution Predoctoral Fellow Smithsonian Tropical Research Institute 2009 - 2010 Gamboa Panama Research Technician University of Texas-Austin 2002 - 2006 Austin TX, USA Education # PhD Microbiology University of Wisconsin-Madison 2006 - 2011 Madison WI, USA Dissertation title: Microbial ecology of leaf-cutter ant gardens and refuse dumps.\nIn addition to my work on leaf-cutter ants, I also worked on honey bee microbiomes, beetle-fungal-bacterial interactions, and the evolution of fungus farming in insects.\nBSc Aquatic Biology University of Texas-Austin 1998 - 2002 Austin TX, USA Minor in Anthropology/Archaeology Training \u0026amp; Certifications # PADI Diver Certification Courses Panama Dive School 2017 - 2018 Bocas del Toro PANAMA Open Water, Advanced Open Water, \u0026amp; Rescue Diver Certifications PoreCamp University of Exeter Sequencing Center 2016 Penryn, Cornwall UK 1-week hands-on training bootcamp on deploying Oxford Nanopore\u0026rsquo;s portable sequencing platform, the MinION\nView course website\nComplex Systems Summer School (CSSS) Santa Fe Institute 2015 Santa Fe, NM USA An intensive 4-week introduction to complex behavior in mathematical, physical, living, and social systems. The CSSS brings together graduate students, postdoctoral fellows, and professionals to transcend disciplinary boundaries, take intellectual risks, and ask big questions about complex systems. The program comprises a series of lectures and workshops devoted to theory and tools, applications-focused seminars, and discussions with faculty and fellow participants. Participants put what they learn from these sessions into practice through group research projects, conducted throughout the program.\nLearn more about the SFI CSSS\nNSF-UNOLS Chief Scientist Training Cruise The University-National Oceanographic Laboratory System 2014 Barbedos to Bermuda 2-week course aboard the R/V Atlantic Explorer for PhD students and postdocs on how to effectively plan and run multi-disciplinary oceanographic research \u0026amp; education cruises.\nView the final report from the 2014 UNOLS training cruise\nFire Academy Southern Maine Community College 2013 - 2014 Portland, ME USA Program provides an occupational foundation for fire suppression in municipal and industrial settings by focusing on the art and science of controlling and extinguishing fires. The program is based on the National Fire Protection Association (NFPA) 1001 Firefighter Professional Qualifications Standard, Firefighter Levels I and II and Maine Bureau of Labor Standards. Students must complete pre-class and post-class assignments and operate as part of a firefighting team.\nCertifications:\nFirefighter I \u0026amp; II Emergency Vehicle Oporations Microbial Diversity Course Marine Biological Labs 2007 Woods Hole, MA USA An intensive 6-week course that provides advanced training in the discovery, cultivation, and analysis of microorganisms that drive diverse biochemical and ecological processes. The curriculum includes modern genetic, biochemical, and computational approaches that advance the study of microbial diversity and function. Students isolate and characterize novel microbes from local marine and freshwater habitats, integrating physiological data with genomic and metabolic analyses and applying advanced sequencing and annotation pipelines to interpret genomic, transcriptomic, and biochemical datasets. Participants receive integrated training in microbial physiology, metabolism, and genomics, focusing on cultivation of bacteria, archaea, and microbial eukaryotes, as well as their associated viruses.\nSee the course website for more information\nArchaeological Field Techniques The Programme for Belize Archaeological Project 2000 Rio Bravo BELIZE A 6-week intensive field course providing hands-on experience in field archaeology, including excavation, survey, mapping, artifact processing, and artifact analysis with a particular emphasis on Mayan art, architecture, \u0026amp; iconography. Subjects include excavation objectives, lithic analysis, ceramic analysis, osteological analysis, and Maya prehistory.\nSee the course website for more information\nFellowships # Smithsonian Institution Genomics Postdoctoral Fellowship Smithsonian Tropical Research Institute 2012 - 2014 PANAMA The role of intestinal microbiomes in the nutritional ecology of dominant Neotropical ant species. Declined Wisconsin Distinguished Graduate Fellowship University of Wisconsin 2010 - 2011 Madison, WI USA The influence of forage material on microbial communities in leaf-cutter ant colonies. Smithsonian Institution Predoctoral Fellowship Smithsonian Tropical Research Institute 2009 - 2010 PANAMA Microbial community assembly in the refuse dumps of the leaf-cutter ant, Atta colombica. ","externalUrl":null,"permalink":"/research-portfolio/experience/","section":"Research Portfolio","summary":"Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.