tag:blogger.com,1999:blog-15118293723513414192024-03-05T03:09:40.893-08:00Wild Plants PostA place to discuss the ecology and evolution of plants as well as the functioning of ecosystems.
Companion to Resource Strategies of Wild Plants, Princeton University Press.JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.comBlogger287125tag:blogger.com,1999:blog-1511829372351341419.post-4920126962896803232017-11-14T06:39:00.000-08:002017-11-14T06:39:09.927-08:00Testing trends in global N cycling<div dir="ltr" style="text-align: left;" trbidi="on">
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<tr><td style="text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7hShpGHZ73aUVJFh1rurnC00Z7FYxjtkf5L95Gbm_catFPkq4vvMBgfe_S8Sn6ADr9fOMbhuF4SRnVLxCsopbBdPOjwZCE1jyKe6LQex1AJREC-zWb2w0vazue6MlBcLenateeoXG3KZj/s1600/15NstdDecade1850.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="900" data-original-width="900" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7hShpGHZ73aUVJFh1rurnC00Z7FYxjtkf5L95Gbm_catFPkq4vvMBgfe_S8Sn6ADr9fOMbhuF4SRnVLxCsopbBdPOjwZCE1jyKe6LQex1AJREC-zWb2w0vazue6MlBcLenateeoXG3KZj/s320/15NstdDecade1850.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Some of the best evidence that N availability has been declining globally. <br />Standardized patterns of wood d15N for forests across the US. From McLauchlan et al. 2017.</td><td class="tr-caption"><span style="font-size: 12.800000190734863px;"><br /></span></td></tr>
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Because we monitor, weather all around the world, we can detect changes in global temperatures and precipitation patterns.<br />
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Because we monitor gas concentrations throughout the world, we can quantify the increases in CO2 concentrations as well as other gases like methane and N2O.<br />
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But what about the N cycle? Has N availability to plants been increasing or decreasing throughout the world?<br />
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We really have no idea. There is no global N monitoring network. We cannot tell if plants have been experiencing increased or decreased N availability over the past, say, 100 years.<br />
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Considering how crucial the N cycle is to plant productivity worldwide, it seems important to have some index of whether N availability has been going up or down.<br />
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Through different projects over the last decade or so, I've been involved in trying to reconstruct N availability over time. Most of these have involved N isotopes in one way or the other, examining patterns in herbarium samples, tree rings, and sediments.<br />
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Most of these papers have shown declines in N availability over time.<br />
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There's one study left that I never got to, though. And it's been bugging me for about 5 years.<br />
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That's seeing if we can see a trend over time in foliar N isotopes at the global scale.<br />
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Most simply, if N availability has been increasing globally, all other things equal, d15N should be increasing. If N availability has been decreasing globally, all other things equal, d15N should be declining.<br />
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The last time we synthesized global foliar 15N patterns, we stopped data collection in 2006 and had about 12,000 data points. In order to update the database, I've read through about 500 papers that were flagged as potentially having appropriate data. About 250 did. So, Andrew Elmore and I started sending out emails to assemble the new global database.<br />
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With the new synthesis, we're now over 40,000 data points assembled so far with a couple dozen more datasets left to incorporate.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9SiF8HxnrcYBYqF-x48zEfW1SVG1hBy60Elm0foUAqAOUmscvsRRpikvkGGs9qvtLKcnOLuhx3FV9ABoS60iZOyBX-qTxFsEOWQJsQVh0pnMvsVRfFiOB4pFYNGc1Ah14qo5bG7MRkXZa/s1600/Global15Nmap.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em; text-align: center;"><img border="0" data-original-height="762" data-original-width="1600" height="152" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh9SiF8HxnrcYBYqF-x48zEfW1SVG1hBy60Elm0foUAqAOUmscvsRRpikvkGGs9qvtLKcnOLuhx3FV9ABoS60iZOyBX-qTxFsEOWQJsQVh0pnMvsVRfFiOB4pFYNGc1Ah14qo5bG7MRkXZa/s320/Global15Nmap.jpg" width="320" /></a><br />
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Given all the variability that exists at the global scale, we'll likely need all 40,000 data points to detect any trend that might be there (or to be sure there isn't a trend).<br />
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As Andrew and I talked about how we wanted to conduct this study, we wanted to make sure that the analyses were trusted. We wanted to preclude any criticisms that, for example, we left out data that didn't fit a given desired outcome**.<br />
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**Although most of the other patterns we've uncovered support declining to stable N availability, any of the three outcomes are equally interesting and important, as long as we have strong enough analyses to be certain about the patterns.<br />
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To make this project as trusted as possible, we have pre-registered our data analysis plan with the open science framework. See https://osf.io/thnyf/#. This means all of our hypotheses and analysis plans have been declared ahead of data collection. The R code that we will use to analyze the data has also been written and posted. This pre-registration is important in that it locks in our approach ahead of time and eliminates many forms of scientific bias that can misrepresent results. This transparency will be important to creating trust in whatever results we find.<br />
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We should be finishing up data acquisition by the end of the year, given the current pace of people getting back to us (which has been pretty good--over 75% of the requests have been answered).<br />
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One neat thing about writing all the R code ahead of time is that once we have all the data, we just push the big red button, and we'll see our answer.<br />
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Something to look forward to in 2018.<br />
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McLauchlan, K. K. et al. 2017. Centennial-scale reductions in nitrogen availability in temperate forests of the United States. Scientific Reports 7: 7856.</div>
JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com5tag:blogger.com,1999:blog-1511829372351341419.post-1071947647819080242017-03-25T22:01:00.000-07:002017-03-26T06:56:43.417-07:00Declining protein for cattle in the US<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgks3nGgqGqjNV69d5um_eKjAICvqf33x4Dki-tOPvipop6git2IFhpn6xtTXiutMsP-ktN8dqiI-HmUBfxVxVqAtoa3V0Am_CyIQFNNkZ5ZyJCbYxjmnel2HiCjNykYtUHFLhNEKIbK4Sd/s1600/Untitled.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="175" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgks3nGgqGqjNV69d5um_eKjAICvqf33x4Dki-tOPvipop6git2IFhpn6xtTXiutMsP-ktN8dqiI-HmUBfxVxVqAtoa3V0Am_CyIQFNNkZ5ZyJCbYxjmnel2HiCjNykYtUHFLhNEKIbK4Sd/s320/Untitled.png" width="320" /></a></div>
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By last count, I had coauthored 98 scientific articles. <a href="http://iopscience.iop.org/article/10.1088/1748-9326/aa67a4" target="_blank">Number 99</a> has just been published on-line at Environmental Research Letters. I'll wager that this one is the most important I've written**.<br />
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**It doesn't mean it is important on the absolute scale, just the relative scale...<br />
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I've said <a href="http://wildplantspost.blogspot.com/2016/03/biogeochemical-planetary-boundary_5.html" target="_blank">before</a> that scientists have two jobs. The first is to create intellectual tension. The second is to resolve intellectual tension.<br />
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For global ecologists, some of the most important intellectual tension right now resides in two opposing ideas regarding nitrogen availability. Some theories suggest that global N availability is rising. Other theories suggest that it should be declining.<br />
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Given the central role of N availability in the functioning of the ecosphere, this is some of the most important intellectual tension we have to resolve. There is no doubt that excessive nutrient availability is damaging some aquatic ecosystems. Yet, in terrestrial ecosystems, whether N availability is increasing or decreasing is uncertain. The trajectory of terrestrial N availability determines how the ecosphere will respond to elevated CO2 and what types of policies we must impose. The difference couldn't be starker. If N availability is increasing, then we need to begin to limit anthropogenic N fixation. If the opposite is true, policies that limit N fixation might actually have deleterious effects.<br />
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The question about whether N availability to terrestrial plants is increasing or decreasing has suffered from a lack of data. Quite simply, there are no long-term measurements of terrestrial N availability across broad spatial scales that can be used to assess this question. We do not know the trajectory of N availability in grasslands. We do not know the trajectory of N availability in forests.<br />
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Paper #99 does not directly assess any of these, but it does one of the next best things for grasslands. It utilizes a unique long-term dataset on forage quality for cattle across the US.<br />
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I'll leave the details to the paper, but data suggest that N availability is declining in grasslands across the US. Not one or two experimental plots, but the whole of the Great Plains. Across this broad region, cattle are becoming more protein stressed as their forage is showing declines in protein. It appears that something is causing N availability to decline to plants and plants are responding by reducing their N (and protein) concentrations.<br />
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How much has protein declined over 20 years? The equivalent of a decline that causes plant N concentrations to decline about 10 mg protein g-1, or 0.3% N.<br />
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How much protein is that for US cattle? It would take about $2B in soybeans to replace all of that protein. Or about half of the soybeans produced in all of Iowa in a year.<br />
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By no means is paper #99 the final word on the topic. A fair amount of data support the thesis that N is declining in terrestrial ecosystems. Paper #100, which is still being reviewed, is going to be a major line of evidence in favor of declining terrestrial N availability.<br />
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As for this:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiu8byXusUSANBp2XzDI1-5faM0Nn-eAEitoV38VfIhMrkzOWedQd3IQ_kGD5rukrBGf9eUMdfiLabXMHff93NmjZ2CoEQwnGpKpd3fGgga49RwCv-RiZs_4YHJo3wRbKiFRXDUeC43aJb1/s1600/PB_FIG33_globaia%252B16%252BJan.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiu8byXusUSANBp2XzDI1-5faM0Nn-eAEitoV38VfIhMrkzOWedQd3IQ_kGD5rukrBGf9eUMdfiLabXMHff93NmjZ2CoEQwnGpKpd3fGgga49RwCv-RiZs_4YHJo3wRbKiFRXDUeC43aJb1/s320/PB_FIG33_globaia%252B16%252BJan.jpg" width="256" /></a></div>
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Let's just say that there are some intellectual tensions that aren't resolved.<br />
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I wouldn't believe it yet.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-7274448172328818992016-11-15T17:23:00.002-08:002016-11-15T17:23:31.102-08:00Fishes of Ohio<div dir="ltr" style="text-align: left;" trbidi="on">
I remember clearly over 20 years ago reading <i>Fishes of Ohio </i>by Milton Trautman. First published in 1957, the book is primarily a key and description to the fishes of the state.<br />
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The part I remember most was the introduction. I remember it describing Ohio when settlers first came to settle Ohio. Trautman summarized early records and painted a picture of lands with clear waters and an amazing abundance of fish.<br />
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In my mind, the abundance of fish was represented by a story that the boardwalks of Cleveland were built on the backs of fish.<br />
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I related that story the other day, but thought I should go back and find if I was remembering the details correctly. So, I purchased a copy, sat down, and started working through the 700+ page tome.<br />
