Journal Club 2016

Monday, December 12, 2016
Darwin and Mendel

Join us this Monday for the 2016 finale of Journal Club, where Irwin Goldman will lead a discussion on new evidence regarding the highly speculated and intriguing relationship between Darwin and Mendel. How might an exchange between Darwin and Mendel have reshaped the course of modern biology? What is the impact of phraseology on how we discuss and interpret scientific literature? Is there compelling evidence of a bromance between Darwin and Mendel?

In a perspective piece that celebrates the sesquicentennial anniversary of Mendel’s classic paper, Experiments on Plant Hybrids, Fairbanks and Abbott propose evidence of Darwin’s influence on Mendel’s interpretations and theory. They describe the history of translation and controversy surrounding Mendel’s work, including R.A. Fisher’s “abominable discovery” that Mendel may have falsified his results. To address shortcomings in previous translations of Mendel’s paper, they propose a new translation that (1) improves the accuracy and accessibility of Mendel’s original work and (2) employs Darwin’s phraseology from the Origin of Species, providing a 19th century Darwinian tone that is consistent with the timing of the original publication. This translation, coupled with marginalia from Mendel’s copy of Origin of Species, suggests that Darwin influenced Mendel’s writing in the final sections of his paper, supporting Fisher’s previous observation that “the reflection of Darwin’s thought is unmistakable.” Click here to access the paper by Fairbanks and Abbott.

Coffee, chocolate, and peers are the Elements which go forth to promote the Lebensbedingungen and Variabilität of Journal Club.

Monday, November 28, 2016
Back to the Bayesics

Join us on Monday to discuss the basics of Bayesian statistical inference and potential applications in genetics. We encourage participation regardless of familiarity with the topic, as the goal is to focus on big picture concepts in Bayesian statistics. What are the principles of Bayesian inference? When are Bayesian methods worth the high computational and interpretive investments? Are you currently using or is there an opportunity to integrate Bayesian frameworks in your research?

The advent of high-power computing has ushered in a revolution in statistics, specifically regarding Bayesian frameworks. As we continue to generate large data, there is an increasing need for more robust, efficient, and flexible statistical methods that provide biological insight. In their 2004 review, Beaumont and Rannala compare the use of Bayesian approaches to other statistical methods, explain why the use of Bayesian reasoning has increased in genetics, and highlight the shortcomings and future potential of these methods. Click here to access the article by Beaumont and Rannala.

As an example, we will walk through the Monty Hall problem: Your PI gives you a choice of three doors. There is a degree behind one door, and five more years of grad school behind the other two. You pick door #2, and your PI, who knows what is behind the doors, opens door #3, which shows five more years of grad school. Your PI then asks if you’d like to switch your choice to door #1 – is it to your advantage to switch? Hint: You should always switch your answer! Please click here to access an additional resource by Shoemaker, Painter, and Weir.

Monday, November 21, 2016
Agricultural journals in the Victorian era

Join us Monday where Charlene Grahn will discuss the development and influence of agricultural journals in the Victorian era. How does modern agricultural science compare to its nascent form? What insights can we gain from the successes and failures of past scientific journals? How have technological advancements changed science communication in the past and how might it continue to do so in the future?

Public dissemination of science was instrumental in advancing the farming practices of Victorian England during a period of unprecedented population growth. Early 19th century agricultural scholars lamented that farmers were ‘not a reading class,’ however by the end of the century over half of all English farmers subscribed to at least one agricultural periodical or newspaper. The Journal of the Royal Society of Agricultural Science is one such publication that shaped agriculture during the Victorian era by fostering communication between scientists and farmers. Click here to access a digitized volume of The Journal of the Royal Agricultural Society of England. Original copies of the journal will be available for browsing during journal club!

Gather with your fellow Men of Science for an afternoonified discussion over coffee and chocolate!

Monday, November 14, 2016
Global adaptation of populations

Join us Monday where Shelby Ellison will discuss how genetic adaptation to local environments has helped modern humans spread across the globe. What are the current population genomic tools to detect selection/adaptation within populations? Is the plant community better or worse equipped to use these tools? Are there untapped resources that we can use to better sample global plant populations?