\n","title":"Appointments, Education, \u0026 Training","type":"research-portfolio"},{"content":" Get in touch I would love to hear from you. Please fill out the form and I will get back to you as soon as possible.\nSend me a Message Have a question or want to work together? Drop me a line and I\u0026rsquo;ll get back to you within 24 hours. Name Email Subject Message Send Message Send me a Message Have a question or want to work together? Drop me a line and I\u0026rsquo;ll get back to you within 24 hours. Name Email Subject Message Send Message ","externalUrl":null,"permalink":"/contact-form/","section":"","summary":" Get in touch I would love to hear from you. Please fill out the form and I will get back to you as soon as possible.\n","title":"Contact Form","type":"footer"},{"content":" Header 1 # Fungus-growing ants, as my graduate advisor was fond of saying, \u0026ldquo;are the paradematic example of multipartite coevolution and symbiosis\u0026rdquo;. These ants\u0026ndash;called Attines\u0026ndash;forage as all ant do, but the food they gather\nHeader 2 # Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nHeader 3 # Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nLorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nLorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\n","externalUrl":null,"permalink":"/study/symbiosis/","section":"Research","summary":"Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor.","title":"Symbiosis","type":"study"},{"content":"","externalUrl":null,"permalink":"/study/complexity/","section":"Research","summary":"Remember when we first started…? I’ve missed those days.","title":"Complexity","type":"study"},{"content":"Unless otherwise noted, all content of this website, including text and images, are my own.\nHomepage # Banner image reproduced from The Channeled Scablands of the Columbia Plateau by J Harlen Bretz, The Journal of Geology 31, no. 8 (1923):617 - 645. This work has been marked as dedicated to the public domain. Posts # Accessible Color Palettes for Data Visualization # Banner image generated in R using code modified from Danielle Navarro\u0026rsquo;s Linear cosine palettes post. This work is licensed under a Creative Commons BY 4.0 International License. Reimaging Codon Maps # Codon table provided by Scott Henry Maxwell. This work is licensed under a Creative Commons BY-NC-SA 4.0 International License. Codon wheel provided by Mouagip. This work has been marked as dedicated to the public domain. Codon chart provided by Kosigrim . This work has been marked as dedicated to the public domain. Codon 3D provided by Charles Juvon . This work is licensed under a Creative Commons BY-SA 4.0 International License. ","externalUrl":null,"permalink":"/credits/","section":"","summary":"Unless otherwise noted, all content of this website, including text and images, are my own.\nHomepage # Banner image reproduced from The Channeled Scablands of the Columbia Plateau by J Harlen Bretz, The Journal of Geology 31, no. 8 (1923):617 - 645. This work has been marked as dedicated to the public domain. Posts # Accessible Color Palettes for Data Visualization # Banner image generated in R using code modified from Danielle Navarro’s Linear cosine palettes post. This work is licensed under a Creative Commons BY 4.0 International License. Reimaging Codon Maps # Codon table provided by Scott Henry Maxwell. This work is licensed under a Creative Commons BY-NC-SA 4.0 International License. ","title":"Credits","type":"footer"},{"content":"See all publications ","externalUrl":null,"permalink":"/research-portfolio/featured-publications/","section":"Research Portfolio","summary":"See all publications ","title":"Featured Publications","type":"research-portfolio"},{"content":"","date":"1 December 2023","externalUrl":null,"permalink":"/research-portfolio/publications/","section":"Research Portfolio","summary":"","title":"Publications","type":"research-portfolio"},{"content":" (Last modified: Sep 1, 2026) General Commitment # I, Jarrod J Scott, am committed to ensuring digital accessibility for all people. I am continually improving the user experience for everyone and applying the relevant accessibility standards to ensure my research, teaching materials, and blog posts are universally available.