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"The state of Ohio, situated in the midlands of the United States, is squarish in outline". It's not the most flattering beginning to a book, but it's a true representation of the state.<br />
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After this, Trautman describes historical accounts of Ohio. The waters were so clear that "early pioneers drank as readily from flowing streams as the did from springs." The abundances of fish are characterized, too. Before 1800, in the Maumee River "A spear may be thrown into the water at random, and will rarely miss killing one!"<br />
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After 1800, things start to go downhill.<br />
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I looked through this introduction and couldn't find the line about the boardwalk.<br />
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I went into the sections on individual fish.<br />
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In my mind, the boardwalks were built on the backs of sturgeon or maybe blue pike, a subspecies of walleye.<br />
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The section on lake sturgeon describes them being so abundant that fisherman sometimes placed them in large piles and set fire to them. Nothing on boardwalks.<br />
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Blue pike? 26M pounds caught in the 1950's, but nothing on their use as a base for sidewalks.<br />
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Google books has been no help, nor google. Nor bing.<br />
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I don't think it was in this book.<br />
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I have no idea where I read that.<br />
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Still, it was good to read through it again. Books like these just don't get written much anymore. And certainly there are few individuals left that spend more than 25 years making more than 2000 collections of fish--some half million individuals identified-- to help map the distribution of fish of a state.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-50252627137618448782016-10-04T19:32:00.000-07:002016-10-04T19:32:07.456-07:00Map of streams of US<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3Owgf7KKm1hBlZkNFUIxiqBbswHoEi3IO0dhzwOHpijcFSJvPuP2qxVYWq8eT_Vm9XPexldGK0yNkQvrue86OZ1KCPhAL1Wbd9MRBJSORY-vjaJrkZCbMpM796nItaRtbFyovxlruE5T8/s1600/8747607969_65098e4af6_o.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="225" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg3Owgf7KKm1hBlZkNFUIxiqBbswHoEi3IO0dhzwOHpijcFSJvPuP2qxVYWq8eT_Vm9XPexldGK0yNkQvrue86OZ1KCPhAL1Wbd9MRBJSORY-vjaJrkZCbMpM796nItaRtbFyovxlruE5T8/s400/8747607969_65098e4af6_o.png" width="400" /></a></div>
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I found this map of the US today. It shows all of the streams and rivers in the lower 48 states. You can find it <a href="https://secure.flickr.com/photos/nelsonminar/8747607969/in/set-72157633504361549/" target="_blank">here</a>.</div>
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It seem like everywhere in the US, even dry places, have at least temporary streams. But not everywhere.</div>
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What fascinates me about the map are not that there are so many streams, but the regions where there aren't any.<br />
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That strip in the Dakotas is the Missouri Coteau. It's the western extent of the eastern glaciers. It looks something like this:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHbqb3PpUltHaXYUmLYjXQhI_vqlolTaYtMHg4DkaUWqc7MokuTTJVz8IOyk41zDgIXFw-yrQQERuwsqHNplnfEHXn_s1LHOLiWF9fOXNPQkaP51rMS9Qtp-BnL9V666fmpN7UIAwnn84q/s1600/Missouri_Coteau_%2528656541298%2529.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="240" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHbqb3PpUltHaXYUmLYjXQhI_vqlolTaYtMHg4DkaUWqc7MokuTTJVz8IOyk41zDgIXFw-yrQQERuwsqHNplnfEHXn_s1LHOLiWF9fOXNPQkaP51rMS9Qtp-BnL9V666fmpN7UIAwnn84q/s320/Missouri_Coteau_%2528656541298%2529.jpg" width="320" /></a></div>
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There really are no streams there. Pot hole lakes and well drained soil. But really no streams.</div>
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In the middle, you can also see the Sandhills of Nebraska. Again, almost no streams. At least on the surface. Almost all the water drains through the soil and feeds aquifers. </div>
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You can also see the high plains of Texas to the south of there and south of there the coastal sand plain of Texas. Again, no streams there. </div>
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In the northwest, there are the buttes of the Snake River valley:</div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgboUquxr1Q8DrzpBHnvf6tsDmyKWouqCt4qn7lRAzXFDrz817W35_Xn2_A5CYs1JjwcmWr6aDlQH9YPewKAqhQbjohWbRVC0lOYlfP-XrtDqZNPw_70VKDlUZHrliWGWdYeLRcZC3K4mKo/s1600/SnakeRiver.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="197" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgboUquxr1Q8DrzpBHnvf6tsDmyKWouqCt4qn7lRAzXFDrz817W35_Xn2_A5CYs1JjwcmWr6aDlQH9YPewKAqhQbjohWbRVC0lOYlfP-XrtDqZNPw_70VKDlUZHrliWGWdYeLRcZC3K4mKo/s320/SnakeRiver.jpg" width="320" /></a></div>
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Again, no streams or rivers up there.</div>
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South of the Snake River Valley is the Great Salt Lake Basin. </div>
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Down in Florida, the Everglades are prominent.</div>
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I really have no other insight about the map, except it's an interesting way to look at the geography of the US. </div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com1tag:blogger.com,1999:blog-1511829372351341419.post-4141611725411438642016-09-23T12:36:00.000-07:002016-09-23T12:36:09.196-07:00Book review: Statistics Done Wrong: the Woefully Complete Guide<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibIUYvyuaShiWhuue7hYJ3-qq5krkxSby8r0goSD5cw8xWNLyJ5xkB8uuYsF9ata4voUsGJuFZ3924Ic6ZRrlD12HOMlpQRdFbELIUZH0gx23rfucn-6GWcU96QUdAMN6I43QSSZpjVyNW/s1600/51U1otVSfdL._SX331_BO1%252C204%252C203%252C200_.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEibIUYvyuaShiWhuue7hYJ3-qq5krkxSby8r0goSD5cw8xWNLyJ5xkB8uuYsF9ata4voUsGJuFZ3924Ic6ZRrlD12HOMlpQRdFbELIUZH0gx23rfucn-6GWcU96QUdAMN6I43QSSZpjVyNW/s320/51U1otVSfdL._SX331_BO1%252C204%252C203%252C200_.jpg" width="213" /></a></div>
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<br />
How to Lie with Statistics came out in 1954. It has long been considered a classic with over a half-million copies sold.<br />
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The second edition of Statistics Done Wrong might be a true successor to the classic. The first edition, recently released, is still a good read for any scientist.<br />
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The author, Alex Reinhart, spends covers some basics about statistics and then empirical cases where statistics have been used incorrectly.<br />
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It's a good book. I learned a few things while reading it and was impressed to see that important examples from recent news were included as cautionary tales. I think most scientists should spend the time to read through this. If they don't learn anything, they should at least feel good about that. My guess is that they would.<br />
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That said, the difficulty with the book is that it isn't mature yet. The section on p-values is probably the most important, but I finished the section not quite sure what the author wanted to impress upon the reader. The reader is admonished to use ranges instead of p-values, but it just isn't clear why. As the book matures, the author should have better examples to get his points across. In contrast, his examples for base rate fallacies were mature. They were poignant and the reader should have a clear idea how to calculate what percentage of positives are likely false.<br />
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Another problem with any statistics book is that statistics is too broad to be covered in any thin volume no more than a single book could cover how to lie with language.<br />
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At any rate, Statistics Done Wrong is an admirable effort. At the very least it should set off alarm bells with researchers to ask questions about their statistics a little more deeply.<br />
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I'm looking forward to seeing what the second edition holds.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-14805927913507408602016-09-19T17:48:00.002-07:002016-09-19T17:48:46.139-07:00xkcd cartoon on global mammal weights<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVdgrPiMsig9lZ4pxPoF2ySloirbHYZ_6iNJAzKh5d58Nf1M6E7XhczVk6AcuQFDvMZeaMdipvlCHAaEEWH-PJUYRf1MXk8D_BOXLyes8dXVyDrl6y-EzbjCHKx94ErqWcVzy5MccJ0z2P/s1600/land_mammals.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="255" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVdgrPiMsig9lZ4pxPoF2ySloirbHYZ_6iNJAzKh5d58Nf1M6E7XhczVk6AcuQFDvMZeaMdipvlCHAaEEWH-PJUYRf1MXk8D_BOXLyes8dXVyDrl6y-EzbjCHKx94ErqWcVzy5MccJ0z2P/s320/land_mammals.png" width="320" /></a></div>
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Just a bit sad....</div>
JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-34094596736919008502016-09-13T10:03:00.000-07:002016-09-13T10:04:31.311-07:00The trajectory of nitrogen availability<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEsu3lWHLWpUPJfSY0LVfa1MDlyXvCiZh2vRfX4Sgegme1hRFq1R3TEuFseMNkxeb3fyCTGlym-ofIeBK20ivvrXEr65W4QDxlIQ6znV-CdXDbBJORMbzwBV9gn6Zq_8n1Vsk7uzBDRemg/s1600/Untitled.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="130" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgEsu3lWHLWpUPJfSY0LVfa1MDlyXvCiZh2vRfX4Sgegme1hRFq1R3TEuFseMNkxeb3fyCTGlym-ofIeBK20ivvrXEr65W4QDxlIQ6znV-CdXDbBJORMbzwBV9gn6Zq_8n1Vsk7uzBDRemg/s320/Untitled.png" width="320" /></a></div>
It is a simple fact that N availability is rising throughout the world, likely causing a planetary boundary to be exceeded. Considering that humans have doubled global N2 fixation, it's impossible that it hasn't.<br />
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It is also a simple fact that CO2 concentrations have been rising, which likely should be causing N to become progressively more limiting.<br />
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It is also a simple fact that no one has taken the time to comprehensively address whether N availability has been increasing or decreasing in the ecosystems of the world. There are almost no time series of direct measurements of N supplies or availability to test whether N availability is going up or down.<br />
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As a result, it is unresolved as to whether N availability is increasing or decreasing in ecosystems across the world.<br />
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Andrew Elmore and Dave Nelson (with a little help from me) report in the latest issue of Nature Plants new data that looks at whether N availability is increasing or decreasing in US eastern deciduous forests.<br />
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Short answer: N availability looks to be decreasing.<br />
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Using ratios of N isotopes in wood as a proxy for N availability, Elmore et al. show that N availability has been declining in the forests they examined for some time.<br />
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That's a pretty big result.<br />
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Not only do they show this, but they also show that the declines are tied to spring phenology. Years with warmer springs have the lowest N availability.<br />
<br />
Mechanistically, one link between phenology in N availability is that years with warmer springs have greater increases in plant demand for N than any increases in N supplies, leading to declines in N availability.<br />
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One question that arises from this work...if N availability is declining in these forests, how sure are we that we have crossed a planetary boundary for N? Are the world's terrestrial ecosystems really eutrophying?<br />
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Elmore, A. J., D. M. Nelson, and J. M. Craine. 2016. Earlier springs are causing reduced nitrogen availability in North American eastern deciduous forests. Nat Plants <b>2</b>:16133.</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-73691303497364969612016-09-05T07:43:00.001-07:002016-09-05T14:12:04.064-07:00Study on old trees<div dir="ltr" style="text-align: left;" trbidi="on">
