Thursday, November 24, 2016

Evolution Day Meets Thanksgiving Day (or the progress of the turkey ;)

This year Evolution Day (the anniversary of the public of "The Origin of Species" by Charles Darwin) falls on the same day as the US National Holiday of Thanksgiving, so it *only* seems right to take a nod at the turkey!

This Thanksgiving (and Evolution Day!) brought to you by the letter M (for mineralization)

This year Thanksgiving serendipitously coincides with Evolution Day (the anniversary of the publication of Darwin's "Origin of Species" in 1859), so it seems *only* appropriate to express our thankfulness for mineralization (which allows fossils to be created from decaying organisms). This played a key role in Darwin developing and proving the theories of evolution.

*Sorry about the audio quality---this was filmed on the fly so we didn't grab a real mic for this little clip. Might fix the sound up and add a couple more informative diagrams later. In the meantime, enjoy that Thanksgiving dino-descendant turkey with a side of Darwin!

Science Theory Meme and Definition!

Thank you Inigo for putting that so well!

The intent behind the word "theory" is commonly mistaken because it has a different emphasis when it is used in every day conversation versus when it is applied in science.

Theory commonly means speculation or supposition, or simply an idea for explaining something.

The use of the word "theory" in science, or the term "scientific theory" or "science theory", has a much stronger meaning: "A scientific theory is a well-substantiated explanation of some aspect of the natural world that is acquired through the scientific method (we'll talk later about WHY this part of the definition is sooo important!) and repeatedly tested and confirmed, preferably using a written, pre-defined, protocol of observations and experiments."   ( thank you wiki for the grab of the definition   ; )

Wednesday, November 16, 2016

The Earth is (was) Flat: A Brief History of GIS, How it Benefits Us Today, and How YOU Can Get Involved!

by B. McL

Everyone knows what a map is. We use and see them every day, from a slick infographic on the news, to the handy smart phone app we trust to get us correctly from A to B. Or, for those outdoor adventurers we caller hikers, a crinkly old paper topo map with hard to read text. But what about the science that comes behind these maps?
Since the Canadian government decided to map all its lands in the 1960s, we have called that science GIS or, for the rest of us, Geographic Information Systems. Modern day GIS is a science that deals, essentially, with representing the physical world in a digital environment. Most basically, we choose to make this digital world flat or round or somewhat egg-like, give it the fancy name “geoid” (JEE-oyd), and then we stretch what we observe in reality to make it fit our 2-dimensional (or more and more often 3-dimensional) model. This is what we call a “projection”. Remember that for your next dinner party! The result is often a pretty map, whose simplicity (or complexity!) says little about the databases, projections, programming, surveying, etc. that it takes to produce it.

But GIS, or map making in general, hasn’t always been so sophisticated. Or, rather, it was sophisticated in other ways. While the maps of today are more often than not produced by satellites orbiting our earth hundreds of miles above us, or by GPS-enabled survey equipment that can pinpoint a location down to a fraction of an inch (at the cost of more than your car!!!), all of which is fed into computers that runs programs with thousands of lines of code, the maps of the past were often the result of barebones surveying equipment that relied on star charts and fairly complex trigonometry, and all taken down on paper that could easily be lost, burned, or both. To see how accurately the cartographers of the past mapped our coastlines, countries, and world, with nothing more than a sextant (or a length of chain!), puts many of us modern day mappers to shame.

GIS Data Layer, Over-Lays

So you may ask, “OK, so maps can tell us where we are, and how far interpret from that map. This is what we now call “spatial analysis”, and it affects us in ways we don’t even see, and in some ways we do.
away another place is, but that’s it, right?” Wrong. Maps can do so much more, and have done for hundreds of years. The way that a map can affect every one of our lives is what we

Here are a few examples, spanning the centuries and sciences.

