Spartan Ideas is a collection of thoughts, ideas, and opinions independently written by members of the MSU community and curated by MSU Libraries

In response to the novel coronavirus outbreak, advice about public health measures, and the need to support online teaching and learning, activities at MSU that are deemed non-essential are being stopped at this time. Therefore, selection of blog entries for the Spartan Ideas web site has been suspended. We ask for your patience during this unusual situation for our university and our country

# Does Behe’s “First Rule” Really Show that Evolutionary Biology Has a Big Problem?

Michael Behe has a new book coming out this month called Darwin Devolves. Nathan Lents, Joshua Swamidass, and I wrote a review of that book for the journal Science. (You can also find an open-access copy of our review here.) It provides an overview of the problems we see with his thesis and interpretations. As our …

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# Food Fraud Education Schedule – Quarterly Update + MOOCs Now On-Demand

REGISTRATION AND COURSES OPEN: MSU Food Fraud MOOC programs – Free Food Fraud Overview Food Fraud Audit Guide Food Defense Audit Guide Food Fraud VACCP Implementation (Food Fraud Vulnerability Assessment FFVA & Food Fraud Prevention Strategy FFPS Development) Each MOOC is offered monthly, with the content available on-demand.  Live lecture webinar updates are offered semiannually. …

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# Precision Genomic Medicine and the UK

I just returned from the UK, where I attended a Ditchley Foundation Conference on machine learning and genetic engineering. The attendees included scientists, government officials, venture capitalists, ethicists, and medical professionals. The UK could become the world leader in genomic research by combining population-level genotyping with NHS health records. The application of AI to datasets …

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# The Future of Genomic Precision Medicine

As I mentioned in this earlier post, I’ll be in the UK next week for a Ditchley Foundation conference on the intersection of machine learning and genetic engineering. I’ll present these slides at the meeting. The slides review the rapidly evolving situation in genomic prediction, focusing on disease risk predicted using inexpensive genotyping. There are now …

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Yesterday I had a rather rude reminder (actually, two) of something I’ve known for a while. I was running a Java program that uses CPLEX to solve an integer programming model. The symptoms were as follows: shortly after the IP solver run started, I ran out of RAM, the operating system started paging memory to …

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# Genomic Prediction of Complex Disease Risk (bioRxiv)

Our new paper describes over a dozen genomic predictors for common disease risk, constructed via machine learning on hundreds of thousands of genotypes. The predictors use anywhere from a few tens (e.g., 20 or 50) to thousands of SNPs to compute the risk PGS (Poly-Genic Score) for a specific disease. The figure above (Atrial Fibrillation) …

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# Ghosts and Hybrids: Ancient DNA and Human Origins

Take a break from your holiday Netflix binge and learn something about recent breakthroughs in our understanding of human evolution from ancient DNA. John Hawks (UW Madison) is an excellent speaker and this talk is for non-experts. Get the whole family together to watch — it’s a treat to learn from one of the leading …

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# Two Books – Real Gifts

I have a pile of about 10 books I’m wading through, but two are of special note as I write this. As I noted in my last blog of 2017 I have the privilege of reading, and especially of reading books. For the past few years I’ve read on average between 20-30 nonfiction works cover-to-cover per year. …

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# On Fear, Parades of Horribles, and Emotionally Potent Oversimplifications in Tribal Rights Litigation

Will the state of Oklahoma revert back to the Indians? Will tribes veto non-Indian land use decisions? Will thousands of state prisoners go free? Will non-Indians have to give back their lands to Indians? In the last few years, in cases out of Oklahoma, Wyoming, Michigan, Washington, and elsewhere, advocates for states and non-Indian property owners have invoked …

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# IceCube: neutrino astronomy in Antarctica

Tyce DeYoung (MSU Department of Physics and Astronomy) colloquium on high-energy astrophysics and exploration of the high-energy universe with the IceCube neutrino detector at the South Pole. Several MSU professors are part of the IceCube collaboration. I predict very exciting developments in neutrino astronomy in the coming decade ;-) The situation is similar to that …

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For almost a decade I’ve been involved with the Football Scholars Forum, an online book club that TV wordsmith Ray Hudson labeled “the soccer think tank.” I also like to think of it as an intellectual pick up game. An informal space to read, reflect, try new things, network, learn, and engage in thoughtful conversations with fútbologists around the …

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# The President. The Governor. The Economy 2018.