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a<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTxbMyO-MVyp4n9qNAuRjLyXPa23CGEF7KM7OQJgJv1yTf1n8ljeZi5iqE3pe8RHxMrL9RmE3qEHT6yxllbpwCjN0gathmv-wuClv9VXpGNDzp8ccYCexcfOmuGw-eonLR8WXUUVAsrKFA/s1600/treering.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="190" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTxbMyO-MVyp4n9qNAuRjLyXPa23CGEF7KM7OQJgJv1yTf1n8ljeZi5iqE3pe8RHxMrL9RmE3qEHT6yxllbpwCjN0gathmv-wuClv9VXpGNDzp8ccYCexcfOmuGw-eonLR8WXUUVAsrKFA/s320/treering.png" width="320" /></a></div>
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The oldest trees in the world are often in the most stressful environments, or so it seems. Yet, there has never been a quantitative attempt to assess tree longevity.<br />
<br />
Di Filippo et al. make a first attempt at this by analyzing tree-ring data for broad-leaved deciduous trees in the Northern Hemisphere.<br />
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Given the massive impact of humans on old-growth forests, any study like this will have caveats, but the data are interesting.<br />
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For example, they report that 300-400 years is a good baseline for tree lifespan (if that concept even applies to trees). They also report a maximum longevity of 600-700 years for deciduous trees in general.<br />
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They also show that the really old trees spent a long time growing slowly. The idea is that mortality rates increase with size, so staying small is a good way to avoid mortal blows like wind throw.<br />
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The relationship they show with maximum age for Fagus was interesting. Essentially, in warm places, the maximum age of Fagus was a lot less than in cold places. They cannot answer whether this is a direct or indirect effect, but they did not find the same relationship for Quercus species.<br />
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The authors don't believe the evidence assembled indicates a biological limitation to longevity in trees, e.g. meristems senesce after a certain amount of time.<br />
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Instead, trees can only roll the dice so many times. And it's hard to roll the dice for more than a few hundred years and not lose.<br />
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Di Filippo, A., N. Pederson, M. Baliva, M. Brunetti, A. Dinella, K. Kitamura, H. D. Knapp, B. Schirone, and G. Piovesan. 2015. The longevity of broadleaf deciduous trees in Northern Hemisphere temperate forests: insights from tree-ring series. Frontiers in Ecology and Evolution <b>3</b>.</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-40949641247597270202016-09-01T13:25:00.000-07:002016-09-01T13:25:01.906-07:00Quantifying cattle diet across broad gradients<div dir="ltr" style="text-align: left;" trbidi="on">
Just a quick note on a new <a href="http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0161511" target="_blank">paper</a> that we just published.<br />
<br />
I've worked before with Texas A&M's GANLab to assess patterns across the US of forage quality for cattle. In that paper, we saw that cattle in cool, wet regions had the highest forage quality, which suggested the warming would reduce forage quality. It was an important paper for understanding how global warming would affect the ability of grassland to sustain grazers.<br />
<br />
Although that work showed geographic patterns of forage quality, we couldn't tell how the species that the cattle consumed might be changing.<br />
<br />
Just this month, we published a new paper where we sequenced the plant DNA in fecal samples of cattle across the US to answer that question.<br />
<br />
Those results are pretty interesting, too.<br />
<br />
In short, cattle in warmer grasslands are relying more on forbs than cattle in cooler grasslands. That suggests warming will shift the diet of cattle, potentially to compensate for lower forage quality. This is pretty similar to what we saw for bison.<br />
<br />
The specific results are important, but the general approach is even more interesting. This is the first time the diet of an herbivore was quantified over such a large spatial scale and with such specificity. For example, we could see the species of grasses shift as one moved south, and the unique diet of cattle in southern Texas (a fair amount of live oak there).<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com1tag:blogger.com,1999:blog-1511829372351341419.post-54725800561627692752016-09-01T05:37:00.002-07:002016-09-01T13:13:56.958-07:00Plant productivity and climate: a back and forth<div dir="ltr" style="text-align: left;" trbidi="on">
The process of science is one we do not talk about much. There are reams of studies on statistical tests for a given data set, and meta-analyses have moved science forward for bringing together different data sets to test an idea.<br />
<br />
But how does science decide the "truth" when there are different assumptions between different studies? What process gets used when words are used in different ways? No statistical test or meta-analysis can bridge that gap.<br />
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Here's an example... <br />
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In August of 2014, Michaletz et al. published a paper that analyzed data on plant production for over a thousand forests across the world. It has long been understood that production is greatest in warm, wet forests (think tropical rain forests) and least in cold, dry forests (think bristlecone pine).When we warm or irrigate forests, they grow more, too. Seems like the role of climate is pretty well settled.<br />
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In their review, the authors found that, indeed, production correlated with temperature and precipitation, but according to them, this was too simple. When viewed through metabolic scaling theory, climate had only an indirect effect on production. The authors asserted that "age and biomass explained most of the variation in production whereas temperature and precipitation explained almost none". In short, warm, wet forests are more productive only because they tend to be older and larger there, not because warm or wet conditions promote growth. By this idea, if you compare two forests of equal size and age, but one forest was in a cold, dry environment, and the other was in a warm, wet environment, there would be no difference in their production.<br />
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The authors have published many excellent papers on metabolic scaling, really developing a line of thought to begin to unify some fractured thought on how plants work. If this result held, it would be a <i>coup de grace</i> in many ways.<br />
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So how did the authors rule out that climate directly affected production?<br />
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The authors calculated a rate of monthly production by dividing production by the length of the growing season. This removed the influence of differences in the length of the growing season to compare forests across the world more equally, essentially asking if forests in warm, wet places grow more each month than ones in cold, dry places. When they did this, they found that "In contrast to results for NPP, average growing season temperature,...mean annual precipitation, and mean growing season precipitation explained little to no variation in global [monthly production]."<br />
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And with that result, the authors move on to test other factors, such as stand age and biomass, independent of climate, finding that "A large proportion of variation in NPP...was explained by just two variables: stand biomass and plant age."<br />
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The Michaletz paper was published in Nature, which is often publishes some of the most important results in our discipline only after intense scrutiny. It seemed like that question was settled. Climate only affects how big forests get and how old they are, it doesn't make a given forest grow any faster per se.<br />
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Well, I guess it can be said that one person's assumption is another person's legerdemain.<br />
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This past January a new paper was published in Global Change Biology. Chu et al. reanalyze the Michaletz data and start with the title "Does climate directly influence NPP globally?" The authors assert that the Michaletz study had "flaws that affected that study’s conclusions". They also "present novel analyses to disentangle the effects of stand variables and climate in determining NPP."<br />
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In short, the authors state that ruling out climate's direct effect by calculating monthly production was erroneous. Growing season length and mean climate are highly correlated. In their view, it was incorrect to rule out the direct effect of climate by dividing production by growing season length and then examining the resultant metric against climate variables.**<br />
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**This debate, in part, is the Knops-Vitousek debate all over again...<br />
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Instead, using different analytic techniques, Chu et al. simultaneously test the roles of growing season length and other climate variables on production.<br />
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Their conclusion? Climate does directly affects production.<br />
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At this point, I'm not writing about this to weigh in on which side is right or more right or right under specific conditions.<br />
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I only pose this question.<br />
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Now what?<br />
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How does our discipline resolve the tension here?<br />
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Were the assumptions by Michaletz right? Are the two camps' differences semantic? Which conclusion should be accepted? Does climate directly affect production or only indirectly?<br />
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At this point, if it was convenient for a scientist's argument for climate not to affect production, they just cite the Michaletz paper. If the contrary held, just cite the Chu paper.<br />
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In the legal world, when different circuit courts come to different conclusions, this can lead to "forum shopping" where a plaintiff can simply go to the circuit that is most favorable to their case. That shouldn't be if the goal is to have one set of laws to govern a nation.<br />
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Like the legal world, it seems like being able to cite either one of two opposing ideas is not sustainable for science either.<br />
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It is interesting to note that in the US federal court system, two contrary ideas existing at the same time would be the equivalent of a "circuit split" where two circuit courts come to two different conclusions about how to interpret the law. This tension would often be resolved at the next higher court, the Supreme Court. And the decision of the Supreme Court would resolve the differences of opinion.<br />
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All I note here is that science doesn't have that. We have no formalized process for resolving a split. Split conclusions can theoretically last indefinitely. And scientists can cite whichever side they believe in more or find most convenient.<br />
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I think that is fascinating.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-40469842354473991702016-05-31T09:34:00.003-07:002016-05-31T09:34:55.079-07:00CUDOS in science<div dir="ltr" style="text-align: left;" trbidi="on">
Here's something I hadn't seen before.<br />
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I've thought that it's interesting that there isn't a Hippocratic oath for scientists (scientists didn't exist in the days of Hippocrates). It turns out there are norms of scientific society.<br />
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I read about this in Wootton's book, but hadn't ever heard about them. Apparently, these norms were described in 1942 by Merton in his description of the sociology of science.<br />
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The norms of science go by the acronym of CUDOS:<br />
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Communalism<br />
Universality<br />
Disinterestedness<br />
Organized Skepticism<br />
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The wikipedia<a href="https://en.wikipedia.org/wiki/Mertonian_norms" target="_blank"> page</a> describes them fairly well. As does <a href="http://scienceblogs.com/ethicsandscience/2008/01/29/basic-concepts-the-norms-of-sc/" target="_blank">this</a> blog post.<br />