GIS and Public Health
The godfather (not that kind!) of modern day spatial analysis, and of an often linked science known the method used to find the causes of health outcomes and diseases in populations; was a doctor named John Snow. Yes, like from Game of Thrones, although arguably much more heroic (although less immortal). Doctor Snow was an English physician in London during the mid 1800s. In many GIS and epidemiology texts, he is rightly credited for his investigation into the cause of a cholera epidemic in London in 1854. At the time, many doctors and public health officials thought that disease was spread by “miasma”, or bad air. While we know now that some diseases are indeed airborne, many others are spread through media such as water. Dr. Snow wasn’t as fortunate as us to know about germs, but he also didn’t believe that cholera as being spread through the air in a toxic “miasma”. So he took to the streets, and with the help of a local reverend surveyed the residents of the neighborhood in Soho where the outbreak was worst. From his survey, he produced what many consider to be one of the first recorded instances of spatial analysis. It was a map that tallied the number of people who had become ill due to cholera. In the map, the black bars represent individuals, and they are tallied up per household along each street.
as epidemiology (which the US Centers for Disease Control defines as “
While somewhat hard to read, one can see that the bars are thickest at the center of the map, on Broad Street. This was where the most sicknesses occurred, and this trend let Dr. Snow to believe that the cholera was coming from a water pump on Broad Street. We know today that cholera bacteria are transported primarily through water, but at the time, Dr. Snow was met with much resistance from local officials, although he did succeed in shutting down the tainted pump. Consequently, the cholera outbreak was contained, and many people avoided sickness thanks to his efforts. (Source: Gunn, S. William A.; Masellis, Michele (23 October 2007). Concepts and Practice of Humanitarian Medicine. Springer. pp. 87–. ISBN 978-0-387-72264-1.)

Today, GIS is an integral part of public health planning and disaster response. During the ebola epidemic of 2014-16, governments and public health non-profits used GIS to analyze where
outbreaks were worst, and where they might be heading. This allowed them to prioritize resources to the heaviest hit areas, and ultimately contain the epidemic, although at a high cost in lives. Without the visualization provided by GIS, decision makers would have made blind decisions, which could have extended the epidemic. The map below uses “graduated symbols”, or symbols that get bigger or smaller depending on what they represent, to show the number of ebola cases in different districts of Guinea, Liberia, and Sierra Leone in West Africa. By comparing the size and color of the symbols, they could see where ebola cases were decreasing, and where they were increasing.
GIS and the Environment

GIS has also provided a great many benefits to the managers of our world’s natural resources. All over the world, changes are taking place to the environment that will affect life on earth in many different ways. GIS has been used to map and predict sea level rise due to global climate change, identifying areas that will see the most inundation, and giving people in those areas more information they need to prepare and adapt.

Maps have also helped forestry managers right here in the US identify where forests are struggling to survive due to drought, tree-killing beetles, and other threats from a changing climate. The map below shows how often fires occur in different parts of the US, which will help forest managers make decisions about where to apply fuel-suppressing treatments (burning dead wood to reduce the risk of fire) or other strategies to revitalize dying forests. Forest fires can affect millions of Americans with bad air quality, destruction of infrastructure and homes, and also contributes greenhouse gases to the atmosphere.

GIS in Local Government
Chinese Holy Field Plan
While not the most glamorous or the most global in perspective, GIS used in local government often has wide ranging effects on where, how, and how well we live day to day. City planners have been literally deciding where we live for centuries, and their decisions are informed and enforced by maps. In ancient China, cities were often laid out as a representation of the Holy Field, which was a philosophical concept related to numbers. In the modern day, new philosophies inform how people and activities are grouped together. For example, it is often desirable to keep heavy industry away from residential areas or environmentally sensitive areas such as wetlands or streams. Many cities and counties adopt zoning rules which decide how land is used, although there are many notable exceptions around the world (or better or for worse! I’m looking at you Houston!). 

GIS analysis of traffic patterns and public transit use helps governments plan out road, bus, and rail expansions. As traffic is one of the biggest headaches in the lives of most Americans, imagine how bad it might be if we had no idea where the clogged routes are, and where the alternatives lie. GIS enables informed decision making.

