In our lab, we believe that Black Lives Matter, Love is Love, Women's Rights are Human Rights, Immigrants are Welcome, and of course, that Science is Real. We also believe that it all starts with Being Kind to one another.
My student Alex Drivas (Biochemistry '21) has been spending part of his summer working on printing aluminum parts using our 3D printer. I encouraged Alex to try this approach because, if successful, it would transform our ability to make new equipment in the lab. Generally, if you need something made of metal, you send a drawing out to a company that uses a CNC mill to remove material from a block of metal until you have the desired shape. This is referred to as subtractive manufacturing. Now, our desktop 3D printers have the ability to print in metal or in plastics supplemented with metal at the click of a mouse. Instead of sending something off to an outside manufacturer and paying hundreds or thousands of dollars per piece, we can print a design in the lab in the matter of hours for just the cost of the printer (< $1000) and the cost of the filament (~$165 per kilo). The print does need to be de-bound and sintered offsite, so it's not instant gratification, but it is a huge step forward.
Alex is at the cutting edge of using this technology (a future employer will be very lucky) and I asked him to write up his specifications and thoughts on printing for the benefit of the 3D printing community. Here's what he has to say:
Hot end: 240 °C
Bed temp: 100 °C
Layer thickness: 0.2mm
Perimeters: 4 count
Infill type: Concentric
First layer print speed: 25mm/s
Print speed: 40mm/s
Travel speed: 125mm/s
Cooling Fan: off
Extrusion multiplayer: 90%
First layer extrusion: 93%
Retraction length: 6mm
Retraction speed: 125mm/s
4 count brim
What I learned:
Adhesion and extrusion settings were the most important variables in printing. I had to apply more Dimafix around the corners of the print than the center and introduce a small brim to achieve proper layer adhesion through the print. I had to lower the Z offset (beyond what I would for PLA for ABS) to get better first layer adhesion. In following layers, I manually increased the Z offset just slight. If the nozzle was too far from the plate, the layer would not stick properly, however, if the Z offset was too low, the nozzle would grab material from the print as it extrudes. Improper adhesion would cause the corners of the print to curl and destroy the progress of the print. Applying too much Dimafix however, would make it close to impossible to remove from the bed.
Over-extrusion was a second variable adding to the debris build up around the nozzle. It was difficult at first to differentiate between the two. It will vary in printer type, but I narrowed ours down to the extrusion and retraction settings I had stated above. Decreasing the extrusion of the first layer however, made capturing the proper Z offset very important. Even with the successful print, I was still receiving a little over-extrusion and debris build up around the nozzle and had to pause the print to clean the nozzle. The debris did not build up over time, but rather varied based on contours and geometries at the specific stage of the print. The green part coming off the bed is unclean and needs to be sanded and filed to clean up the past troubles with extrusion.
In terms of the material and how it physically printed, I would compare it to trying to print clay. Coming out of the hot end, it does not stick to the bed as you would expect. Rather, it sticks to itself at times you don’t want it to and doesn’t when you do. Geometrically the material is very limited. Holes below a 10mm radius print unclean and inconsistent through layers. Thicker walls the better. Any internal fillets or contours are difficult and should be avoided. The optimal print for this material would be a gear or some small, geometrically uncomplex, internally uniform object.
Alex's work was supported by a grant from the Center for Undergraduate Excellence at Chapman University.
We are fortunate to have a Picarro L2130i cavity ringdown spectrometer in our new lab here in the Keck Center for Science and Engineering here at Chapman University. The instrument can analyze stable isotopes of oxygen and hydrogen in water vapor or liquid samples via the autosampler (with a dry nitrogen carrier gas). The lab has a number of in-house standards that span the range of typical waters at natural abundance. Many labs are not running highly enriched or depleted liquid samples right now due to memory effects; these problems can be solved with a particularly rigorous approach to sample injection and careful choice of standards; we are willing to take the time to run those samples. We are happy to serve as a resource for the community - please reach out if you have analyses in mind.