The State of the State Podcast discusses issues, questions, answers, policy and research on the hottest topics on the local, state and national stage. State of the State podcasters Interim IPPSR Director Arnold Weinfeld and Charles Ballard, Director of IPPSR’s State of the State Survey, will talk together and share the air with frequent guests …

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# Living Values

In the open letter we wrote to the College of Arts & Letters community in January 2018, we promised to look critically at ourselves, recognize our failures, and rebuild the trust that is required of us. This commitment has led to an intense period of critical self-reflection in the Dean’s Office and across the College in …

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# The Ecosystem for Organized Crime (and how to disrupt Food Fraud vulnerabilities)

This is a summary of Markus Felson’s 2006 report and presentation on The Ecosystem for Organized Crime (Felson, 2006). As is consistent with his other works and Situational Crime Prevention in general, the most efficient focus is on how and why a crime opportunity exists – which is more than just catching bad guys or bad …

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# The Quantum Theory of Fields

Excerpt from Sidney Coleman’s Erice lectures. The period he describes just predates my entry into physics. This was a great time to be a high-energy theorist, the period of the famous triumph of quantum field theory. And what a triumph it was, in the old sense of the word: a glorious victory parade, full of …

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# Of Typewriters and Permutations (V)

Okay, this is the last post on the subject. I promise! If you’re coming into this movie on the last reel, you may need to skim the last few posts to see what it’s about. I’m trying not to repeat myself too much. To summarize where we are at: Hardmath123 posted a solution (generated by …

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# Of Typewriters and Permutations (IV)

I’m continuing the recent theme of solving a quadratic assignment problem that lays out the 26 letters of the English alphabet on a one-dimensional “keyboard” for an 18th century typewriter. I thought this would be the last post, but something new turned up, so there will likely be one more. In the blog post that …

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# Of Typewriters and Permutations (III)

This continues the discussion (okay, monologue) from the two previous posts about the problem of laying out a one-dimensional typewriter keyboard. This is not the last post in the series, but I can at least guarantee that the series is converging. In the previous post, I gave a MIP model (named MIP1) that used binary …

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# Of Typewriters and Permutations (II)

This continues my previous post about the problem of optimally laying out a one-dimensional typewriter keyboard, where “optimally” is taken to mean minimizing the expected amount of lateral movement to type a few selected books. As I noted there, Nate Brixius correctly characterized the problem as a quadratic assignment problem (QAP). I’ll in fact try …

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# Of Typewriters and Permutations (I)

This is going to be the first of a few posts on the same problem. My efforts are based on a blog post by Nate Brixius (@natebrix) titled “Optimizing 19th Century Typewriters“, which in turn is based on a post titled “Tuning a Typewriter” by “Hardmath123”. As the image in Hardmath123’s post shows, an old …

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# Time to Empty Your Pockets

I just made my self read the nine page “Executive Summary” of the recently (November 14) released Providing for the Common Defense: The Assessment and Recommendations of the National Defense Strategy Commission . It was all I could do to keep from gagging. I won’t put myself through the full 116 pages, especially as I scanned the …

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# He did it: He Jiankui talk at HKU conference on gene editing

This is He’s talk from a conference on gene editing, in progress now in HK. (Should start at 1h09.) This article describes serious discussions between He and bioethicists over the last year. It’s important to note that CapEx required for this process is quite modest — not beyond the capability of a medium-sized IVF clinic. …

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# Generation CRISPR?