Citizen GIS
We’ve covered a few different ways GIS is used to better our lives. Be sure, there are many more, and probably a few not-so-good ways as well. If you made it through all this, you might think, wow, GIS is very exciting, but too hard for me to understand or contribute to. That is where you are wrong! There a variety of ways that any citizen with a smart phone or a computer can contribute to the field of GIS, for the betterment of all life on earth. Here are just a few:

·         Open Street Map. OSM is “the Free Wiki World Map – An openly licensed map of the world being created by volunteers using local knowledge”. Anyone can quickly and easily learn how to add to the map. Add your house, or different features around your neighborhood such as trails, parks, restaurants, etc.
·         Missing Maps: This program, founded by the Red Cross and others, directs the improvement of Open Street Map by targeting where maps are missing in the world’s most vulnerable places and recruiting citizen mappers to improve them, from the comfort of your own home!
·         Find It Fix It: Find It Fix It is a public service request app by the City of Seattle. Many cities and counties have similar apps downloadable on the Google Play or Apple store. Find out if your city has a similar map app, and start helping to improve the area you live!
·         What’s Invasive: What’s Invasive is an app that turns you into a citizen scientist! You can report where you observe potential invasive species, help managers respond before it is too late!
·         For other crowd-sourced apps and websites, see this article:

It's GIS Day again!

Our QuestX *accomplices* have all been very busy, but one of them, a GIS Specialist, says that he is going to *create some space* in his busy schedule to write up an overview of GIS just for you!

So... stayed tuned! It won't be today, but it will be very soon!

Monday, November 14, 2016

America ReCycles Day - Nov. 15, 2016

Make a difference today, for tomorrow!

America Recycles Day is an initiative of the Keep America Beautiful Program! For more information about going to an event or creating your own even, go to their website!

 The information in the following poster lets you compare recycling efficiency and waste disposal around the world.

Click for larger poster! (Credit: UNEP)

 Many items can be recycled, but some items are not recyclable, are recyclable in limited areas, or should be composted.

Credit: EcoMaine

Thursday, November 10, 2016

Jellyfish blooms, why?!? [science translated! specialized science *lingo* translated for a very wide audience]

[Sometimes specialized science language can get sooo specialized and/or change so rapidly that even scientists in similar fields can find it a challenge to be sure what is meant, or an interested amateur can end up feeling lost and "out"; the language used isn't meant to exclude any reader, it is used so the *scientists* can communicate what they mean more clearly and (believe it or not ;)  ) more quickly! The best thing to do if you're ineterested is ferquently to copy the article and stick the definitions of the words you're not sure of right in to the text so you can become more familiar with the words *in context*. Definitions are given in (= definition)]

by S. Abboud

A bloom is a consequence (= result) of seasonal life cycles when there is localized increases in asexual reproduction and growth typical of all metagenic (= the reproduction cycle of organisms that alternate between a sexual generation and an asexual generation) organisms that result in normal or abnormal seasonal biomass (Figure 1: an alternate photo of a bloom has been inserted). Blooms can be influenced by localized anthropogenic (= human caused) effects attributed to oceanic sea surface temperature, nutrient inputs (Purcell et al. 2007, Brodeur et al. 2008), disturbances (Brodeur et al. 2002) including over-harvesting fisheries and translocations (Purcell 2005, Howarth et al. 2002). Apparent sudden jellyfish population increases (i.e. blooms, Figure 2) are possible due to increased recruitment (= increase in a natural population as offspring grow and new animals arrive) from local asexual reproduction (Madin & Deibel 1998), high fecundity (i.e. enhanced fertilization success), aggregation (= gathering) of mature medusae (Strathmann 1990, Purcell and Madin 1991, and Hamner et al. 1994), and previously mentioned ecophysiological (= adaptation of an organism's physiology/function to environmental conditions) and reproductive versatility (= adaptive reproductive strategies) (Hadfield & Strathmann 1996, Lucas 2001, Deibel & Lowen 2011).