We also have the ability to extract water from environmental samples (e.g. soil, plants, and other biological tissue) using the method proposed by Koeniger et al. (2011 in RCMS). The basic principle is that a sample under vacuum is heated in the dry block heater and the evaporated water is in turn condensed in liquid nitrogen. This approach has not been as widely applied as cryogenic vacuum distillation systems built with glass or metal manifolds; however, the principles of use are identical. Again, we are happy to serve as a resource for the community - please reach out if you have analyses in mind or if you would like the parts list that we developed for how to build this instrumentation.
Folks in the lab are pursuing a number of different innovative projects right now, ranging from understanding how environment contributes to the evolution of new species in the Tropics to how water moves through landscapes. What is interesting is how many of those innovative projects are leaning on very classic methods - we are measuring soil texture, quantifying stem anatomical traits, and counting stomata. Looking forward to seeing the results!
How do we know that what we observe at one location holds true at another?
For the past three years, my collaborators and I have been studying the spatial patterns in stable isotopes of water as they move through forest ecosystems. My hope was that looking at variations in space would reveal something variations in time cannot – the application of stable isotopes water to ecohydrology has long been focused on repeatedly sampling the same location. The first three papers are now a matter of public record, largely thanks to the efforts of Scott Allen, Sabine Braun, James Kirchner and Rolf Siegwolf, with a few more papers on the way.
I had hoped that we would gain some fundamental insights into process. For instance, can sampling spatial variation in soil water isotopes tell us more about how soil characteristics contribute to variation? However, what has captured my attention is very different:
-Many applications of stable isotopes of water benefit from spatially and temporally explicit estimations of precipitation inputs. Interpolated maps of precipitation isotopes have become a fundamental tool. In a paper published in Geophysical Research Letters, Scott Allen develops a method using sine curve functions to describe the temporal patterns in precipitation isotopes across the entirety of Switzerland, then maps each of the three sine curve parameters (amplitude, phase, and offset). Each parameter contains compelling information: amplitude describes the strength of the seasonal cycle, phase describes the timing of the peak values, and offset describes the mean values. Beyond the many existing applications of precipitation “isoscapes,” I cannot wait to see how the community uses this new information.
-For a long time, we have been using variation in stable isotopes of water in the soil and comparing it to stable isotopes of water in plants as a means of inferring something about the depth of plant water uptake. In a paper in Hydrology and Earth Systems Sciences (currently in open review), Scott Allen develops a new index of plant source water that I believe much more accurately reflects what we are measuring – the seasonal origin of the water being taken up by plants. This approach is agnostic to the current debate about the methodological concerns of soil water isotope extraction. Moreover, I am hoping that it will reframe and advance the field in new directions. This is not to say that the results of the study– over 900 trees at 182 sites across the entirety of the country of Switzerland –are not incredibly compelling in and of themselves….
-At the beginning of this post, I posed a question. How do we know that what we observe at one location holds true at another? How do we know that the soil water isotopes sampled in one location are similar to those 5 m distant, 50 m distant, or 500 m distant. This is of critical import because we frequently use soil water isotopes sampled at one location as the foundation for inferring the depth of root water uptake among any number of neighboring trees. On average, studies have sampled 4 replicate individuals of 3 different plant species and matched them with 3 replicate soil profiles (n = 76 studies from 2010-2016; Evaristo & McDonnell, 2017). We hope that those 3 soil profiles are representative. In a study I led in the journal Ecohydrology, we demonstrate that accurately characterizing the spatial variation (both lateral and vertical) in soil water isotopes requires considerable sampling. Our simulations show that due to tremendous variability, inferences of root water uptake using two-end member mixing models (or really most of the methods reviewed in the compelling paper by Rothfuss and Javaux 2017) cannot be interpreted with confidence at our temperate forest site. We will have to hold ourselves accountable for this while interpreting research carried out to date and in designing new research in the future.
As always, I invite your comments and feedback. Many thanks to all of the individuals who have contributed to this research, the funding agencies that have made it possible, and the reviewers and the handling editors who have helped us effectively communicate it.
