Uncommon Ground

Academics, biodiversity, genetics, & evolution

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A crack in creation

In August, 2012 a paper entitled “A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity” appeared in Science (doi: 10.1126/science.1225829). I probably saw the title in the table of contents of the August 17th issue and skipped right by. Bacterial immunity isn’t a topic a pay a lot of attention to. OK. Let’s be honest. I don’t pay any attention to bacterial immunity.

Not too long after that paper appeared, I started hearing about something called CRISPR-Cas9. I didn’t know what it was or what it might be useful for, only that a lot of people who were interested in molecular genetics were paying attention to it, especially those who were interested in using molecular tools to edit genomes of complex, multicellular organisms. I started to see newspaper and magazine articles talking about how this new technology would revolutionize biology and medicine in the same way that the discovery and use of restriction endonucleases had revolutionized them in the mid-1970s.

Some of the most ambitious projections suggested that we could be entering an era of designer genes in which gene therapy might be used not only to modify or replace genes that lead to diseases like sickle cell anemia, but in which it might be used to enhance “normal” functions. Not too long after that I started hearing about biologists who realized that CRISPR-Cas9 could be used to build gene drives that might be used to control pest populations. A lot of people began worrying about the ethical issues associated with use of CRISPR-Cas9 (e.g., doi: 10.1093/bmb/ldx002).

In June, two pioneers in the work leading to development of CRISPR-Cas9 published a book outlining the history of the work and exploring some of the ethical implications. I am a little less than halfway through A crack in creation, but so far I have found it very readable and informative. Reading this book is the only reason I know about the Science paper from 2012. Only now, 5 years later, am I taking the time to learn about this new technology. I had an inkling of its power and utility before I started reading, and I was (am still am) uneasy about some potential applications. Since so much of the basic science is very distant from my expertise and experience, I can’t judge the historical accuracy of the story Douda and Sternberg tell, but they seem generous in giving credit to other scientists who made contributions and very aware that their creative insights depended on previous work by many other people. That makes me think that if there are inaccuracies in the story, they are inadvertant and unintentional.

If you’ve been waiting for a good time to learn more about CRISPR-Cas9, your wait is over. Click on the image above, go to Amazon, and buy yourself a copy of A crack in creation or check it out from your library. You won’t be disappointed.

(In case you’re wondering, I don’t know either of the authors, and I won’t get any Amazon affilliate credits if you buy the book from Amazon. I’m endorsing the book only because I’ve found it very informative. It’s also written very clearly, clearly enough that I think your non-biologist friends and relatives would find it interesting and informative, too.)

BioOne has a new look

BioOne logos

The new organizational logo for BioOne (left) and the new logo for the BioOne Complete collection (right)

Some of you know that I have chaired the BioOne Board of Directors since a year after its initial incorporation in 1999. In the last 17 years, BioOne has seen many changes. The most recent is an updated set of logos for BioOne, the not-for-profit organization that supports innovative approaches to scholarly publication in organismal and environmental life sciences. BioOne is a collaboration between not-for-profit publishers and libraries, both of whom share an interest in ensuring that scholarly research is widely accessible and that not-for-profit publishers can recover the revenues they need to support their publishing operations. BioOne Complete is BioOne’s core product, “a database of 200 subscribed and open-access titles in the biological, ecological, and environmental sciences.”

A week ago BioOne and BioOne Complete launched the new logos above. More information about the new logos is available at http://www.bioonepublishing.org/news/1412/.

Revitalizing Graduate STEM Education for the 21st Century

The National Academy of Sciences has a committee that is leading a study of graduate education in science, technology, engineering, and mathematics (STEM). The goals of the study include:

  • Identifying policies, programs and practices that could better meet the diverse education and career needs of graduate students,
  • Identifying strategies to improve the alignment of graduate education courses, curricula, labs and fellowship/traineeship experiences for students with the needs of prospective employers
  • Identifying policies and effective practices that provide students and faculty with information about career paths for graduates holding master’s and Ph.D. degrees and provide ongoing and high quality counseling and mentoring for graduate students.
  • Creating a set of national goals for graduate STEM education that can be used by research universities.

The committee released a discussion document describing a set of competencies that might form core educational elements for both master’s and PhD programs in STEM fields. It seeks community input on the discussion document. The deadline for comment is 22 September 2017 and may be submitted either by a web form at http://nas.gradedinput.sgizmo.com/s3/ or via e-mail to STEMGradEd@nas.edu. If you are interested in STEM graduate education, I encourage you to read the document and submit comments.

Disclaimer: I was part of the Council of Graduate Schools Committee that developed the Alignment Framework for the Master’s Degree that the document uses to describe core educational elements for STEM master’s degrees.

Rediscovering Adonis cyllenea

Adonis cyllenea

Adonis cyllenea – Photographed at the 8th International Alpine Conference, Nottingham, UK. Photo by Todd Boland (from the North American Rock Garden Society)

Adonis cyllenea was described in 1856 from a specimen collected in the Peloponnese Mountains of Greece (http://bit.ly/2xgG1lS). It was thought to be extinct in the wild until 1976 when it was rediscovered (https://en.wikipedia.org/wiki/Adonis_cyllenea). It was recorded in the Giresun province of Turkey in 1867 and was just rediscovered there (http://bit.ly/2vfDPcO). Occasionally, there is good news about plants that were thought to be extinct. Mostly when they disappear, they are gone for good.