Akin to artificial selection within plants, selective pressures in response to regional conditions have influenced global human genomic diversity. Identification of genetic variation associated with adaptation is in part due to improved genomic technologies, statistical analyses, and larger sample sizes. In this review, Fan et al. illustrate the use of emerging data sets and tools to better understand recent human evolution. Click here to access the article by Fan et al.

Monday, November 7, 2016
BLAST to the past

Join us Monday where Guillaume Ramstein will discuss the use of genetics in paleoanthropology. How can DNA information be so useful as to help elucidate the multiplicity of origins in prehistoric farming? How familiar are we already to the methods that the authors used to reach such fascinating conclusions?

There is more to statistical genetics than just association studies… Analyses typical of this field can yield conclusions like “this gene is positively associated to [some trait of interest]”. But interestingly, it can also yield conclusions like “the first farmers of the southern Levant and the Zagros Mountains were strongly genetically differentiated, and each descended from local hunter–gatherers”!… The study of Lazaridis et al. is remarkable not only because it exemplifies the power of DNA information and sequencing technologies, but also because it provides new insight about ancient human demography. Please click here to access the article by Lazaridis et al.

Monday, October 31, 2016
Halloween special: Reanimating zombie data!

Join us on Monday for a special Halloween edition of Journal Club. Joe Gage will lead a discussion on a topic that terrifies all scientists: best practices in scientific computing. Which practices do you currently implement in your research? What resources exist to facilitate use of these guidelines? How can you best arm yourself to fight zombie analyses?

Reanimating old data or scripts is the scientific equivalent of a zombie apocalypse – you dig into the depths of an archived folder, only to find the poorly annotated remains of a previously robust analysis. What was that variable again? Is that script written in an ancient alien language? How long will you be bunkered up to troubleshoot? In this guide, Wilson et al. use their combined expertise to outline “good enough” practices for scientific computing, providing the armaments needed to combat challenges in data management and organization for researchers with all levels of technical skill. Please click here to access the article by Wilson et al.

Monday, October 24, 2016
Symposium Highlight: Dr. John Kress

Join us Monday where Lynn Maher will highlight research on DNA barcoding by Dr. John Kress, who will be speaking at the Annual Plant Sciences Symposium on November 4! What are DNA barcodes and why should we care? Can this type of network construction be applicable in our own research? Join us to find out!

We will look at the use of DNA barcodes to understand complex plant-herbivore interactions in an effort to create and maintain biodiversity. Discussion will include an overview of the methodology, broader uses of DNA barcodes and how Dr. Kress has used this method in his work. Click here to access the article by Kress et al.

Understand the complexity of your dietary network with free coffee and cookies!

Monday, October 17, 2016
Symposium Highlight: Dr. Jessie Alt

Join us next Monday where Kevin Cope will discuss the discovery of a new soybean aphid biotype. This discovery was made in part by Dr. Jessie Alt, a research scientist at DuPont Pioneer and a speaker at this year’s Annual Plant Sciences Symposium. Why is it important to understand the precise mechanisms of resistance? How can these resistance traits be incorporated into commercial lines of soybean? How would you identify resistance to Biotype 4 in soybean breeding lines?

The soybean aphid (Aphis glycines) was first reported in the United States in 2000 as an invasive pest of soybean (Glycine max).  It is now one of the most damaging pests in soybean production, causing upwards of 50% yield loss during heavy infestation. Previously, there were three soybean aphid biotypes that had been identified, but a new biotype, collected near Lomira, WI, was reported by Jessie Alt and Molly Ryan-Mahmutagic in 2013. We will discuss how they confirmed the isolate was a distinct biotype, as well as the various sources of resistance to aphid biotypes 1, 2, and 3 via antibiosis or antixenosis. Click here to access the article by Alt and Ryan-Mahmutagic.

Coffee and cookies will be provided to break down resistance to attending journal club.

Monday, October 10, 2016
Symposium Highlight: Dr. Dan Chitwood

Join us Monday where Adam Bolton will lead a special edition discussion on an article by Dr. Dan Chitwood, who will be presenting at the Annual Plant Sciences Symposium on November 4! Dan will be sharing developments from his research on the morphometric analysis of leaves. How close do you think we can get to capturing the holophenotype of a single organism? Even if we could measure the entirety of a phenotype, how would we even begin to interpret  it? Would the effect size of existing QTL decrease? How can we best quantify a phenotype over developmental time?