In collaboration with Christian Ammendola from the incomparable 42Matters (Zurich, Switzerland), I recently presented at a poster on the citizen science ecosystem at the annual meeting of the AAAS. This work builds on my longstanding interest in the role of technology in facilitating informal science learning. The abstract follows below, but I'll reduce this to just a single sentence:
There has been an incredible growth in mobile apps to facilitate citizen science, but most are unused and subsequently abandoned by the developers.
Abstract: Citizen science has become an increasingly popular means of engaging the public in the collection of scientific data. In parallel, scientists are creating mobile platforms to facilitate their citizen science projects. Such mobile apps hold the potential to significantly increase our capacity to do scientific research, as well as our ability to provide informal science education to broad audiences. However, our understanding of the development, use, and efficacy of mobile applications for citizen science remains limited. How do we know what apps are available and how they are being engaged? We used web crawlers to search for citizen science mobile applications on the Android and iOS platforms. We used a number of different keywords to capture all possible applications and then reviewed each one to ensure it met criteria for inclusion. We identified 138 unique citizen science mobile applications, including 48 common to both platforms. The median range of downloads for applications on the Android platform was 500-1000, indicating that very few experience widespread adoption. We also observed that more than 70% of the applications have not been updated for more than a year. This raises interesting questions regarding the return on the investment in developing these apps. As such, we searched for peer-reviewed science or science education literature associated with each application and found articles relating to only 15% of them to date. At this time, it appears that very few mobile citizen science applications are resulting in published data and that little is known about how those applications affect public engagement in science. However, of those applications with widespread adoption, analysis of the text of user reviews indicated that participants liked facilitating science, appreciated application functionality, and were engaging applications to seek scientific information. While such results are promising, there is clearly a critical need for the community to study how we engage technology for citizen science and science education, as well as translate these findings into best practices that can inform how we invest our resources in the future.
We are soliciting for the first of two postdoctoral research associates who will drive the research for a new NSF Dimensions of Biodiversity grant. Dr. Jennifer Funk and I will advertise the second position in the coming months.
DESCRIPTION: The Ecology and Evolutionary Biology Department (https://www.eeb.ucsc.edu/) at the University of California, Santa Cruz (UCSC) invites applications for the position of Postdoctoral Scholar under the direction of Associate Professor Kathleen Kay under a five-year NSF Dimensions of Biodiversity grant (“Biotic and abiotic drivers of Neotropical plant speciation”). The scholar will investigate the phylogeny, population genomics, and quantitative genetics of the spiral gingers (monocot genus Costus). The project is a collaboration among PIs Kathleen Kay (UCSC), Jennifer Funk (Chapman University), Carlos Garcia-Robledo (University of Connecticut), Santiago Ramirez (UC Davis) and Dena Grossenbacher (Cal Poly SLO) to uncover patterns and mechanisms of speciation in a recent, rapid radiation throughout Central and South America. The first years will be focused on phylogenetics and population genomics, whereas later years will be focused on QTL mapping and field testing of key traits and loci involved in adaptive divergence and reproductive isolation. Primary responsibilities include experimental design, coordinating and conducting sequence data collection, managing and analyzing large datasets, mentoring undergraduate and graduate students, coordinating research collaborators, and contributing to the dissemination of results through manuscripts, presentations, public outreach, and agency reports. Applicants with the following preferred qualifications are strongly encouraged to apply: experience generating and analyzing next gen sequence data from non-model plants, excellent bioinformatics skills, a strong interest in plant speciation and adaptation, and a track record of publishing in leading journals. The position requires excellent time management and written/oral communication skills. The scholar will be based at UCSC, with opportunities for lab exchanges and fieldwork in Costa Rica and Panama. More information on the Kay Lab can be found at https://kay.eeb.ucsc.edu/
ACADEMIC TITLE AND SALARY: Postdoctoral Scholar. Minimum annual salary of $48,216, commensurate with qualifications and experience. Minimum annual salary rates are made based on the individual’s Experience Level, which is determined by the number of months of postdoctoral service at any institution. See current salary scale for Postdoctoral Titles athttps://apo.ucsc.edu/compensation/salary-scales/index.html
BASIC QUALIFICATIONS: Ph.D. or foreign equivalent in Biology or related field, as well as a minimum of two years experience in phylogenetic and/or population genetic laboratory research.