\nConformance Status # The Web Content Accessibility Guidelines (WCAG) defines requirements for designers and developers to improve accessibility for people with disabilities. 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In the navigationn bar at the top of each page there are three option that allow you to modify the look of the site:\na) Accessibility options,\nb) Light \u0026amp; dark mode toggle,\nc) Color theme picker.\nIf you click the Accessibility icon (a) a dropdown will appear giving you several additional options including changing the default font size.\nI also have a post on designinging Accessible Color Palettes for data visualization. After all, why not strive for accessibility across the board.\n","date":"1 September 2026","externalUrl":null,"permalink":"/accessibility-statement/","section":"","summary":" (Last modified: Sep 1, 2026) General Commitment # I, Jarrod J Scott, am committed to ensuring digital accessibility for all people. I am continually improving the user experience for everyone and applying the relevant accessibility standards to ensure my research, teaching materials, and blog posts are universally available.\n","title":"Accessibility Statement","type":"footer"},{"content":"Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus non magna ex. Donec sollicitudin ut lorem quis lobortis. Nam ac ipsum libero. Sed a ex eget ipsum tincidunt venenatis quis sed nisl. Pellentesque sed urna vel odio consequat tincidunt id ut purus. Nam sollicitudin est sed dui interdum rhoncus.\n. ","externalUrl":null,"permalink":"/research-portfolio/visuals/","section":"Research Portfolio","summary":"Lorem ipsum dolor sit amet, consectetur adipiscing elit. Vivamus non magna ex. Donec sollicitudin ut lorem quis lobortis. Nam ac ipsum libero. Sed a ex eget ipsum tincidunt venenatis quis sed nisl. Pellentesque sed urna vel odio consequat tincidunt id ut purus. Nam sollicitudin est sed dui interdum rhoncus.\n","title":"Data Visualizations","type":"research-portfolio"},{"content":"","externalUrl":null,"permalink":"/study/ethnobotany/","section":"Research","summary":"Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor.","title":"Ethnobotany","type":"study"},{"content":" (Last modified: Aug 31, 2026) The views, thoughts, and opinions expressed on this website belong solely to the author, Jarrod J Scott, and do not necessarily reflect the official policy, position, or views of any institution or organization I happen to be affiliated with, its administration, or any funding agencies.\nContent Accuracy \u0026amp; Liability # All content provided on this website is for informational and educational purposes only. While every effort is made to ensure the accuracy of the research data, publications, and commentary presented, the author makes no representations as to the completeness, currentness, or validity of any information on this site. The author will not be liable for any errors, omissions, or delays in this information or any losses, injuries, or damages arising from its display or use.\nExternal Links # This website contains links to external websites, including academic journals, research repositories, and institutional pages. These links are provided for convenience and educational purposes only. The author does not guarantee, approve, or endorse the information or products available on these external sites.\n","date":"31 August 2026","externalUrl":null,"permalink":"/disclaimer/","section":"","summary":" (Last modified: Aug 31, 2026) The views, thoughts, and opinions expressed on this website belong solely to the author, Jarrod J Scott, and do not necessarily reflect the official policy, position, or views of any institution or organization I happen to be affiliated with, its administration, or any funding agencies.