Very strange. This guy left his university a few years ago to concentrate on this research. Are his claims real? Genome-edited baby claim provokes international outcry (Nature News) The startling announcement by a Chinese scientist represents a controversial leap in the use of genome-editing. A Chinese scientist claims that he has helped make the world’s …

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# Back to Blue; Future Ahead

﻿ The State of the State Podcast discusses issues, questions, answers, policy and research on the hottest topics on the local, state and national stage. State of the State podcasters Interim IPPSR Director Arnold Weinfeld and Charles Ballard, Director of IPPSR’s State of the State Survey, will talk together and share the air with frequent …

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# In Other Words (Week of November 5)

To the Right: https://rightmi.com/in-the-beginning/ Even from the beginning of Michigan’s current reapportionment process, there was chaos, Right.com notes. https://rightmi.com/michigan-2018-election-results/ A lineup of Michigan’s win’s and losses in Election 2016 with analysis about top races from Right.com. https://www.michigancapitolconfidential.com/whos-moving-up-in-next-years-michigan-legislature Michigan Capitol Confidential.com outlines the new state Legislature broken down by party and notes some key details, after …

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# The Indian Child Welfare Act at 40

On this date in 1978, President Carter signed the Indian Child Welfare Act into law. Senator Abourezk introduced the bill to the Senate on April 1, 1977, and the Senate voted on it on November 4, 1977. Interestingly, while Sen. Goldwater supported the purpose of the bill, he did not vote on the Senate’s version …

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# The Narcotic of Power

I still have two chapters to go before I finish Philippe Sands penetrating 2005 book, Lawless World: America and the Making and Breaking of Global Rules, so what follows might have been improved if I had finished before sharing these thoughts.  I can’t be sure if what follows is inspired by that engaging book, or the …

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# The Limits of Our Thoughts

The reading pile keeps getting bigger. Each morning upon grabbing the coffee and nestling into a corner of the couch, I reach for one of the books in my reading pile. On the coffee table in front of the couch are the magazines that pile up – The Sun, The Atlantic, The Nation, Yes Magazine. Today I grabbed a …

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Can there be an “adulterated food” that does not include an “adulterant”? Yes. Confused yet? Keep reading. The bottom line is that to avoid confusion it is recommended to use the terms “Food Fraud” or “adulterant-substance” when referring to the type of fraud that is a substance intentionally added for economic gain. This blog post …

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# 1 In 4 Biostatisticians Surveyed Say They Were Asked To Commit Scientific Fraud

In the survey reported below, about 1 in 4 biostatisticians were asked to commit scientific fraud. I don’t know whether this bad behavior was more prevalent in industry as opposed to academia, but I am not surprised by the results. I do not accept the claim that researchers in data-driven areas can be ignorant of …

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# Stepwise Regression Code Revisited

I’ve added a few more tweaks to the stepwise regression code I published back in 2011. (If you wish, see here for the original post and here for a subsequent update.) The code does stepwise regression using F tests (or, equivalently, p-values of coefficients), which is a bit old fashioned but apparently how it is …

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# Backpropagation in the Brain?

Ask and ye shall receive :-) In an earlier post I recommended a talk by Ilya Sutskever of OpenAI (part of an MIT AGI lecture series). In the Q&A someone asks about the status of backpropagation (used for training of artificial deep neural nets) in real neural nets, and Ilya answers that it’s currently not …

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# Pseudocode in LyX

Fair warning: This post is for LyX users only. When I’m writing a paper or presentation in LaTeX (using LyX, of course) and want to include a program chunk or algorithm in pseudocode, I favor the algorithmicx package (and specifically the algpseudocode style). There being no intrinsic support for the package in LyX, I have …

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# B.S.-ing Precisely

In a recent blog post titled “Excessive Precision“, John D. Cook points out the foolishness of articulating results to an arbitrarily high degree of precision when the inputs are themselves not that precise. To quote him: Excessive precision is not the mark of the expert. Nor is it the mark of the layman. It’s the …

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# Physics as a Strange Attractor

Almost every student who attends a decent high school will be exposed to Special Relativity. Their science/physics teacher may not really understand it very well, may do a terrible job trying to explain it. But the kid will have to read a textbook discussion and (in the internet age) can easily find more with a …

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# Population-wide Genomic Prediction of Health Risks

The UK is ahead of the US in the application of genomics in clinical practice. Part of this is due to their leadership in projects like the UK Biobank (500k genomes with extensive biomedical phenotyping), and part is due to having a single-payer system that can adopt obviously beneficial (and cost-beneficial) practices after some detailed …

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# Quantum Information Science Workshop at MSU