POSITION AVAILABLE: April 1, 2018. Start date could be as late as October 1, 2018. Ph.D. must be in hand at time of the initial appointment.
MAXIMUM DURATION OF SERVICE IN A POSTDOCTORAL TITLE: Postdoctoral Scholar appointments are full-time; the initial appointment is for two years, with the possibility of reappointment. Reappointment will be contingent upon positive performance review and availability of funding. The total duration of an individual’s postdoctoral service may not exceed five years, including postdoctoral service at any institution. Under limited circumstances, an exception to this limit may be considered, not to exceed a sixth year.
APPLICATION REQUIREMENTS: Applications should be emailed to Kathleen Kay email@example.com. All documents and materials must be submitted as PDFs. Please refer to Position # EEB Postdoctoral Scholar-18T in all correspondence. Informal inquiries may be sent to firstname.lastname@example.org
Cover letter describing past research experience and qualifications for this position (required)
Current curriculum vitae (required)
A list of three references that includes their contact information (required)
Up to three copies of published manuscripts-submitted as separate pdfs (required)
There is a new version (1.3) of Plant-O-Matic available on the iTunes store. The update focuses on the user experience, including two new key features:
These are modest changes a long time coming, but my hope is that they significantly improve the user experience.
As we reported in our open access description of the methods underlying Plant-O-Matic, much of the information we make available to support the identification of the 88,000 species in the database is currently quite limited. This most recent update has revealed once again just how much of this information is missing; we have a lot of work to do in order to collate the available data and even more to do to fill the gaps where no data exists. We’re excited about the challenge.
I am excited to be joining the faculty in the Department of Biological Sciences in the Schmid College of Science and Technology at Chapman University in fall 2017. In addition to teaching and research, I will also direct the Grand Challenges Initiative, a new program empowering undergraduates in the sciences with the interdisciplinary critical thinking and problem-solving skills that they need to solve problems of global importance.
The university is really a gem – I could not be more impressed by the administration, the faculty, and the students –and is engaging in some truly innovative initatives. Campus is beautiful and we have a brand new science and technology building coming online in 2018. There is a lot to be excited about.
In the near-term, I am happy to serve as a host for postdoctoral research associates and visiting scientists, please feel free to reach out if you are interested.
Jim Kirchner (ETH Zurich) and I are very excited to be advertising a postdoctoral research position focused on spatiotemporal patterns in soil water isotopes across Switzerland. The postdoctoral research associate will be based at ETH Zurich. Additional details follow below. Feel free to reach out if you have any questions.
Applications are invited for a postdoctoral research associate to conduct research focused on interpreting spatial and temporal patterns in soil water isotopes. The project leverages a unique long‐term water isotope data set collected throughout Switzerland. The long‐term goal of the project is to use environmental water isotopes to improve our understanding of soil water storage and plant water relations in a manner that can inform environmental decision‐making.
The successful candidate will be an independent and highly motivated scientist with a strong background in environmental water isotopes and/or stable isotope biogeochemistry. Additional expertise in geospatial statistics, (eco)hydrology, or soil physics is particularly welcome.
The research associate will be based in the Department of Environmental Systems Science at ETH Zurich, Switzerland, and will be co‐supervised by James Kirchner (ETH) and Greg Goldsmith (Paul Scherrer Institute & Chapman University).
As Europe's leading technical university, ETH Zurich has excellent infrastructure and research support. Collaborative links with other Swiss universities and federal research institutes provide additional depth and breadth in ecohydrology and biogeochemistry, and the Swiss landscape is an unparalleled natural laboratory.
The initial appointment is for two years with the possibility for extension. Applicants should supply a single PDF containing:
‐ a statement of their research interests, experience and technical background
‐ a CV and complete list of publications
‐ and contact information for three references.
Applicants may also supply up to three (but no more) examples of their best published work, again as PDFs. Applicants who are attending AGU and are available for interviews there should note this in their applications.
As part of the ETH's efforts to promote women in science, qualified female researchers are particularly encouraged to apply. Applications should be sent to apply_PES@env.ethz.ch
Review of applications will begin 15 November 2016 and continue until the position is filled.