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Jeffrey Hall, a retired professor at Brandeis University, shared the 2017 Nobel Prize in medicine for discoveries elucidating how our internal body clock works. He was honored along with Michael Young and his close collaborator Michael Roshbash. Hall said in an interview from his home in rural Maine that he collaborated with Roshbash because they shared...
This is an all-too-often heard story. The difference is that now a Nobel Prize winner is telling it about himself!Syndicated copies to:
In my post “The Kolmogorov Option,” I tried to step back from current controversies, and use history to reflect on the broader question of how nerds should behave when their penchant for speaking unpopular truths collides head-on with their desire to be kind and decent and charitable, and to be judged as such by their culture. I was gratified to get positive feedback about this approach from men and women all over the ideological spectrum. However, a few people who I like and respect accused me of “dogwhistling.” They warned, in particular, that if I wouldn’t just come out and say what I thought about the James Damore Google memo thing, then people would assume the very worst—even though, of course, my friends themselves knew better. So in this post, I’ll come out and say what I think. But first, I’ll do something even better: I’ll hand the podium over to two friends, Sarah Constantin and Stacey Jeffery, both of whom were kind enough to email me detailed thoughts in response to my Kolmogorov post.
Matthew knew the deal when he joined his department: 10 years of work, and then you have to apply for tenure. “But,” he told me, “nobody talks about, ‘What if I run out of money beforehand?’”
We’ve really got to reorganize how research is done in this country. The brain drain is destroying our tremendous lead in basic research.Syndicated copies to:
I’m now so many wonderful episodes in, that it was far past time to give something back to Jeremy for the hours of work he’s put in to give me so much entertainment, enjoyment, and even knowledge. So I just made a pledge to support him on Patreon.
If you haven’t been paying attention, Eat This Podcast is a fantastic series on food, but it it uses the “foods we eat to examine and shed light on the lives we lead, from authenticity to zoology”. Food becomes his “vehicle to explore the byways of taste, economics and trade, culture, science, history, archaeology, geography and just about anything else.”
It’s unlike much of anything I’ve seen or followed in the food space for some time. As someone who is a fan of the science of food and fantastic writers like Harold McGee, Herve This, Alton Brown, Tom Standage, Michael Pollan, Nathan Myhrvold, Maxime Bilet, Matt Gross, and Michael Ruhlman (to name only a few), Eat This Podcast is now a must listen for me.
Not only are the episodes always interesting and unique, they’re phenomenally well researched and produced. You’d think he had a massive staff and production support at the level of a news organization like NPR. By way of mentioning NPR, I wanted to highlight the thought, care, and skill he puts into not only the stunning audio quality, but into the selection of underlying photos, musical bumpers, and the links to additional resources he finds along the way.
And if my recommendation isn’t enough, then perhaps knowing that this one person effort has been nominated for the James Beard Award in both 2015 and 2016 may tip the scales?
If you haven’t listened to any of them yet, I highly recommend you take a peek at what he has to offer. You can subscribe, download, and listen to them all for free. If you’re so inclined, I hope you’ll follow my lead and make a pledge to support his work on Patreon as well.
New discoveries about the human mind show the limitations of reason.
… and they’ve got help.
The New York Times bestselling winner of the 2016 James Beard Award for General Cooking and the IACP Cookbook of the Year Award. A grand tour of the science of cooking explored through popular American dishes, illustrated in full color. Ever wondered how to pan-fry a steak with a charred crust and an interior that's perfectly medium-rare from edge to edge when you cut into it? How to make homemade mac 'n' cheese that is as satisfyingly gooey and velvety-smooth as the blue box stuff, but far tastier? How to roast a succulent, moist turkey (forget about brining!)―and use a foolproof method that works every time? As Serious Eats's culinary nerd-in-residence, J. Kenji López-Alt has pondered all these questions and more. In The Food Lab, Kenji focuses on the science behind beloved American dishes, delving into the interactions between heat, energy, and molecules that create great food. Kenji shows that often, conventional methods don’t work that well, and home cooks can achieve far better results using new―but simple―techniques. In hundreds of easy-to-make recipes with over 1,000 full-color images, you will find out how to make foolproof Hollandaise sauce in just two minutes, how to transform one simple tomato sauce into a half dozen dishes, how to make the crispiest, creamiest potato casserole ever conceived, and much more.
Went on vacation or fell asleep at the internet wheel this week? Here’s some of the interesting stuff you missed.
An exclusive look at data from the controversial web site Sci-Hub reveals that the whole world, both poor and rich, is reading pirated research papers.
Sci Hub has been in the news quite a bit over the past half a year and the bookmarked article here gives some interesting statistics. I’ll preface some of the following editorial critique with the fact that I love John Bohannon’s work; I’m glad he’s spent the time to do the research he has. Most of the rest of the critique is aimed at the publishing industry itself.