\n","title":"Disclaimer","type":"footer"},{"content":"","externalUrl":null,"permalink":"/study/sciart/","section":"Research","summary":"Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor.","title":"SciArt","type":"study"},{"content":" Expand to see Tech Stack Tech Stack Technologies I use to build things\nLanguages R Python Bash Go Bioinformatics \u0026amp; Network Analysis \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e anvi\u0026#39;o \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e Mothur dada2 \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e Phyloseq miaverse \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e SPAdes Cytoscape \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e image/svg+xml Gephi Development Environments \u0026amp; Editors RStudio VS Code Jupyter Design \u0026amp; Graphics Gimp Inkscape Document Publishing \u0026amp; Static Sites Quarto Quarto Hugo Markdown \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e RMarkdown Frontend \u0026amp; Styling HTML5 CSS3 Tailwind CSS Git \u0026amp; DevOps git GitHub GitHub Actions \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e Snakemake Package \u0026amp; Environment Management \u003c?xml version=\"1.0\" encoding=\"utf-8\"?\u003e file_type_conda Conda \u003c?xml version=\"1.0\" encoding=\"UTF-8\"?\u003e Mamba Homebrew COMING SOON Field Work # Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nLorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nLorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nLorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nMarine # Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nTerrestrial # Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\nLaboratory # Molecular # Microbiology # Bioinformatic # Publishing # Visualization # Lorem ipsum dolor sit amet consectetur adipiscing elit. Quisque faucibus ex sapien vitae pellentesque sem placerat. In id cursus mi pretium tellus duis convallis. Tempus leo eu aenean sed diam urna tempor. Pulvinar vivamus fringilla lacus nec metus bibendum egestas. Iaculis massa nisl malesuada lacinia integer nunc posuere. Ut hendrerit semper vel class aptent taciti sociosqu. Ad litora torquent per conubia nostra inceptos himenaeos.\n","externalUrl":null,"permalink":"/research-portfolio/expertise/","section":"Research Portfolio","summary":" Expand to see Tech Stack Tech Stack Technologies I use to build things\n","title":"Skills \u0026 Expertise","type":"research-portfolio"},{"content":" (Last modified: Aug 31, 2026) © 2026 Jarrod J Scott. All rights reserved unless otherwise stated below. I believe in open science and the free exchange of academic knowledge. To facilitate collaboration, different materials on this website are made available under the following open-source licenses:\nWritten Content \u0026amp; Teaching Materials: Except where otherwise noted, the text, blog posts, lecture slides, and original diagrams on this site are licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). You are free to share and adapt these materials for non-commercial purposes, provided you give appropriate credit to the author.\nResearch Code \u0026amp; Software: Any source code, scripts, or software repositories hosted or linked on this site are open-source and distributed under the MIT License, allowing for free reuse, modification, and distribution with attribution.\nPublished Papers: PDF copies of peer-reviewed journal articles and conference proceedings are shared here in accordance with publisher self-archiving policies (Green Open Access). Copyright for these materials remains with the respective publishers or authors as indicated in each document.\n","date":"31 August 2026","externalUrl":null,"permalink":"/licensing-terms-of-use/","section":"","summary":" (Last modified: Aug 31, 2026) © 2026 Jarrod J Scott. All rights reserved unless otherwise stated below. I believe in open science and the free exchange of academic knowledge. To facilitate collaboration, different materials on this website are made available under the following open-source licenses:\n","title":"Licensing \u0026 Terms of Use","type":"footer"},{"content":"On this page are some web-based products I made using publishing tools tools like R Markdown, Quarto, and Hugo. Included here are project websites, reproducible workflows, tutorials, and slides from talks. Each web product has a link to the corresponding code repository on GitHub just in case you want to see the code.\nI call these data-driven because at the root of each site is an underlying data set that is used to generate many of the figures, tables, analyses, etc. This means that unlike static documents like PDFs or Word documents, if the underlying data changes (e.g., adding new samples), the site can be rebuilt without recreating the analytical outputs. All of that is handled by the code.\nNote Some of these are a little older and may not be optimized for mobile devices or accessibility standards.