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In short, these norms describe the ideals of science. The results should be open to everyone. Ideas (and opportunities) are evaluated blind to the characteristics of the individual. Scientists report results independent of the consequences of the outcome. All ideas are subject to scrutiny.<br />
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Wootton's analogy between science and the law in these norms is pretty interesting. The legal profession holds similar ideas**. For example, evidence should never be withheld to opposing parties, which is similar to communalism.<br />
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**Though Wootton does not delve into it, the adversarial nature of legal actions is not replicated generally in science even though there is still a tradition of a "defense" of theses or dissertations.<br />
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Most scientists believe they deserve more kudos for the work they do. Apparently CUDOS are built into science.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-78689896700627339912016-05-30T06:48:00.001-07:002016-05-30T09:00:54.037-07:00Book review: The Invention of Science<div dir="ltr" style="text-align: left;" trbidi="on">
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Currently, science is undergoing a convulsion. The very way that science operates is changing. It's a change that appears to be unprecedented in modern times.<br />
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For the first time, science is being forced to deal with bias. Questions of reproducibility have become a crisis. The review process is under renewed scrutiny. The nature and openness of publishing is being assaulted legally and illegally. Everyone from editors to scientists to funding agencies are being forced to reckon with consequences of retractions at an unprecedented rate.<br />
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The Invention of Science, a new book by David Wootton addresses none of these modern ills. But, sometimes, modern crises are an important time to revisit our history. The Invention of Science is an unparalleled examination of the long, slow (and sometimes convulsive birth of science).<br />
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Note, this thing is a wrist-breaker. 600 pages before you get to the endnotes. That's a good thing. Understanding the history of a topic is not something to do in Cliff Notes form. You need a comfortable chair and a pen for the margins to absorb the lessons.<br />
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The thesis of this book is that science (as we currently define it) once did not exist. Knowledge was generated through means other than science. In order for science to be invented, a number of conventions had to be created, too. We needed a new vocabulary. People needed to act and interact differently. The conceptual framework that we recognize as scientific had to not only be assembled, it had to displace previous frameworks.<br />
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A book of this scope is hard to summarize with any justice.<br />
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Here is the first sentence of the book. "Modern science was invented between 1572, when Tyco Brahe saw a nova...and 1704, when Newton published his Opticks...." Science took a bit over 100 years to invent. It's only a bit over 300 years old.<br />
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Over a hundred years to invent something that seems so simple that we do it every day? Why so long?<br />
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The book answers why it wasn't as easy as people might think.<br />
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The middle chapters are the ones I've spent the most time on. These are their titles: Facts, Experiments, Laws, Hypotheses/Theories, Evidence and Judgment.<br />
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These chapters lay out the history of the main elements of the modern scientific approach.<br />
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I'm going to have to read these chapters one or two more times before I can crystallize them, but their scopes are the raw material for anyone trying to understand if not shape modern science.<br />
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For example, the word "fact" (with its modern meaning) did not exist in any language. The Greeks and Romans had no word for "fact". The concept of a "fact" did not exist. And facts are not the same as the truth.<br />
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Let me quote here.<br />
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"What is a fact? It is a sort of trump card in an intellectual game...Facts are a linguistic device which ensures that experience always trumps authority and reason."<br />
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Facts are a linguistic device? Since when is the truth a device? Facts must be something other than what we recognize them to be.<br />
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The experiments chapter describes a number of the early experiments. Here's a quote: "This is the first 'proper' experiment, in that it involves a carefully designed procedure, verification (the onlookers are thereto ensure this really is a reliable account), repetition and independent replication, followed rapidly by dissemination."<br />
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When did this happen? 1648 when a brother-in-law of Pascal climbed a mountain with a barometer.<br />
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But note his definition of an experiment. It involves verification. Repetition. Replication. Followed by dissemination. Our modern crisis comes about because of a lack of verification, repetition, and replication (or reproducibility as we refer to it). Only touched on, the author highlights the motto of an Italian society. The motto was: <i>provando i reprovando. </i>Test and retest.<i> </i>Hard to imagine that as any modern society's motto.<br />
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The evidence and judgement chapter has interesting nuggets, too. In part, it examines the legal frameworks of different European countries, which affects how scientists came to prove things. Drawing techniques for a judicial system that relies on judges vs. juries leads to different ways of conducting science. That thumbprint is still with us today. Like any organism that has evolved, modern science still bears the marks of its history and past forms.<br />
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Here's a quick example he provides:<br />
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"A friend of mine was once in hospital in Paris. The doctors told him that they had an hypothesis regarding the nature of his illness which they intended to prove, where in England they would have told him that he had certain symptoms which suggested a diagnosis which they would run tests to confirm."<br />
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This is a subtle difference, but one whose distinctions should be obvious to anyone practicing science. Different paths do not always lead to the same destination, so choose the path wisely.<br />
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Right now, our science is in the middle of a transformation. The question is whether a new layer will simply be added or whether parts will be torn down and rebuilt. Anyone who offers an opinion on how science should be reformulated is wise to know it's history. This is a good book to start on that.<br />
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But buy it in hardcover so you can write in the margins.<br />
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The only drawback is that the margins are not wide enough.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-25832032166259920172016-05-24T07:28:00.002-07:002016-05-24T07:31:21.179-07:00Why we cite papers<div dir="ltr" style="text-align: left;" trbidi="on">
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Scholarly works are set apart from other types of writings by the use of citations. An essay on natural history might cover a scientific topic, but it is just an essay until it contains citations. Scientific papers are not scientific without citations.***<br />
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***This blog post is certainly not scientific...no citations here. OK, maybe one.<br />
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Most scientists do not question the need for citations nor the role they play in the paper itself. When we do not have a common understanding of the role of citation, we have trouble determining when citations are improper and what to do when what we think to be true shifts.<br />
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Most of us think that the big debates about citations is formatting. Do we number our citations or list the authors and dates each time? There are deeper issues that that. They have nothing to do with formatting.<br />
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The first time I really thought about citations is I remember that Stephen Jay Gould once got into trouble for citing a paper in his thesis that was not contained in his school's library.* His advisors questioned the link between the statement he was making and the original citation. They were not refuting that his statement wasn't true. Only that he didn't know it was true, because he could not have examined the original source. Another author's judgment on the assessment of truth was insufficient. That's how rigorous citation can be.<br />
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*This is a place where a citation is really needed. But, I can't remember which of his books I read this in. Structure of Evolutionary Theory? Panda's Thumb? I'm fuzzy on the details here, but whether it happened or not, it could have happened, which is all that is necessary here.<br />
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When I think about how I use citations, I feel there are two types of citations that I use.<br />
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The first I call vertical citations.<br />
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Vertical citations are the links between what has been found to be true in the past and a statement we currently would like to make to establish the truth.<br />
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For example, here is the first sentence of a paper that I just submitted to a journal:<br />
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<i>There are approximately 1 billion cattle in the world with cattle populations steadily increasing over the past few decades (Estell et al. 2014).</i><br />
<i><br /></i>
This is a vertical citation. I am going back into the literature to provide evidence of the truth of a statement. I personally have not counted how many cattle there are in the world. Nor have I determined whether cattle populations are increasing or decreasing over the past few decades. So, instead of going out and counting cattle, I cite a paper that has established this to be true or has cited the papers that have established this to be true. The paper I chose to cite is Estell et al. 2014***<br />
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***<i>et al.</i> stands for <i>et alia</i> (in the neuter form), which means <i>and others</i> in Latin. <i>Et alia</i> is almost always abbreviated <i>et al., </i>which is funny because we really aren't saving that many characters. Really just one. I think, in part, it gets abbreviated because the actual Latin phrase depends on whether the "others" are male, female, or both. Easier to write "et al." than determine whether <i>et alii, et aliae, et alia </i>is more appropriate.<br />
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So, when are vertical citations necessary?<br />
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Any time we make a statement in a scientific paper about what we consider to be true outside of the personal experience we are describing, a citation is necessary.<br />
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<i>Any time.</i><br />
<i><br /></i>
If we want to say that there are a billion cattle in the world, we need a citation. If we want to say that atmospheric CO2 concentrations are increasing, we need a citation. The sky is blue? Citation. Gravity exists? Citation.<br />
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Now, if we want to say that we performed a certain procedure in an experiment, we do not need a citation. We hold it true that we might have measured something at a certain temperature, but there is no citation for this since it comes from our experience, not the literature.<br />