Phenotyping is a critical, and often difficult, component to any genetics or breeding program. The last few years has seen an shift in focus from genomics to phenomics, which attempts to measure multiple scalar traits to capture the phenome of an organism. An article by Daniel Chitwood and Christopher Topp proposes the terms holophenotype, to mean the totality of and organism’s phenotype, and cryptotype, which is the combination of individual traits that maximizes the separation of types. Click here to access the paper by Chitwood and Topp.

Coffee and cookies will be provided to positively influence the phenome of journal club.

Monday, October 3, 2016
Cold-hardiness in fruit crops

Join us Monday where Madeline Wimmer will help welcome the cold weather with a discussion on breeding cold hardy perennial fruit crops. How do perennial crops differ from annual and biennial crops? What traits are most important for cold hardiness? Which crops are adaptable?

There are many breeding efforts for perennial fruit crops in Minnesota and Wisconsin, including dramatic fluctuations in temperature. This discussion will focus specifically on cold climate wine grapes, but a reference article on perennial fruit crop breeding by J.J. Luby is referenced for background on breeding perennial crops for cold hardiness. Madeline will walk us through this exciting topic using wine grapes as a case study! Click here to access the article by Luby.

Adaptation to journal club conditions will be encouraged with coffee and cookies.

Monday, September 26, 2016
From region to reason

Join us Monday where Chris D’Angelo will discuss the use of CRISPR-directed mitotic recombination to identify causal variants. What avenues does this technology open for scientific discovery? What are the possible trade-offs and/or bottlenecks of this technology? How accessible is this approach to the general research community?

The advent of linkage and association studies has identified thousands of genomic regions contributing to phenotypic variation. However, fine mapping and causal variant analysis is often not pursued due to limitations with recombination rate. In a recent Science publication, Sadhu et al. outline a method for CRISPR-directed mitotic recombination, which will allow researchers to rapidly identify casual variants for phenotypic variation by inducing “loss of heterozygosity” (LOH). Click here to access the article by Sadhu et al.

Monday, September 19, 2016
Is sharing caring?

Join us this Monday, September 19 at noon in Moore 473 for a discussion on the ethics and logistics of data sharing. What resources exist to facilitate data sharing? How can these resources be improved? What are the ethical concerns? Is there a way to capture the advantages of data mining while still involving the original researchers?

The sciences are facing many new challenges in the information age, especially how to manage large data sets and making them accessible to other researchers. Data sharing has many advantages, including increasing transparency and repeatability in research. However, widespread access to data often overlooks the context of the data collection, such as why certain parameters were chosen and experimental constraints. A recent editorial by Longo and Drazen in the New England Journal of Medicine discusses these issues in the context of clinical trials and provide insight into possible alternatives to promote data sharing and synergistic collaborations. Click here to access the article by Longo and Drazen.

Journal club is dedicated to the sharing of coffee, cookies, and scientific discussion in a synergistic environment.

Monday, September 12, 2016
The Spandrels of San Marco

Welcome back, Plant Scientists! The PSGSC is excited to kick off another semester of informal and intellectual discussion! What do spandrels, diminutive tyrannosaurus arms, and evolution have in common? To find out, please join us Monday to discuss “The Spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme” by S.J. Gould and R.C. Lewontin.

The most compelling stories of evolution often involve a competitive adaptation that arises via natural selection. We can become so fascinated by the origin of a single trait that we lose sight of the big picture, perhaps overlooking indirect explanations resulting from developmental constraints or population structure. In their classic 1979 article, Gould & Lewontin provide the famous analogy to spandrels, which they define as triangular spaces formed by the intersection of two rounded arches in domed churches. Spandrels are an architectural constraint, but also provide a convenient, seemingly intentional, space for mosaics. With captivating rhetoric, Gould & Lewontin argue that  biologists often ascribe trait origins to an adaptive advantage without due consideration for alternatives, although in the case of architecture it is clear that “spandrels do not exist to house evangelists.” Click here to access the article by Gould and Lewontin.

Does this article provide a convincing critique of adaptationist thinking? How are the topics presented relevant in modern science? What parallels can we draw to our own research? How can we broaden our perspective to avoid “just-so” storytelling? For those interested, click here for an eloquent criticism of this article by Jeremy Fox.