The solar eclipse at UConn

Solar eclipse

Solar eclipse prediction for Storrs from Wolfram

This afternoon at 2:45pm EDT the solar eclipse will reach its maximum in Storrs, about 70%. The figure above is a screenshot from my iPhone of the Wolfram Precision Eclipse Computation for Storrs. Follow that link to get the results for your location. The Physics Department at UConn will be hosting an eclipse viewing party on Horsebarn Hill. There will be solar telescopes and a short public lecture in addition to other activities. Unfortunately, I won’t be able to attend. I will be welcoming the new class of graduate fellows from 2:00-3:00pm and welcoming all new and continuing fellows and their faculty advisors at an ice cream social from 3:00-4:00pm. We will be meeting in the Alumni House, so we should see the darkening outside, and I may suggest that we take a short break a little before 2:45pm to go outside.

It’s almost certainly too late to get eclipse glasses, so if you don’t have them already you’ll have to find welder’s goggles or a solar telescope. If you can’t find any of those, you can still build yourself an eclipse viewer with a cardboard box and a few simple tools. Whatever you do, don’t look at the eclipse without protection for your eyes. A man in Portland, Oregon looked at an eclipse for no more than 20 seconds when he was in high school in 1963. It burned a holed in the retina of his right eye. Don’t let that happen to you.

Keep your data tidy

If you’ve spent any time using R, you probably know the name Hadley Wickham. He’s chief scientist at RStudio, the author of 4 books on R, and the author of several indispensable R packages, including ggplot2, dplyr, and devtools. I was reminded recently that several years ago, he wrote a very useful paper for the Journal of Statistical Software, “Tidy data” (August 2014, Volume 59, Issue 10, https://www.jstatsoft.org/article/view/v059i10).

If you are familiar with Hadley’s contributions to R, you won’t be surprised that tidy data has a simple, clean – tidy – set of requirements:

  1. Each variable forms a column.
  2. Each observation forms a row.
  3. Each type of observational unit forms a table.

That sounds simple, but it requires that many of us rethink the way we structure our data, no more column headers as values, no more storing of multiple variables in one column, no more storing some variables in rows and others in columns. Fortunately, Hadley is also the author of tidyr. I haven’t used it yet, but given how bad I am at starting with tidy data, I suspect I’ll be using it a lot in the future.

I’m sorry. P < 0.005 won't save you.

Recently, a group of distinguished psychologists posted a preprint on PsyArxiv arguing for a re-definition of the traditional signifance threshold, lowering it from P < 0.05 to P < 0.005. They are concerned about reproducibility, and they argue that “changing the P value threshold is simple, aligns with the training undertaken by many researchers, and might quickly achieve broad acceptance.” That’s all true, but I’m afraid it won’t necessarily “improve the reproducibility of scientific research in many fields.”

Why? Let’s take a little trip down memory lane.

Almost a year ago I pointed out that we need to “Be wary of results from studies with small sample sizes, even if the effects are statistically significant.” I illustrated why with the following figure produced using R code available at Github: https://github.com/kholsinger/noisy-data

What that figure shows is the distribution of P-values that pass the P < 0.05 significance threshold when the true difference between two populations is mu standard deviations (with the same standard deviation in both populations) and with equal sample sizes of n. The results are from 1000 random replications. As you can see when the sample size is small, there’s a good chance that a significant result will have the wrong sign, i.e., the observed difference will be negative rather than positive, even if the between-population diffference is 0.2 standard deviations. When the between-population difference is 0.05, you’re almost as likely to say the difference is in the wrong direction as to get it right.

Does changing the threshold to P < 0.005 help. Well, I changed the number of replications to 10,000, reduced the threshold to P < 0.005, and here’s what I got.

Do you see a difference? I don’t. I haven’t run a formal statistical test to compare the distributions, but I’m pretty sure they’d be indistinguishable.

In short, reducing the significance threshold to P < 0.005 will result in fewer investigators reporting statistically significant results. But unless the studies they do also have reasonably large sample sizes relative to the expected magnitude of any effect and the amount of variability within classes, they won’t be any more likely to know the direction of the effect than with the traditional threshold of P < 0.05.

The solution to the reproducibility crisis is better data, not better statistics.

 

Using weather to predict growth of forest trees

Last January I mentioned that I co-authored a paper that appeared on bioRxiv in which we combined tree ring and growth increment data to predict growth from weather and biophysical data. The paper has now appeared in Ecosphere, an open acces journal from the Ecological Society of America. Here’s the abstract. You’ll find the full citation below.