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Vertical citations go back into the literature to provide justification for the truth of statements we are making. Think of the Newton's phrase, if I have seen further, it is by standing on the shoulders of giants...When we cite a previous work, we are placing our foot on the shoulder of a giant that has come before us. We are reaching down vertically to build something taller.<br />
<br />
As opposed to vertical citations, there are also horizontal citations. Like vertical citations, they reach down into the literature to establish the truth, but the purpose is different.<br />
<br />
Horizontal citations are primarily for context. In the introduction, horizontal citations are typically used to identify intellectual tension. Study A found this. Study B found that. This and that cannot be both true under our current intellectual framework. We cite these papers to show what other researchers have found to justify our work.<br />
<br />
In the discussion, horizontal citations are used in a similar manner, but it is not to establish that there is intellectual tension, but to see if there is intellectual tension. Study A found this. Study B found that. We found this, too. Therefore, it seems like this is more likely to be true than that.<br />
<br />
With horizontal citations, we are not citing other giants, but instead other dwarfs (or other Isaac Newtons).**<br />
<br />
**the original metaphor was "dwarfs standing on the shoulders of giants". Citation <a href="https://en.wikipedia.org/wiki/Standing_on_the_shoulders_of_giants" target="_blank">here</a>. We think of Newton as a giant now, but originally he would have been a dwarf in the metaphor.<br />
<br />
So, when I think about how I reference the literature, it is generally vertically or horizontally. I am either reaching down to stand taller, or reaching across to build linkages.<br />
<br />
That's probably a long enough post for now. Down the line, I should cover the consequences of failing to cite the literature correctly and the consequences of determining that the findings of a published paper was not true: what happens when a giant tumbles?<br />
<br />
***<br />
Mostly as a note to myself, comparing legal citations and scientific citations is also instructive. The law only cares about what was legally true at the time the law was being examined. Science cares about what is known to be true at the time the scientific fact was established and after. Hence, changes in the law and changes in scientific understanding have much different consequences.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-19818807176142871112016-03-09T10:38:00.001-08:002016-03-09T10:38:16.014-08:00Declines in tree nutrient concentration over past 25 years<div dir="ltr" style="text-align: left;" trbidi="on">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8qM44tNl29Arf7qlAPJ3sKHRs7-xfTkyMmmhwpCwgNn0cjdJTFV2w0aAEnM9dbQtmcwmMBSXRM8T0NneqcP7UQYLnlxcXDd9z6W_JiAbgKpGP2Unm_BjBOVcrkIj5FjrVTlyoQ_JQOdV6/s1600/map.png" imageanchor="1" style="text-align: center;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj8qM44tNl29Arf7qlAPJ3sKHRs7-xfTkyMmmhwpCwgNn0cjdJTFV2w0aAEnM9dbQtmcwmMBSXRM8T0NneqcP7UQYLnlxcXDd9z6W_JiAbgKpGP2Unm_BjBOVcrkIj5FjrVTlyoQ_JQOdV6/s320/map.png" width="342" /></a></div>
<br />
I've been trying to catch up on journals lately. Apparently, I hadn't read anything from Global Change Biology over the past 2 years. Must have been distracted. No time like the present...<br />
<br />
Here's one that struck me as amazing.<br />
<br />
Researchers in Europe resampled forest leaves from 1992 - 2009 across a large number of plots in Europe. At each site for a subset of species they assessed nutrient concentrations and leaf mass--a pretty simple and standard measurement. Doing this allowed them to examine the trajectory of nutrient concentrations (and contents). Nutrient concentrations in leaves are critical to determining tree productivity as well as interactions with herbivores, so knowing whether concentrations are going up or down is critical to modeling the future productivity of these forests.<br />
<br />
Here's the simplified result: almost all nutrient concentrations were declining. 20 nutrients had declining concentrations. 2 were increasing.<br />
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Here's an example of the pattern for beech. white bars are concentrations, grey contents.<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuE7Sg3m-XkaU1OmgukooESEVEbi2m9mTp4kt8RMn96dCAQnqUzOssZ-Xmxp6UhTso_BFxvifX8eW43VPhA_ftmS_FAMvN_UfJdlsLOkHjTX4xBmQP5eZR81Vn5frlQBJApZS1cL12NGB4/s1600/Fagus.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="207" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiuE7Sg3m-XkaU1OmgukooESEVEbi2m9mTp4kt8RMn96dCAQnqUzOssZ-Xmxp6UhTso_BFxvifX8eW43VPhA_ftmS_FAMvN_UfJdlsLOkHjTX4xBmQP5eZR81Vn5frlQBJApZS1cL12NGB4/s320/Fagus.png" width="320" /></a></div>
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The authors focus on P nutrition the most, emphasizing the role of N deposition in promoting P limitation. Yet, even N concentrations were declining. These declines must be more than just N deposition causing imbalances, especially since N deposition has been declining over the time period. </div>
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The authors suggest elevated atmospheric CO2 might also be playing a role, as well as droughts and warming, but this paper mostly describes the pattern, which is fine.</div>
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The big question is: What is causing this massive, continental decline in nutrient concentrations?</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-47429118408111624142016-03-07T08:05:00.001-08:002016-03-07T08:05:27.803-08:00ASA statement on P-values<div dir="ltr" style="text-align: left;" trbidi="on">
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<br />
<br />
The American Statistical Associations statement on the use of p-values can be found <a href="http://amstat.tandfonline.com/doi/pdf/10.1080/00031305.2016.1154108" target="_blank">here</a>.<br />
<br />
The short list is:<br />
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<li style="margin: 0px 0px 5px; padding: 0px;"><em style="margin: 0px; padding: 0px;">P-values can indicate how incompatible the data are with a specified statistical model. </em></li>
<li style="margin: 0px 0px 5px; padding: 0px;"><em style="margin: 0px; padding: 0px;">P-values do not measure the probability that the studied hypothesis is true, or the probability that the data were produced by random chance alone. </em></li>
<li style="margin: 0px 0px 5px; padding: 0px;"><em style="margin: 0px; padding: 0px;">Scientific conclusions and business or policy decisions should not be based only on whether a p-value passes a specific threshold. </em></li>
<li style="margin: 0px 0px 5px; padding: 0px;"><em style="margin: 0px; padding: 0px;">Proper inference requires full reporting and transparency. </em></li>
<li style="margin: 0px 0px 5px; padding: 0px;"><em style="margin: 0px; padding: 0px;">A p-value, or statistical significance, does not measure the size of an effect or the importance of a result. </em></li>
<li style="margin: 0px 0px 5px; padding: 0px;"><em style="margin: 0px; padding: 0px;">By itself, a p-value does not provide a good measure of evidence regarding a model or hypothesis. </em></li>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">My personal take is that there are a few corrections in how p-values are used. </span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">1) p< 0.05 is arbitrary. report the exact p-values and think of them as a continuum. Don't think a paper should be accepted just because p < 0.05. Don't reject a paper just because p > 0.05. </span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;"><br /></span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">2) the p-value reported needs to be contextualized with the number of comparisons made. this is where p-hacking shows up. if you do 20 independent analyses, 1 is likely to have p-value < 0.05. You need to state that you did an additional 19 analyses if you are reporting the 20th. if you went and added more data or looked more carefully for outliers because a p-value wasn't low enough, this needs to be reported.</span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;"><br /></span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">3) p-values and effect sizes must be reported together. an independent assessment of whether the measured effect is biologically relevant is needed. </span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;"><br /></span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">#2 on the list is the hardest to comprehend because it involves logical assumptions of the test. </span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;"><br /></span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">The manuscript's explanation of this is:</span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;"><br /></span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">Researchers often wish to turn a p-value into a statement about the truth of a null hypothesis, or about the probability that random chance produced the observed data. The p-value is neither. It is a statement about data in relation to a specified hypothetical explanation, and is not a statement about the explanation itself.</span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;"><br /></span></div>
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<span style="color: #222222; font-family: Lucida Grande, Lucida Sans Unicode, Helvetica, Arial, sans-serif; font-size: x-small;">At RetractionWatch, the author explains it this way:</span></div>
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<strong style="margin: 0px; padding: 0px;">Retraction Watch: Some of the principles seem straightforward, but I was curious about #2 – I often hear people describe the purpose of a p value as a way to estimate the probability the data were produced by random chance alone. Why is that a false belief? </strong></div>
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Ron Wasserstein: Let’s think about what that statement would mean for a simplistic example. Suppose a new treatment for a serious disease is alleged to work better than the current treatment. We test the claim by matching 5 pairs of similarly ill patients and randomly assigning one to the current and one to the new treatment in each pair. The null hypothesis is that the new treatment and the old each have a 50-50 chance of producing the better outcome for any pair. If that’s true, the probability the new treatment will win for all five pairs is (½)<sup style="margin: 0px; padding: 0px;">5</sup> = 1/32, or about 0.03. If the data show that the new treatment does produce a better outcome for all 5 pairs, the p-value is 0.03. It represents the probability of that result, <em style="margin: 0px; padding: 0px;">under the assumption that the new and old treatments are equally likely to win.</em> It is <u style="margin: 0px; padding: 0px;">not</u> the probability the new treatment and the old treatment are equally likely to win.</div>
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This is perhaps subtle, but it is not quibbling. It is a most basic logical fallacy to conclude something is true that you had to assume to be true in order to reach that conclusion. If you fall for that fallacy, then you will conclude there is only a 3% chance that the treatments are equally likely to produce the better outcome, and assign a 97% chance that the new treatment is better. You will have committed, as Vizzini says in “The Princess Bride,” a classic (and serious) blunder.</div>
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**</div>
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I'm still looking for the right wording on this one, but it seems like the probability that the null hypothesis is true given the effect size observed. </div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-3914950259658575982016-03-05T19:27:00.002-08:002016-03-06T09:55:06.714-08:00Biogeochemical Planetary Boundary: Beyond the zone of uncertainty? (Part II)<div dir="ltr" style="text-align: left;" trbidi="on">
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<br />
I think of scientists as having two jobs.<br />
<br />
One is to create intellectual tension.<br />
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The other is to resolve it.<br />
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Creating intellectual tension is generating hypotheses. Hypotheses that we do not know whether they are true or false represents intellectual tension. Competing hypotheses about how the world works are also intellectual tension. We do not know which is true. This is the tension.<br />
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Resolving intellectual tension can sometimes occur by identifying logical flaws in one hypothesis. Generally, intellectual tension is resolved by collecting data. It is a fair question about whether a hypothesis can ever be proven or disproven and therefore whether intellectual tension is ever fully resolved, but the process of science works to reduce intellectual by favoring hypotheses.<br />