Description (Lucas & Dawson 2013)
A true bloom is a consequence of seasonal life cycles when there is localized increased asexual reproduction (= producing offspring without a sexual act) and growth typical of all metagenic organisms, resulting in normal or abnormal seasonal biomass. A true bloom is categorized as an endemic (= native / to a restricted area) bloom staying in the same location over time. Though apparent blooms are either transient blooms (blooms that move spatially over time) or an accumulation within enclosed habitats, not reflecting true blooms
A long-term summation of fluctuations (= changes/ variability) in relative number compared on temporal (= time) and spatial (= space) scales without causation
mass occurrence
Similar to an accumulation but larger in magnitude (= number - like a baby elephant or adult elephant is one elephant) and/or biomass (= total amount of animal by total mass of animals present rather than by number - a baby elephant is much smaller than an adult, so even though it is also ONE elephant it has a much smaller individual biomass- a group of 12 baby elephants would have a smaller biomass than a group of 12 adult elephants)
Accumulation of individuals likely emigrated (= left) from natural or apparent blooms due to passive drifting, active behavior, or a combination of the two
A very dense aggregation (= group) of individuals coming together primarily through individual motion than currents alone
Extraordinary increases in biomass over a short time period within a reproductive season that is typically associated with anthropogenic (= human caused) ecosystem changes

            Due to the pelagic mobility of jellyfish, it is often difficult to properly describe a mass of jellyfish as a bloom or any of the other previously described related events. These events similar to jellyfish blooms differ by location of reproduction, mode of how they came together and other factors that influence jellyfish distributions (Mills 2001; Graham et al. 2001; Hamner & Dawson 2009; and Richardson et al. 2009; also see Lucas & Dawson submitted 2012). It is imperative to consistently use the following relative terms to facilitate interpretation of scientific literature and best present cause and consequences (translation of entire section = To make communication between those interested in this topic as clear as possible it is very important that everyone use the same terms, and with the same meaning!) (Lucas & Dawson 2013): bloom, accumulation, mass occurrence, aggregation, swarm, and outbreak (Table 1).Due to the pela et al. 2001; Hamner & Dawson 2009; and Richardson et al. 2009; also see Lucas & Dawson submitted 2012). It is imperative to consistently use the following relative terms to facilitate interpretation of scientific literature and best present cause and consequences  (Lucas & Dawson 2013): bloom, accumulation, mass occurrence, aggregation, swarm, and outbreak (Table 1).

            The key to understanding the distributions of jellyfishes is in identifying the original source of jellyfish blooms. Bloom biology focus is on the meditative medusae form, which, in large numbers, can have negative economic impacts on commercial fisheries from fish larvae consumption (Sandlifer et al. 1974), on aquaculture by destroying equipment and stock (Purcell et al. 1999; Delano 2006), and on power station operations by impairing equipment (as seen in Brodeur et al. 2008; Clark 2008).