Webpage / Program / Abstracts. My opening remarks: On behalf of Michigan State University it is my pleasure to welcome all of you to this workshop on quantum information science. In the fall of 1983 (my freshman year!) Feynman taught a graduate course at Caltech called Potentialities and Limitations of Computing Machines. Chapter 6 of …

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# Intuition and the two brains, revisited

﻿ Iain McGilchrist, author of The Master and His Emissary: The Divided Brain and the Making of the Western World, in conversation with Jordan Peterson. I wrote about McGilchrist in 2012: Intuition and the two brains. Albert Einstein: “The intuitive mind is a sacred gift and the rational mind is a faithful servant. We have …

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# To Rally or Not to Rally?

As I approach this week the “Stand Up for Peace” rally that I have been helping to plan for months, I began to think about what drives people to attend rallies or to stay home. As someone who has not planned a rally before but who has participated in many over the decades, I started to wonder …

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# Beyond the Soccer Mom

The white, middle class, minivan-driving suburban “Soccer Mom” has been part of U.S. political discourse since at least the 1996 presidential election. Two decades later, soccer is so embedded in mainstream American culture that a candidate is using past college playing experience to boost her campaign. Democrat Amy McGrath is challenging GOP incumbent Andy Barr …

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# Coordinating Variable Signs

Someone asked me today (or yesterday, depending on whose time zone you go by) how to force a group of variables in an optimization model to take the same sign (all nonpositive or all nonnegative). Assuming that all the variables are bounded, you just need one new binary variable and a few constraints. Assume that …

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# Sniffing out pandas’ social secrets

I find I tend to write most of my blog posts from the field – I guess this is what I think readers will find most exciting, which is probably because it’s what I find most exciting. I thought that I was done with fieldwork back in April, but while doing analyses for my dissertation …

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# The French Way: Alain Connes interview

I came across this interview with Fields Medalist Alain Connes (excerpt below) via an essay by Dominic Cummings (see his blog here). Dom’s essay is also highly recommended. He has spent considerable effort to understand the history of highly effective scientific / research organizations. There is a good chance that his insights will someday be put …

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# Choosing “Big M” Values

I seem to bring up “big M” models a lot, so apologies if I end up repeating myself in places here. Not long ago, someone passed along highlights of a “big M” type model to me and asked if he could somehow reformulate to get rid of $$M$$. I did not see any good way …

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# Adding Items to a Sequence

A question posed on OR-Exchange in 2017 asked the following: Given a tour of nodes, how does one best add two new nodes while respecting the ordering of the original tour. Specifically, the author began with a tour 0 – 1 – 2 – 4 – 6 – 0 (where node 0 is a depot) …

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# NP Confusion

I just finished reading a somewhat provocative article on the CIO website, titled “10 reasons to ignore computer science degrees” (when hiring programmers). While I’m not in the business of hiring coders (although I recent was hired as a “student programmer” on a grant — the Universe has a sense of humor), I find myself …

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# Scientists of Stature

The link below is to the published version of the paper we posted on biorxiv in late 2017 (see blog discussion). Our results have since been replicated by several groups in academia and in Silicon Valley. Biorxiv article metrics: abstract views 31k, paper downloads 6k. Not bad! Perhaps that means the community understands now that genomic …

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# Genomic Prediction: A Hypothetical (Embryo Selection), Part 2

The figures below are from the recent paper Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations (Nature Genetics), discussed previously here. As you can see, genomic prediction of risk allows to identify outliers for conditions like heart disease and diabetes. Individuals who are top 1% in polygenic risk score are …

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# Genomic Prediction of disease risk using polygenic scores (Nature Genetics)

It seems to me we are just at the tipping point — soon it will be widely understood that with large enough data sets we can predict complex traits and complex disease risk from genotype, capturing most of the estimated heritable variance. People will forget that many “experts” doubted this was possible — the term …

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# A Few Reflections on the TOME Initiative

WASHINGTON, DC – Today a group of colleagues from the Association of American Universities, Association of Research Libraries, and Association of University Presses met to advance the Towards an Open Monograph Ecosystem (TOME) initiative. It was heartening to see the progress the initiative has made since our first gathering in the summer of 2016. At the time, I was enthusiastic …

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