\n","externalUrl":null,"permalink":"/research-portfolio/products/","section":"Research Portfolio","summary":"On this page are some web-based products I made using publishing tools tools like R Markdown, Quarto, and Hugo. Included here are project websites, reproducible workflows, tutorials, and slides from talks. Each web product has a link to the corresponding code repository on GitHub just in case you want to see the code.\n","title":"Web Products","type":"research-portfolio"},{"content":" (Last modified: Aug 31, 2026) Your privacy is important to me. This Privacy Policy explains how Jarrod J. Scott or jarrodscott.github.io (\u0026ldquo;I\u0026rdquo;, \u0026ldquo;my\u0026rdquo;, or \u0026ldquo;this website\u0026rdquo;) collects, uses, and protects your personal information when you visit this site and use its contact features.\nInformation Gathered Through Contact Forms If you choose to contact me using the Contact Form on this website, you will be asked to provide your name, email address, and the content of your message.\nPurpose: This information is used strictly to reply to your inquiry, collaborate on academic research, or answer questions about my work.\nStorage \u0026amp; Sharing: Your messages are treated as confidential correspondence. I will never sell, rent, or distribute your email address or personal details to third parties for marketing purposes.\nAutomated Data Collection (Analytics \u0026amp; Cookies). Like most academic websites, this site may automatically collect non-personal tracking data to help me understand how visitors interact with my content. This may include:\nAnonymized IP addresses Browser type and operating system Pages visited and time spent on the site Referring websites This site may use cookies (small text files placed on your device) to power these basic analytics or website performance tools. You can choose to disable cookies through your browser settings at any time without losing access to the website\u0026rsquo;s content.\nThird-Party Links and Embedded Content This website features links to external academic journals, universities, and research networks (e.g., ResearchGate, Google Scholar). Articles on this site may also include embedded content (e.g., videos, charts). Embedded content from other websites behaves in the exact same way as if the visitor has visited the other website. These third parties may collect data about you, use cookies, or embed additional tracking. I am not responsible for the privacy practices of external sites.\nData Security I take reasonable security measures to protect the personal information submitted to me. However, please note that no method of transmission over the internet or electronic storage is 100% secure.\nYour Rights (Including GDPR Compliance) Depending on your location, you may have rights under regional privacy laws (such as the EU General Data Protection Regulation) regarding your personal data. This includes the right to request a copy of the data I hold about you, or to request that I delete any contact emails or personal information you have sent me.\nContact Information If you have any questions about this Privacy Policy or wish to have your data removed, please contact me directly via the Contact Form on this website or via Direct Email.\n","date":"31 August 2026","externalUrl":null,"permalink":"/privacy-policy/","section":"","summary":" (Last modified: Aug 31, 2026) Your privacy is important to me. This Privacy Policy explains how Jarrod J. Scott or jarrodscott.github.io (“I”, “my”, or “this website”) collects, uses, and protects your personal information when you visit this site and use its contact features.\n","title":"Privacy Policy","type":"footer"},{"content":"","externalUrl":null,"permalink":"/research-portfolio/media/","section":"Research Portfolio","summary":"","title":"Media Features","type":"research-portfolio"},{"content":"","date":"1 September 2026","externalUrl":null,"permalink":"","section":"","summary":"","title":"","type":"footer"},{"content":" Welcome to my website! I\u0026rsquo;m really happy you stopped by.\nResearch Collaboration \u0026amp; Services ","date":"1 September 2026","externalUrl":null,"permalink":"/","section":"Jarrod","summary":" Welcome to my website! I’m really happy you stopped by.\n","title":"Jarrod","type":"page"},{"content":"","date":"1 December 2023","externalUrl":null,"permalink":"/authors/alaina-r.-weinheimer/","section":"Authors","summary":"","title":"Alaina R. 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Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.\nRecent Teaching Experience # I teach the way I learn. My goal is to create a venue where students can be curious, get their hands dirty, make mistakes, \u0026amp; explore. I\u0026rsquo;m here to help students see what\u0026rsquo;s possible, not tell them what to do.