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In the previous post, I identified some important intellectual tension in the scientific world.<br />
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There is the hypothesis that the planet has exceeded a biogeochemical "planetary boundary". Too much nitrogen is being fixed and entering ecosystems. This is the hypothesis.<br />
<br />
Yet, it is unclear whether this is causing planetary-scale eutrophication of terrestrial ecosystems or aquatic ecosystems.<br />
<br />
On the one hand, we have a hypothesis where the world is awash in nitrogen. We fix more nitrogen than ever and apply it to ecosystems on a massive scale. As a result, nitrogen is leaking out into waterways creating dead zones in the oceans. Nitrogen is also entering the atmosphere and raining down on even the most remote ecosystems on earth. As a result, terrestrial ecosystems are becoming eutrophied. Species adapted to low nitrogen availability are being crowded out by faster growing plants. Biodiversity is plummeting. Productivity is increasing unsustainably. With all this extra nitrogen, we have exceeded a biogeochemical planetary boundary. Civilization as we know it is threatened.<br />
<br />
Yet, the intellectual tension on this hypothesis actually takes the form of a competing hypothesis. It is possible that not only have we not exceeded a planetary boundary for nitrogen, but ecosystems might be becoming more nitrogen limited over time. As temperatures warm and atmospheric CO2 builds up, this might stimulate the demand for N more than it is being supplied. Plants and microbes become more limited by N. Plant N concentrations decline. Photosynthesis declines. Plants that compete well for N become more dominant. Less N leaks out of ecosystems into streams. Productivity becomes more and more constrained by the lack of nitrogen. Vegetation sequesters less and less carbon than they could be, all because there is not enough nitrogen. As a result, more CO2 accumulates in the atmosphere than could be if forests had more nitrogen. Climates warm even faster. Civilization as we know it is threatened.<br />
<br />
Intellectual tension like this could not be as stark.<br />
<br />
If you reduce the world to one pixel, there is either too much nitrogen. Or there is too little.<br />
<br />
Resolving this tension requires data. On the one hand, we know that N is being fixed in ever greater amounts. On the other hand, CO2 continues to increase which shifts demand for N even higher. Back again, N is raining down on ecosystems still at an elevated rate. Yet, the NO3- concentrations of water in streams is so low, stream water is approaching the NO3- concentrations of distilled water.<br />
<br />
The only way to resolve this tension is to collect data on N availability.<br />
<br />
Yet we need long-term measurements of N availability to know for sure whether N is becoming more or less limiting.<br />
<br />
We don't have these.<br />
<br />
We could use the species composition of plant communities in conjunction with indices of what plants represent low or high N availability, but again we have not invested in long-term monitoring of our plant communities.<br />
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The tension of whether the world is becoming more eutrophic or more oligotrophic has existed for a long time now.<br />
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It probably is not a bad thing to think that civilization is threatened. But we should at least know whether it is because there is too much nitrogen or too little before we try to fix it. Or else our remedies might exacerbate the situation.<br />
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Without the right data, we cannot resolve this tension. That means we start monitoring key indices like N availability and species composition now and try to answer the question in 10 years.<br />
<br />
Or we find a different dataset that allows us to reconstruct N availability on broad spatial scales far enough back in time to discern the trajectory of N availability.<br />
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Do we have the data to resolve this tension?<br />
<br />
I think we might...<br />
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Let's see what reviewers say.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-30766530853972120022016-03-05T06:57:00.000-08:002016-03-05T06:57:01.833-08:00Biogeochemical Planetary Boundary: Beyond the zone of uncertainty? (Part I)<div dir="ltr" style="text-align: left;" trbidi="on">
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The cycling of nitrogen in a terrestrial ecosystem determines its primary (and secondary) productivity, its diversity, and how much (and how) nitrogen is lost to the atmosphere and waters. In general, plant productivity is limited by the availability of nitrogen. Add a little more nitrogen, and not much changes. Productivity increases, but qualitatively, the ecosystem functions the same. Add a little more, and the ecosystem changes quantitatively, but not qualitatively. Productivity increases. N concentrations increase a bit, but it still is qualitatively similar to the unfertilized ecosystem.<br />
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Keep fertilizing the ecosystem with N, and eventually the ecosystem reaches a threshold. Not only does productivity increase, but a lot of other things change. Suddenly, plant N concentrations increase a lot. The plant community shifts towards plants that thrive under higher N. They have high N concentrations, they use alkaloids instead of tannins to defend themselves, their leaves are built to capture as much light as possible, rather than avoid capturing too much light. In the soil, the soil microbial community shifts and the richness of N causes N to start leaving the soils in ways it hadn't before. More NO3- comes out in the waters. More gaseous N is lost to the atmosphere.<br />
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This threshold has been repeated experimentally in individual ecosystems throughout the world. And we've seen it when we non-experimentally add a lot of N to pastures or croplands or even forests.<br />
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What we see at the plot level or even at the level of the stand or region could potentially have analogs at the planetary level. As humans fix more and more N and more and more N is added to the ecosystems, could the whole planet flip states and autocatalyze from a oligotrophic world to a eutrophic world? Could N limitation become the exception, rather than the rule.<br />
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In 2009, Rockstrom et al. published their summary of the state of the earth in respect to Planetary Boundaries (see my 2012 post on the issue <a href="http://wildplantspost.blogspot.com/search?q=planetary" target="_blank">here</a>). These planetary boundaries are planet-wide environmental boundaries or ‘tipping points’. Exceed these thresholds, and humanity is at risk.<br />
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That paper was updated last year by Steffen et al. As before, the authors state that for climate change, we have entered a "zone of uncertainty" with "increasing risk". Despite all the warming, the sea level rise, the collapsing ice sheets, the potential for a shutdown of the thermohaline circulation, losses of coral reefs, thawing of permafrost, and climatic reorganization underway, their summary is that humanity is still in a safe operating space climatically.<br />
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In contrast, for the global nitrogen cycle, the status is the same as in 2009. We are apparently beyond the zone of uncertainty, and humanity is currently at high risk of exceeding a planetary threshold.<br />
<br />
That sounds pretty dire.<br />
<br />
But are we?<br />
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The basis for this assessment is from a recent paper by de Vries et al. 2013.<br />
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Reading the paper, apparently, for the planet to have exceeded a planetary boundary for N requires that one of the following (according to the authors) has exceeded safe operating space:<br />
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1) eutrophication of terrestrial ecosystems<br />
2) eutrophication of marine ecosystems<br />
3) acidification of soils and fresh waters<br />
4) NOx, a greenhouse gas<br />
5) ozone formation<br />
6) groundwater contamination<br />
7) stratospheric ozone depletion<br />
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There is really no evidence of too much tropospheric ozone or too much groundwater contamination for humans to safely inhabit planet. Soils do not appear to be becoming acidified due to N deposition and fertilization globally. NOx levels are not deathly high. Stratospheric ozone levels are still recovering from CFC phase-outs.<br />
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Therefore, if humanity has exceeded a biogeochemical planetary boundary, then there must be evidence of planetary-scale eutrophication of terrestrial or marine ecosystems.<br />
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In a future post, I'll examine the intellectual tension about this idea...<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-54799490888828686732015-12-07T09:24:00.000-08:002015-12-07T09:24:03.484-08:00Highlights from Nature Climate Change in 2015<div dir="ltr" style="text-align: left;" trbidi="on">
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Catching up on a year's worth of articles from Nature Climate Change. It's like binge-watching your favorite program. There are a lot of great "episodes", but here are some that stood out for me:<br />
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<b>Central US experience a greater frequency of floods most likely due to a greater frequency of heavy rainfall events and rain-on-snow events.</b><br />
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<i>Mallakpour, I. and G. Villarini. 2015. The changing nature of flooding across the central United States. Nature Climate Change 5:250-254.</i><br />
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<b>Growing season length is increasing almost everywhere.</b></div>
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<i>Buitenwerf, R., L. Rose, and S. I. Higgins. 2015. Three decades of multi-dimensional change in global leaf phenology. Nature Climate Change 5:364-368.</i></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidbWthTLDzfQKAIu5scAWDGpsQSzDnxcDF89OeOGo69wt3ED45pIYCwD_-TO4bk-DgpxcDGsplyg6UOyh823V9qHj6wO6U0_2cajiam9EpdpiiLQcJ0v-ILaIvcDjtvceFHXvKda_cF3gA/s1600/Untitled+2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEidbWthTLDzfQKAIu5scAWDGpsQSzDnxcDF89OeOGo69wt3ED45pIYCwD_-TO4bk-DgpxcDGsplyg6UOyh823V9qHj6wO6U0_2cajiam9EpdpiiLQcJ0v-ILaIvcDjtvceFHXvKda_cF3gA/s320/Untitled+2.png" width="318" /></a></div>
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<b>Increasing CO2 decreases plant N:P, while warming and water increase it. </b></div>
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<i>Yuan, Z. Y. and H. Y. H. Chen. 2015. Decoupling of nitrogen and phosphorus in terrestrial plants associated with global changes. Nature Climate Change 5:465-469.</i></div>
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<b>Temperature is more tightly coupled with greenhouse gases than insolation. </b>"This confirms the existence of a positive feedback operating in climate change whereby warming itself may amplify a rise in GHG concentrations." Note the new analytical techniques here to evaluate complex systems.</div>
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<i>van Nes, E. H., M. Scheffer, V. Brovkin, T. M. Lenton, H. Ye, E. Deyle, and G. Sugihara. 2015. Causal feedbacks in climate change. Nature Climate Change 5:445-448.</i></div>
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<b>Microbial decomposition generates heat that thaws permafrost faster.</b></div>
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<i>Hollesen, J., H. Matthiesen, A. B. Møller, and B. Elberling. 2015. Permafrost thawing in organic Arctic soils accelerated by ground heat production. Nature Climate Change 5:574-578.</i></div>
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<b>European forests are more efficient with their water use, but l</b><b>onger growing season, warmer temperatures, and increased leaf area lead to</b><b> transpiring more water. </b><i>Frank, D. C., B. Poulter, M. Saurer, J. Esper, C. Huntingford, G. Helle, K. Treydte, N. E. Zimmermann, G. H. Schleser, A. Ahlström, et al. 2015. Water-use efficiency and transpiration across European forests during the Anthropocene. Nature Climate Change 5:579-583.</i></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiz9SSyv85e1LYOwMkTqbGHFCkhZ-5EzVs9FwhyphenhyphenB9GzjPp4F-CFpQfNDiIeNe4HEmVs8HnHkGHEnlCfbnUfZn-fEvtLe7AYD2HhZZQ5d6JAzgCqVDHqibko0tkITxLMW5xBokwe1RZNw7uU/s1600/Untitled+7.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="124" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiz9SSyv85e1LYOwMkTqbGHFCkhZ-5EzVs9FwhyphenhyphenB9GzjPp4F-CFpQfNDiIeNe4HEmVs8HnHkGHEnlCfbnUfZn-fEvtLe7AYD2HhZZQ5d6JAzgCqVDHqibko0tkITxLMW5xBokwe1RZNw7uU/s320/Untitled+7.png" width="320" /></a></div>