            Due to the complexity of jellyfish life histories and the consequences of their blooms, Parsons (1993) and Mills (1995) implored jellyfish scientists to study the functional role of jellyfish in maintaining the ecology of the oceans. This call resulted in much of the current information that we know and highlighted what remains to be known about jellyfish blooms.
Phylogenetics (= development and differences within species or structure within species) and population genetics have proven to be useful for understanding jellyfish biology (Hamner & Dawson 2008; 2009), their geographic distribution (e.g., Dawson 2005), and genetic variation between populations. Jellyfish that aggregate, bloom, or swarm are clustered taxonomically and phylogenetically (translated section = Jellyfish that "live together" tend to be similar in development and in relatedness to each other), though taxa that bloom and swarm are typically more diverse than non-accumulating sister taxa (Hamner & Dawson 2008).
Hamner and Dawson (2009) presents an inventory for species that occur en masse (= together), encompassing jellyfish biodiversity (= variety of life), jellyfish molecular phylogenetics, species richness, and phenotypic diversity on a global scale. Conclusions include that taxa are not randomly distributed within medusoid Cnidaria, and there are synergistic (= interconnected) effects of environmental attributes and organismal traits promoting en masse occurrences. Phylogenetics can be used to differentiate between aggregations, blooms, and swarms (Hamner & Dawson 2009), and population genetics can differentiate between evolutionary significant units at the population level (Waples 1994). The integration of these molecular analyses with ecology can distinguish endemic (= native) versus transient blooms and identify putative environmental and genetic influences. This integration allows for the previously mentioned knowledge gaps to be addressed, since jellyfish blooms are characterized by increased biomass ascribed to local conditions (= increase in the amount of jellyfish is impacted by local conditions). Therefore, it is necessary to know the condition exposure overtime, not just a snap-shot of present conditions, to fully understand the spatial distribution of jellyfish. Combining population dynamics and population genetics is essential for tracking jellyfish blooms throughout the season. Categorizing a bloom as endemic or transient will provide necessary information to identify putative causes.

Similar to the development of molecular ecology, using more a evolutionary approach incorporating molecular techniques and focusing on the mechanisms of evolution to understand ecology is how best to understand jellyfish blooms. Many questions in ecology are not framed to include evolution as part of the question asked or as part of the solution in finding its answer. Though, an evolutionary context is necessary to find a resolved and robust answer (Dobzhansky 1964, 1973) through providing a framework allowing for correct assumptions to be made.  Current jellyfish molecular studies emphasize the macroevolution ('deep' timeline between taxa, e.g. Gingerich 1987, Benton 2015), but few consider jellyfish microevolution ('shallow' timeline evident through population genetics, eg. Dobzhansky 1937, Kothe et al. 2016). Microevolutionary studies typically exist in the space between ecological and evolutionary processes since their population dynamics both are influenced by overlapping processes (Lucas & Dawson 2012). After all, there cannot be ecology without the mechanisms of evolution: mutation, genetic drift, gene flow, and selection.  Therefore it is necessary to integrate ecology and population genetics in a novel framework (Lucas & Dawson 2012) to identify types and causes of blooms (Figure 3). This integration can distinguish endemic versus transient blooms and tease out environmental or genetic influences on blooms. Beyond using population genetics as a tool to find (1) what causes jellyfish blooms, and providing the foundation for (2) how jellyfish affect ecosystems/communities: there are some other necessary techniques that should be utilized in concert. Some of these techniques rely on specific methodology. More rigorous sampling is necessary within a jellyfish season (intra-annual) and also between jellyfish seasons (inter-annual) to understand if the bloom has normal or abnormal biomass and whether it is endemic or transient. Additionally, understanding dispersal (a mode of gene flow) through mathematical and oceanographic modeling will result in more accurate identification of possible environmental variables that cause blooms, which would then be empirically tested with laboratory manipulations.  The combination of these techniques must be applied through integrating population genetics and ecology to answer (a) how frequent is genetic structure between species (phylogenetics) and populations (within species)? & (b) on what geographic scale does genetic structure exist (macroevolution or microevolution)? With these answers we can finally have more substantiated conclusions about the causes of jellyfish blooms and what actions we can take to minimize them as the oceans continue to change.

Figure. 2. Hypothetical preliminary quantitative evolutionary-ecological framework (adapted Lucas & Dawson 2013) to define jellyfish en masse events. The abscissa shows a single jellyfish season (May-September) and the ordinate axis shows distance along a northern flowing current. Jellyfish abundance & biomass increase with diameter. The theoretical blooming event dictated by the arrows for two separate possible patterns for these blooms due to reproduction and then subsequent decrease due to mortality or emigration. (A) shows an endemic bloom that remains at the same location throughout the season. (B) shows a transient bloom that moves throughout the season.

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