From a journalistic standpoint, I find it disingenuous that the article didn’t actually hyperlink to Sci Hub. Neither did it link out (or provide a full quote) to Alicia Wise’s Twitter post(s) nor link to her rebuttal list of 20 ways to access their content freely or inexpensively. Of course both of these are editorial related, and perhaps the rebuttal was so flimsy as to be unworthy of a link from such an esteemed publication anyway.
Sadly, Elsevier’s list of 20 ways of free/inexpensive access doesn’t really provide any simple coverage for graduate students or researchers in poorer countries which are the likeliest group of people using Sci Hub, unless they’re going to fraudulently claim they’re part of a class which they’re not, and is this morally any better than the original theft method? It’s almost assuredly never used by patients, which seem to be covered under one of the options, as the option to do so is painfully undiscoverable past their typical $30/paper firewalls. Their patchwork hodgepodge of free access is so difficult to not only discern, but one must keep in mind that this is just one of dozens of publishers a researcher must navigate to find the one thing they’re looking for right now (not to mention the thousands of times they need to do this throughout a year, much less a career).
Consider this experiment, which could be a good follow up to the article: is it easier to find and download a paper by title/author/DOI via Sci Hub (a minute) versus through any of the other publishers’ platforms with a university subscription (several minutes) or without a subscription (an hour or more to days)? Just consider the time it would take to dig up every one of 30 references in an average journal article: maybe just a half an hour via Sci Hub versus the days and/or weeks it would take to jump through the multiple hoops to first discover, read about, and then gain access and then download them from the over 14 providers (and this presumes the others provide some type of “access” like Elsevier).
Those who lived through the Napster revolution in music will realize that the dead simplicity of their system is primarily what helped kill the music business compared to the ecosystem that exists now with easy access through the multiple streaming sites (Spotify, Pandora, etc.) or inexpensive paid options like (iTunes). If the publishing business doesn’t want to get completely killed, they’re going to need to create the iTunes of academia. I suspect they’ll have internal bean-counters watching the percentage of the total (now apparently 5%) and will probably only do something before it passes a much larger threshold, though I imagine that they’re really hoping that the number stays stable which signals that they’re not really concerned. They’re far more likely to continue to maintain their status quo practices.
Some of this ease-of-access argument is truly borne out by the statistics of open access papers which are downloaded by Sci Hub–it’s simply easier to both find and download them that way compared to traditional methods; there’s one simple pathway for both discovery and download. Surely the publishers, without colluding, could come up with a standardized method or protocol for finding and accessing their material cheaply and easily?
“Hart-Davidson obtained more than 100 years of biology papers the hard way—legally with the help of the publishers. ‘It took an entire year just to get permission,’ says Thomas Padilla, the MSU librarian who did the negotiating.” John Bohannon in Who’s downloading pirated papers? Everyone
Personally, I use use relatively advanced tools like LibX, which happens to be offered by my institution and which I feel isn’t very well known, and it still takes me longer to find and download a paper than it would via Sci Hub. God forbid if some enterprising hacker were to create a LibX community version for Sci Hub. Come to think of it, why haven’t any of the dozens of publishers built and supported simple tools like LibX which make their content easy to access? If we consider the analogy of academic papers to the introduction of machine guns in World War I, why should modern researchers still be using single-load rifles against an enemy that has access to nuclear weaponry?
My last thought here comes on the heels of the two tweets from Alicia Wise mentioned, but not shown in the article:
— Alicia Wise (@wisealic) March 14, 2016
— Alicia Wise (@wisealic) March 14, 2016
She mentions that the New York Times charges more than Elsevier does for a full subscription. This is tremendously disingenuous as Elsevier is but one of dozens of publishers for which one would have to subscribe to have access to the full panoply of material researchers are typically looking for. Further, Elsevier nor their competitors are making their material as easy to find and access as the New York Times does. Neither do they discount access to the point that they attempt to find the subscription point that their users find financially acceptable. Case in point: while I often read the New York Times, I rarely go over their monthly limit of articles to need any type of paid subscription. Solely because they made me an interesting offer to subscribe for 8 weeks for 99 cents, I took them up on it and renewed that deal for another subsequent 8 weeks. Not finding it worth the full $35/month price point I attempted to cancel. I had to cancel the subscription via phone, but why? The NYT customer rep made me no less than 5 different offers at ever decreasing price points–including the 99 cents for 8 weeks which I had been getting!!–to try to keep my subscription. Elsevier, nor any of their competitors has ever tried (much less so hard) to earn my business. (I’ll further posit that it’s because it’s easier to fleece at the institutional level with bulk negotiation, a model not too dissimilar to the textbook business pressuring professors on textbook adoption rather than trying to sell directly the end consumer–the student, which I’ve written about before.)
(Trigger alert: Apophasis to come) And none of this is to mention the quality control that is (or isn’t) put into the journals or papers themselves. Fortunately one need’t even go further than Bohannon’s other writings like Who’s Afraid of Peer Review? Then there are the hordes of articles on poor research design and misuse of statistical analysis and inability to repeat experiments. Not to give them any ideas, but lately it seems like Elsevier buying the Enquirer and charging $30 per article might not be a bad business decision. Maybe they just don’t want to play second-banana to TMZ?