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<b>Tall, leafy trees are most likely to get nailed by drought in the future</b>. McDowell, N. G. and C. D. Allen. 2015. Darcy's law predicts widespread forest mortality under climate warming. Nature Climate Change 5:669-672.</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com1tag:blogger.com,1999:blog-1511829372351341419.post-8341279305956161172015-12-01T04:08:00.002-08:002015-12-01T07:09:50.653-08:00Ecological and environmental funding priorities<div dir="ltr" style="text-align: left;" trbidi="on">
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The above graph does not display patterns of ecological priorities. It's about funding at NIH (recently published in <i><a href="http://www.sciencemag.org/content/350/6263/900.full.pdf" target="_blank">Science</a></i>). </div>
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The y-axis is millions of dollars spent in 2010. The x-axis is <a href="https://en.wikipedia.org/wiki/Disability-adjusted_life_year" target="_blank">disability adjusted life years</a>--the cumulative number of years lost to ill-health, disability, or death. (DALY).</div>
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The relationship is a good one, in statistical terms. Diseases with a low burden are funded less than diseases with a high burden. There are residuals, too. Diseases with a global presence (malaria, AIDS) appear to be funded at a greater rate than their US DALY. Lung cancer, migraines, and suicide, which are not as trendy (or likely thought to be the fault of the stricken) are funded less.</div>
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My question today is why don't we have a graph like this for ecology/environmental science? </div>
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The first question would be what do we put on the x-axis? Do we have an ecological equivalent of DALY? Probably not. That right there is one of the biggest failings on how to prioritize. We don't have a standard to compare for prioritizing**. </div>
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**If anything, we make expert lists like "Top 50 Priorities in [insert discipline]"</div>
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That means ecological funding graph is likely to be a bar chart. Still, I'd like to see that.**</div>
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**I guess another way to do it would be to put it in terms of societal benefit. Ecological goods and services. X-axis would be dollars, then.</div>
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Then what are the categories? </div>
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We can't do it by standard categories like carbon cycling, population dynamics, community composition. These do not necessarily speak to societal challenges. </div>
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You need the equivalent of diseases. So, disease would be one category. Climate change, elevated CO2, nitrogen deposition, drought, biodiversity loss, water quality...</div>
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Then I guess you'd need to categorize funding for a given year from NSF and maybe EPA, USGS...</div>
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That graph wouldn't be as good as the DALY-funding graph, but I'd still like to see it. </div>
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The reason is that my suspicion is that funding priorities are all out of whack relative to societal need. If we could have a bivariate plot, it'd be messier than the DALY graph.</div>
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My other suspicion is that the y-axis would be a lot smaller. Many of the most important ecological/environmental issues of our time wouldn't even hit the psoriasis level of funding, no less autism.**</div>
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**Heck, all of NSF Directorate for Biological Science ~$700M is about what NIH spends on depression.</div>
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If we could put together this graph, that should help arguments on how ecology/environmental science is funded. </div>
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Because my last suspicion is that we're underfunded. We wish we were funded like peptic ulcers, or even migraines relative to the importance of the issues.** </div>
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**I think down the line there is going to be a grand bargain where Congress will want NSF to justify their funding based on societal need. It might be a bargain worth taking if the ecological/environmental science gets funded at similar proportions to societal need as disease.</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-54306826515048569652015-11-15T10:09:00.001-08:002015-11-15T10:09:29.584-08:00Global patterns of rumen microbes<div dir="ltr" style="text-align: left;" trbidi="on">
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Ruminants are walking fermentation vats. They ingest plants and let a host of microbes metabolize the plant material. Ruminants then absorb some of the microbial byproducts and also digest the microbes.<br />
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It's been known for awhile that these microbes include bacteria, archaea, and ciliates. The identity of the microbes is still being determined, no less their ubiquity.<br />
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Henderson et al. took a huge step towards understanding these patterns. They examined over 700 rumen samples from 32 ruminant species. Samples were collected globally.*<br />
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*How this paper ended up in Scientific Reports and not Nature is beyond me. My guess is bias against livestock.<br />
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Among their results, the authors show that there is a core set of bacteria and archaea (but not protozoa) in ruminants that they rely on for digestion. The also show clear differences between animals fed browse and concentrate.<br />
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This paper is going to take a while to digest (pun intended), but there are some pretty amazing patterns.<br />
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**<span style="font-family: 'Times New Roman'; font-size: 12px; text-indent: -36px;">Henderson, G., F. Cox, S. Ganesh, A. Jonker, W. Young, C. Global Rumen Census, and P. H. Janssen. 2015. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep </span><b style="font-family: 'Times New Roman'; font-size: 12px; text-indent: -36px;">5</b><span style="font-family: 'Times New Roman'; font-size: 12px; text-indent: -36px;">:14567.</span><br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-53766286302366731662015-10-08T05:16:00.000-07:002015-10-08T05:20:19.327-07:00Up in smoke<div dir="ltr" style="text-align: left;" trbidi="on">
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Gene Towne and I were working on revising a paper reviewing what is known about the effects of differences in the timing of burning on grasslands and grazers.<br />
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We had written "burning in late-April after the green vegetation has emerged, exacerbates smoke production and accompanying air pollution, which is at the forefront of the burning controversy."<br />
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This sentence seemed obvious to us. If you burn green biomass, it's smoky as heck. Still, the sentence did not have a citation. Rightly so, it should have.<br />
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I spent some time going through papers to see if what we had observed empirically had basis in the literature.<br />
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After a few hours reading papers, it seems that the statement wasn't wrong, but I did make a mistake in not reading these papers sooner. Probably the best paper was Andrae and Merlet from 2001, which is frustrating because I apparently could have learned all of this 15 years ago.<br />
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1) Smoke is complex. It contains O3, CO, water vapor, NOx, HCN (!), SO2, CH4, C2H2, xylene, benzene, etc. as well as particulates of certain sizes.<br />
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**Technical point: smoke researchers talk a lot about emission ratios (amount of a product produced in a fire relative to a standard like CO2) and emission factors (same, but relative to amount of biomass burned). They also talk about CE, combustion efficiency, with is an emission ratio of all the products besides CO2 relative to CO2 produced in a fire.<br />
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2) Fire is complex. It has stages: ignition, flaming + glowing + pyrolysis, glowing + pyrolysis (a.k.a. smoldering), glowing, and extinction. Each has different chemistry and emissions.<br />
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3) Flaming involves relatively complete oxygenation (burning) of products. Smoldering does not. Smoldering (burning without flame) is more likely to produce some products like CO and NH3 than flaming, which is more likely to produce products like CO2 and NOx.<br />
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4) It's interesting to read how stuff catches fire. When biomass starts to burn, the first step is the drying/distillation step. This releases water and volatiles. Then comes pyrolysis with "thermal cracking" of the molecules which produces char, tar, and volatiles. Here, stuff is breaking up, but not burning. As the biomass gets hotter, the tar and gas begin to oxidize, which produces the flame.<br />
occurs. Once the volatiles have burned off, then the biomass begins to smolder (glowing fire) and many of the incomplete oxidation products are produced.<br />
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For us, we're likely to rewrite the sentence a bit to acknowledge the complexity of fire and smoke.<br />
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In all, when green grass is burned, it's nitrogen concentration is higher than senesced grass, which leads to greater production of NOx, which is a precursor to ozone production that causes health problems. Whether green grass has a lower combustion efficiency hasn't quite been resolved (Mebust and Cohen 2013). It should be lower with wetter biomass, but this apparently hasn't been definitively demonstrated. If so, then burning green vegetation is going to produce a lot more junk.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-21729136036498432015-10-05T12:29:00.001-07:002015-10-06T04:24:08.115-07:00Investing for research<div dir="ltr" style="text-align: left;" trbidi="on">
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Just a mini thought here.<br />
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In economics, there are a number of theories on how entities invest. One of those is has to do with the relationship between the amount of investment and interest rates.<br />
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Essentially, theorems such as the marginal rate of efficiency or the marginal rate of investment state that firms continue to invest until the marginal rate of return is no different than the interest rate. In short, when making a decision on where to invest money, money will always be invested in the investment that produces the highest rate of return, until there are no options that differ than the prevailing interest rate.<br />
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By analogy, when governments are deciding how allocate scare research dollars, similar economic decisions should be at play.<br />
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In reality, these decisions are nothing close to rational, in the economic sense.<br />
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For one, we cannot quantify the rate of return on investing research dollars. Comparing two proposals for funding, reviewers likely can estimate the rate of return. The equation is something like: # of publications x impact factor of likely journals**.<br />
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**<i>This formula is likely discounted a bit for age. Old researchers are more likely to publish, but have a shorter lifetime return on investment. Funding young researchers before tenure makes it more likely they will be publishing in 10 years...</i><br />
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At a broader scale, this type of analysis is impossible or irrelevant. Funding agencies need to decide whether to invest in one discipline vs. another. This equation is useless for deciding whether to invest in physics vs. biology, for example.**<br />
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**<i>If it was used, it would just favor the more prolific discipline. Publishing papers is not the likely goal for funding agencies, per se. Papers aren't bitcoins. </i><br />