Fusing tree-ring and forest inventory data to infer influences on tree growth

Better understanding and prediction of tree growth is important because of the many ecosystem services provided by forests and the uncertainty surrounding how forests will respond to anthropogenic climate change. With the ultimate goal of improving models of forest dynamics, here we construct a statistical model that combines complementary data sources, tree-ring and forest inventory data. A Bayesian hierarchical model was used to gain inference on the effects of many factors on tree growth—individual tree size, climate, biophysical conditions, stand-level competitive environment, tree-level canopy status, and forest management treatments—using both diameter at breast height (dbh) and tree-ring data. The model consists of two multiple regression models, one each for the two data sources, linked via a constant of proportionality between coefficients that are found in parallel in the two regressions. This model was applied to a data set of ~130 increment cores and ~500 repeat measurements of dbh at a single site in the Jemez Mountains of north-central New Mexico, USA. The tree-ring data serve as the only source of information on how annual growth responds to climate variation, whereas both data types inform non-climatic effects on growth. Inferences from the model included positive effects on growth of seasonal precipitation, wetness index, and height ratio, and negative effects of dbh, seasonal temperature, southerly aspect and radiation, and plot basal area. Climatic effects inferred by the model were confirmed by a dendroclimatic analysis. Combining the two data sources substantially reduced uncertainty about non-climate fixed effects on radial increments. This demonstrates that forest inventory data measured on many trees, combined with tree-ring data developed for a small number of trees, can be used to quantify and parse multiple influences on absolute tree growth. We highlight the kinds of research questions that can be addressed by combining the high-resolution information on climate effects contained in tree rings with the rich tree- and stand-level information found in forest inventories, including projection of tree growth under future climate scenarios, carbon accounting, and investigation of management actions aimed at increasing forest resilience.

Evans, M. E. K., D. A. Falk, A. Arizpe, T. L. Swetnam, F. Babst, and K. E. Holsinger. 2017. Fusing tree-ring and forest inventory data to infer influences on tree growth. Ecosphere 8(7):e01889. doi: 10.1002/ecs2.1889

A journal I don’t trust – Journal of Forensic Medicine Forecast

I won’t say that the Journal of Forensic Medicine Forecast is a predatory open-access journal. I will say that I am suspicious. Why? Beccause I received an invitation over the weekend to join its editorial board. If you’re reading this post, you know enough about me to know that I have no expertise at all in forensic medicine. How could I not be suspicious any journal, open access or not, that invites me to join its editorial board when I lack expertise relevant to its subject.

Here’s the text of the e-mail I received, with a name redacted to protect the individual’s privacy:.

Dear Dr. Kent E Holsinger,

Greetings!

Journal of Forensic Medicine Forecast is an international, Open Access and peer-reviewed journal has been launched by ScienceForecast Publications. The journal devoted to Clinical forensic medicine, digital and multimedia sciences, forensic analytical chemistry, forensic anthropology, forensic biology, forensic education, forensic entomology, forensic genetics, forensic microbiology, forensic odontology, forensic osteology, forensic pathology, forensic physical evidence, forensic psychiatry, forensic radiology, forensic serology, blood spatter analysis, drug delivery, crime scene investigation, dna fingerprinting, toxicological, human toxicology, applied toxicology, experimental toxicology, environmental toxicology, investigative toxicology.

At the onset, we are going to invite editorial board members, journal is seeking energetic, qualified and high profile researchers to join its editorial board. We believe the quality of a journal is depends on the quality of its Editorial Board.

Based on your high expertise in the field of forensic medicine, we are inviting you to join as editorial board member of our journal. As an EB member of our journal you may be required to occasionally review papers, solicit articles from your colleagues/acquaintances and help promote the journal at initial stage.

If you are interested to join as our Editorial Board member, please reply with your latest CV, photograph along with research interests as an email attachment.

To visit Desktop site: www.scienceforecastoa.com

We look forward to receiving your valuable response.

Best Regards,
<name redacted>
Editorial Office: Journal of Forensic Medicine Forecast
Tipple, View drive W
Ohio – 43016
USA

This is not a spam email. If you are not interested to join as Editorial Board Member of this journal, please reply to this email with “unsubscribe” in the subject line.

Lecture notes in population genetics – final version from Spring 2017

I’ve finally had time to clean and post the final version of lecture notes from my graduate course in population genetics last spring. The individual lectures have been since I revised them for class, meaning that the last set of them was available in late April. You will find links to the individual lecture notes at http://darwin.eeb.uconn.edu/uncommon-ground/eeb348/notes/. If you’re interested in a particular topic in population genetics and I have a lecture that covers the topic, that’s probably where you’ll want to go.

If you want a single-volume reference to population genetics (including some old notes that I no longer maintain), you’ll find a PDF (5.89MB, 322 pages) at Figshare (doi: 10.6084/m9.figshare.100687.v2). If you want to print the PDF, I recommend that you print it on a double-sided printer. You can then put the pages in a binder and flip through them as if it were a bound book.

If you use LaTeX (and you’re a glutton for punishment), the LaTeX source and EPS files (for figures) is available in a Github repository (https://kholsinger.github.io/Lecture-Notes-in-Population-Genetics/).

These notes are released under a Creative Commons Attribution-ShareAlike license (http://creativecommons.org/licenses/by-sa/4.0/). I hope you find them useful. If you find errors in them, please let me know.