\nLead Instructor Entangled Social \u0026amp; Ecological Systems Field Course 2024 PANAMA 5-week intensive field course for beginning graduate students that weaves together natural history, social science, tropical ecology, and cultural exchange. Students conduct both marine and terrestrial field work across Panama. This year\u0026rsquo;s course had 12 students from 7 different countries.\nPrimary Duties included:\nDesign course content. Guide student project design \u0026amp; implementation. Lectures \u0026amp; instruction on reproducible analytical workflows using Quarto. Assist students with field work. Natural history of neotropical marine \u0026amp; terrestrial ecosystems. Snorkeling \u0026amp; marine safety classes for students. Field Sites: Barro Colorado Island , Ft Sherman Canopy Crane , Pipeline Road Forests , Mount Totumas Cloud Forest , and Isla Coibita .\nData Specialist \u0026amp; Project Coordinator STRI-McGill NEO Tropical Biology Field Course 2022 PANAMA A 5-week experiential field course where undergraduate and graduate students learn research techniques in biology, ecology, conservation, environmental policies, and participatory evaluation techniques while exploring marine and terrestrial ecosystems on various excursions throughout Panama.\nPrimary Duties included:\nCoordinate student project design \u0026amp; implementation. Teach reproducible analytical workflows using R Markdown. Assist students with field work. Natural history of neotropical marine \u0026amp; terrestrial ecosystems. Snorkeling \u0026amp; marine safety classes for students. Field Sites: Barro Colorado Island , Bocas del Toro , Ft Sherman Canopy Crane , Pipeline Road Forests , Agua Salud , and Isla Coiba .\nSee the Course tutorial website for more information.\nTeaching Assistant STRI-McGill NEO Tropical Biology Field Course 2020 PANAMA A 5-week experiential field course where undergraduate and graduate students learn research techniques in biology, ecology, conservation, environmental policies, and participatory evaluation techniques while exploring marine and terrestrial ecosystems on various excursions throughout Panama.\nPrimary Duties included:\nHelp students design and implement field projects. Teach reproducible analytical workflows using R Markdown. Assist students with field work. Drive field trucks \u0026amp; coordinate field activities. Snorkeling \u0026amp; marine safety classes for students. Field Sites: Barro Colorado Island , Bocas del Toro , Ft Sherman Canopy Crane , Pipeline Road Forests , Agua Salud , and Isla Coiba .\nYou can chack out the Course blog to read essays by student participants or the Course tutorial website for general information.\nMarine Biology Instructor STRI-McGill NEO Tropical Biology Field Course 2019 PANAMA Part of the STRI-McGill NEO Tropical Biology Field Course, this one week module takes place in and around Isla Coiba off the Pacific coast of Panama. During this module students learn how to conduct fish surveys, assess coral reef health, and conduct field experiments.\nPrimary Duties included:\nCoordinate project design \u0026amp; implementation. Assist students with field work. Snorkeling \u0026amp; marine safety classes for students. Field Site: Isla Coibita .\nCreator, Organizer, \u0026amp; Host Marine Microbiome Workshop 2018 Bocas del Toro, PANAMA Workshop Title: From model organisms to ecosystems: scaling-up our understanding of host-microbe symbiosis in the sea.\n1-week intensive workshop that brought together 20 top researchers in marine ecology, symbiosis, microbiology, and chemical ecology. During this workshop we summarized and synthesized the current state of our knowledge on the mechanisms and the role of animal-microbe interactions in the sea. The goal of the workshop was to connect people working on different marine systems and discuss future research goals based on systems level approaches\u0026ndash;to move beyond descriptive studies to synthetic eco-evolutionary dynamics.\nPrimary Duties included:\nConceived, created \u0026amp; designed workshop. Workshop logistics \u0026amp; organization. Led discussions \u0026amp; working groups. See the Workshop website for more information.\n","externalUrl":null,"permalink":"/research-portfolio/teaching/","section":"Research Portfolio","summary":"Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.\n","title":"Teaching Experience","type":"research-portfolio"}]