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The number of likely citations is also not a good metric, because it's circular. The number of times papers in a discipline are cited on average are determined by the number of papers published in that discipline (and the average number of citations in a typical paper).<br />
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If we cannot use expected rates of returns on publications, then how do we assess worth?<br />
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This is the Achilles' heel of rational investing in science. We cannot find a common currency to evaluate the relative worth of research.<br />
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Without this, funding becomes irrational.<br />
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Right now, changes in funding levels occur at the margins. Politicians and directors do not regenerate funding levels each fiscal cycle. Instead, they make a case that funding for one area should be increased or decreased relative to what it is currently. There are no equations that are employed to determine relative funding levels or relative changes in funding levels.<br />
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Until we have a concrete way to assess the value of research, either in terms of dollars, or social equity, or longevity, funding is likely to be irrational.<br />
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Stepping back, not only the relative amounts of funding, but absolute amounts of funding for research need development. In the US, NIH budgets are 4x higher than NSF. Why the relative difference is one question. Another, is why are there combined budgets almost $40 billion? Should they be $20B or $80B?<br />
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If the decisions are fundamentally irrational (economically), then we either need to make them economically rational, or commit to irrational (economically) arguments. </div>
JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-9349395996078053412015-09-22T06:49:00.002-07:002015-09-22T06:49:58.130-07:00Gut fungus in herbivores<div dir="ltr" style="text-align: left;" trbidi="on">
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Most of the energy in grass is locked up in cellulose and other complex recalcitrant molecular compounds like lignin and waxes. Stomach acid alone cannot degrade these compounds into components that yield energy for the animals that eat grass. When faced with how to survive off an abundant, yet inaccessible food source, grazers turned to microbes that have been degrading compounds like these for millions of years. </div>
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The digestive system of herbivores is a soup of microbes. Archaea, bacteria, fungi, protozoans... they're all in there. Most for a good reason.</div>
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A paper from a couple of years ago sheds a little light on the mutualisms between grazers and fungi.</div>
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The paper sequenced fungi in the fecal matter of bison, cattle, pronghorn, and prairie dogs at either Sevilleta (New Mexico) or Wind Cave (Wyoming).</div>
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A few interesting points.</div>
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First, half of the sequences they identified in bison and cattle were from Neocallimastigales. These are anaerobic fungi that produce the compounds responsible for hydrolysing cellulose and hemicellulose. We rarely ever hear about them, but they are the analog to brown-rot fungi that are important for wood decay.</div>
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Second, it appears that some of the fungi found in the fecals could only have gotten there from the animals ingesting roots. Some of these coprophilous fungi become endophytes, especially in roots. Bison and cattle occasionally eat roots of grasses. Prairie dogs a lot more.</div>
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Third, pronghorn fungal communities are just different (and less diverse). Pronghorn are browsers and just wouldn't have the same need for degradation as grazers. </div>
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One interesting side note. Paleoecologists are using the presence of dung fungal spores as evidence of the presence (and abundance) of grazers on the landscape. Fungal spores in sediments are identified as Sporormiella, a genus of Pleosporales. More Sporormiella in the sediment means more grazers on the landscape. Yet, although the authors of this paper identified many genera of Pleosporales, none of them were from Sporomiella. You have to wonder if a revision of what actually hits sediments is in order and whether sequencing the spores could provide more information on who was there.<div>
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Herrera, J., R. Poudel, and H. H. Khidir. 2011. Molecular characterization of coprophilous fungal communities reveals sequences related to root-associated fungal endophytes. Microbial Ecology <b>61</b>:239-244.</div>
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Davis, O. K. and D. S. Shafer. 2006. Sporormiella fungal spores, a palynological means of detecting herbivore density. Palaeogeography, Palaeoclimatology, Palaeoecology <b>237</b>:40-50.</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-56863651560428898582015-09-21T09:41:00.001-07:002015-09-22T05:59:19.250-07:00The diets of animals<div dir="ltr" style="text-align: left;" trbidi="on">
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The roots of ecology rise from questions about trophy. Darwin, Elton, Hutchinson...as far back as you wish to trace ecological thought, trophic questions have been central in the discipline. One organism consuming another (or part of another) is critical for population regulation, community assembly, ecosystem-level transfers of energy and material, no less the evolution of species.<br />
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Ecologists have been watching organisms consume other organisms for a long time, but, curiously, we still know little about what organisms eat.<br />
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Part of the reason is that it is hard to quantify consumption. Visual observations are difficult to translate to data. I've watched bison graze grasslands at a distance of feet and even after 30 seconds couldn't come up with a list of what they just consumed. Worse is that most consumption happens out of view. Dissections or regurgitations are necessarily disruptive and identification is still difficult. Isotope analysis gives crude answers. Microhistological analysis of fecal material suffers from differential digestion and lack of specificity.<br />
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In short, food web diagrams are hard to generate.<br />
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The rise of next generation sequencing has opened new opportunities to quantify what animals eat with resolution that never existed before. Fecal samples from an animal can be sequenced to determine what plants, invertebrates, fungus, or vertebrates they have been eating.<br />
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Noah Fierer and I have been working on helping people understand what animals eat for a bit.<br />
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So far, we've sequenced fecal material from over 20 different species that range from bats to bison, from prairie chickens to whooping cranes, from moose to mule deer.<br />
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I've talked with each of the ecologists afterwards about their data and there is one commonality to all of these discussions: surprises. There are always items in the diet that the ecologists didn't expect. And not just rare diet items. Perceptions (mine included) were always a good ways off of what the animals consumed most. For example, bison were long considered to eat mostly grass. Not so. Their diet can be dominated by forbs and shrubs at certain times of year.<br />
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A good technique is only as valuable as the importance of the question that it helps you answer.<br />
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Next generation sequencing of fecals is an amazing technique that will open up major insights into how populations are regulated, how communities assemble, and how energy and materials flow through the ecosystem. The technique will open up new insights into the coevolution of predator and prey.<br />
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A few bottlenecks still restrict advances.<br />
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1) We need better genetic barcode databases. There are still too many gaps for the technique to be commonplace. Many other people are working on this, but we need to sequence key barcodes for all collected taxa. When a sequence appears, we need to be able to compare it to the sequences from known taxa.<br />
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2) We need better species specificity. Give or take, current sequencing of diets can get down to ~genus level fairly well, but we need to develop different techniques like hierarchical sequencing to get us to the species level better.<br />
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3) We need to be able to quantify the diets of omnivores better. Currently, we can quantify the relative proportion of plants in diets. Or animals in diets. But, knowing the relative proportion of each is difficult. Over the course of a day, a bear (for example) could eat plants, fungi, insects, and vertebrates. But how much of each? Plus, DNA from the diet of prey is present in fecals, but we cannot necessarily tell whether the predator or prey ate a given taxa (or both).<br />
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There will always be more technique development necessary, but the biggest bottleneck is still utilization of the technique. Ecologists need to start using it. We're learning a great deal every time we use the technique.<br />
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com0tag:blogger.com,1999:blog-1511829372351341419.post-72202476675355185892015-06-02T19:49:00.001-07:002015-06-02T19:49:10.607-07:00Diet of large herbivores in Africa<div dir="ltr" style="text-align: left;" trbidi="on">
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Tyler Kartzinel's (and coauthors') new paper is out on diets of African herbivores.<br />
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This has the potential to be a classic. Or at least the start of a number of classic studies.<br />
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The authors examine the diets of 7 large mammalian herbivores at Mpala in Africa. Taken over a 2 month period, it's essentially a snapshot of the diets of the animals. The authors' main goal was to better understanding dietary niches in order to better understand the maintenance of herbivore diversity.<br />
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The authors do a great job of just quantifying the diets of the herbivores. This has never been done with so many animals in one place. Even just determining the proportion of grasses and legumes for the herbivores is interesting. Seeing how much mallow buffalo (generally considered a grazer) upends their dietary strategy.<br />
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The authors also then look essentially species by species at dietary overlap (see above). It's a fine-grained approach to understanding who eats what plants.</div>
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One of the authors' main conclusions is probably the most important for rethinking large herbivores: "dietary similarity was sometimes greater across grazing and browsing guilds than within them."</div>
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Yes, grazers and browsers can be identified, but it is much more complex than that. </div>
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As more samples are taken over time and more sites compared, the broader web of interactions among plants and their herbivores are likely to be better understood. </div>
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For example, how consistent are these diets over time?</div>
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Are their times of year when niche overlap (and maybe competition) is greatest?</div>
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How flexible are the diets of these animals?</div>
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Only time will tell....</div>
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Kartzinel, T. R., P. A. Chen, T. C. Coverdale, D. L. Erickson, W. J. Kress, M. L. Kuzmina, D. I. Rubenstein, W. Wang, and R. M. Pringle. 2015. DNA metabarcoding illuminates dietary niche partitioning by African large herbivores. Proceedings of the National Academy of Sciences:201503283.</div>
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JMChttp://www.blogger.com/profile/06001175696291253716noreply@blogger.com1