Monday, May 2, 2016
Reviving the pulse of pulses

Happy International Year of the Pulses! To celebrate these delicious legumes, join us Monday where Carlos Arbizu will lead a discussion on Andean bean diversity. What are the major challenges influencing pulse production and how are they being addressed? What efforts can we make to improve the utilization of pulses in the diet and in land management?

The United Nations, in collaboration with the FAO, declared 2016 the International Year of Pulses (IYP) to improve public awareness, encourage production, and increase dietary use of pulses. Pulses, which include beans, chickpeas, and lentils, are cultivated in many countries and are valued for their high amounts of protein, fiber, and micronutrients. Large-seeded dry beans (kidney and cranberry beans), also known as “Andean beans,” are an important source of food in the Americas and Africa. Despite their dietary importance, research on these crops is lagging behind their Mesoamerican counterparts. A study conducted by Cichy and collaborators (2015) genotyped and phenotyped a diversity panel, aiming to improve use of Andean bean germplasm in breeding efforts. Click here to access the article by Cichy et al.

In solidarity with the UN and FAO, journal club will be provide pulse-inspired treats and a beverage made from coffee beans.

Monday, April 25, 2016
To regulate or not to regulate, that is the question…

Join us Monday where Lynn Maher will discuss the regulation of organisms edited with CRISPR-Cas9. Is this a new era for GMOs? As scientists, how can we reframe the public discourse and stigmas surrounding gene-editing technology? What opportunities does this precedent offer, at the industry and academic level, for other products developed using CRISPR-Cas9?

The advent of novel DNA-editing technologies, such as zinc finger nucleases, TALENs, and CRISPR-Cas9, has raised questions regarding the existing regulatory framework for genetically modified organisms. Last week, USDA-APHIS informed Yinong Yang, a plant pathologist at Penn State, that a mushroom he developed using CRISPR-Cas9 would not be regulated, making it the first organism edited with CRISPR-Cas9 system to escape USDA oversight. The mushroom in question was engineered to resist browning by knocking out a polyphenol oxidase (PPO) gene, the same mechanism used to reduce browning in Arctic apples and Innate potatoes, which were subject to USDA scrutiny. Click here to access the Scientific American article we will discuss. And click here to access the article by Webber.

“Whether ’tis nobler in the mind to deliberate
The intricacies and bureaucracy of regulation
Or to eat cookies and drink a sea of coffee,
And by listening gain knowledge.”

Monday, April 18, 2016
The business of scientific publishing

Please join us Monday where Guillaume Ramstein will lead a discussion on the business models of scientific publishing.  

The industry of publishing is going through an interesting era! The “publishing giants” have typically applied a model based on subscriptions or one-article fees and, as the recent merger between Nature Publishing Group and major publisher Springer illustrates, they tend to get bigger! On the other hand, open-access journals (like PLoS ONE) and repositories (like arXiv) distribute articles for free, and are gaining importance in the game. Remarkably, strong and unlawful reactions to the traditional subscription model are also arising, through a science-paper equivalent of Napster: Sci-Hub. As a (future) scientist, what do you condone or condemn in these models? What evolution would like to see in the diffusion of (your) scientific knowledge? Come and share your opinion next Monday! Two articles about the changing landscape in the publishing industry can be accessed here: van Noorden. And here: New York Times.

Monday, April 11, 2016
Germplasm and seeds

Join us Monday for a discussion about germplasm conservation and seed industry consolidation. Crop wild relatives are widely lauded as a valuable source of genetic diversity, but how well do conservation efforts truly capture ecological diversity?

A recent study by Alvarez et al. quantified the global conservation and availability of wild accessions for 81 crops, highlighting collection gaps and the corresponding lack of diversity. The authors stress the need for a concerted effort to develop more comprehensive gene banks, which are constrained by lack of funding, political challenges, and biological limitations. The availability of genetic resources also stands to be impacted by recent consolidation within the seed industry (e.g. Dow & Dupont, Syngenta & Chem China). What are options for improving existing gene banks? Is there a trade-off between industry consolidation and conservation priorities (e.g. access to genetic resources and utilization of crop diversity)? Click here to access the article by Alvarez et al.

Does coffee and cookie consumption increase the diversity of scientific discourse? Find out by enjoying complementary coffee and cookies at journal club.