Interestingly there’s a survey at the end of the article which indicates some additional sources of academic copyright infringement. I do have to wonder how the data for the survey will be used? There’s always the possibility that logged in users will be indicating they’re circumventing copyright and opening themselves up to litigation.
I also found the concept of using the massive data store as a means of applied corpus linguistics for science an entertaining proposition. This type of research could mean great things for science communication in general. I have heard of people attempting to do such meta-analysis to guide the purchase of potential intellectual property for patent trolling as well.
Finally, for those who haven’t done it (ever or recently), I’ll recommend that it’s certainly well worth their time and energy to attend one or more of the many 30-60 minute sessions most academic libraries offer at the beginning of their academic terms to train library users on research tools and methods. You’ll save yourself a huge amount of time.Syndicated copies to:
As it was published, I had read Kevin Hartnett’s article and interview with Christoph Adami The Information Theory of Life in Quanta Magazine. I recently revisited it and read through the commentary and stumbled upon an interesting quote relating to the history of information in biology:
These two historical references predate Claude Shannon’s mathematical formalization of information in A Mathematical Theory of Communication (The Bell System Technical Journal, 1948) and even Erwin Schrödinger‘s lecture (1943) and subsequent book What is Life (1944).
For those interested in reading more on this historical tidbit, I’ve dug up a copy of the primary Forsdyke reference which first appeared on arXiv (prior to its ultimate publication in History of Psychiatry [.pdf]):
🔖 [1406.1391] ‘A Vehicle of Symbols and Nothing More.’ George Romanes, Theory of Mind, Information, and Samuel Butler by Donald R. Forsdyke 
Submitted on 4 Jun 2014 (v1), last revised 13 Nov 2014 (this version, v2)
Abstract: Today’s ‘theory of mind’ (ToM) concept is rooted in the distinction of nineteenth century philosopher William Clifford between ‘objects’ that can be directly perceived, and ‘ejects,’ such as the mind of another person, which are inferred from one’s subjective knowledge of one’s own mind. A founder, with Charles Darwin, of the discipline of comparative psychology, George Romanes considered the minds of animals as ejects, an idea that could be generalized to ‘society as eject’ and, ultimately, ‘the world as an eject’ – mind in the universe. Yet, Romanes and Clifford only vaguely connected mind with the abstraction we call ‘information,’ which needs ‘a vehicle of symbols’ – a material transporting medium. However, Samuel Butler was able to address, in informational terms depleted of theological trappings, both organic evolution and mind in the universe. This view harmonizes with insights arising from modern DNA research, the relative immortality of ‘selfish’ genes, and some startling recent developments in brain research.
Comments: Accepted for publication in History of Psychiatry. 31 pages including 3 footnotes. Based on a lecture given at Santa Clara University, February 28th 2014, at a Bannan Institute Symposium on ‘Science and Seeking: Rethinking the God Question in the Lab, Cosmos, and Classroom.’
The original arXiv article also referenced two lectures which are appended below:
[Original Draft of this was written on December 14, 2015.]
This has to be the best article of the entire year: “No, It’s Not Your Opinion. You’re Just Wrong.”
It also not coincidentally is the root of the vast majority of the problems the world is currently facing. There are so many great quotes here, I can’t pick a favorite, so I’ll highlight the same one Kimb Quark did that brought my attention to it:
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Previously, I had made a large and somewhat random list of books which lie in the intersection of the application of information theory, physics, and engineering practice to the area of biology. Below I’ll begin to do a somewhat better job of providing a finer gradation of technical level for both the hobbyist or the aspiring student who wishes to bring themselves to a higher level of understanding of these areas. In future posts, I’ll try to begin classifying other texts into graduated strata as well. The final list will be maintained here: Books at the Intersection of Information Theory and Biology.
These books are written on a generally non-technical level and give a broad overview of their topics with occasional forays into interesting or intriguing subtopics. They include little, if any, mathematical equations or conceptualization. Typically, any high school student should be able to read, follow, and understand the broad concepts behind these books. Though often non-technical, these texts can give some useful insight into the topics at hand, even for the most advanced researchers.
Possibly one of the best places to start, this text gives a great overview of most of the major areas of study related to these fields.
One of the best books on the concept of entropy out there. It can be read even by middle school students with no exposure to algebra and does a fantastic job of laying out the conceptualization of how entropy underlies large areas of the broader subject. Even those with Ph.D.’s in statistical thermodynamics can gain something useful from this lovely volume.
A relatively recent popular science volume covering various conceptualizations of what information is and how it’s been dealt with in science and engineering. Though it has its flaws, its certainly a good introduction to the beginner, particularly with regard to history.
One of the most influential pieces of writing known to man, this classical text is the basis from which major strides in biology have been made as a result. A must read for everyone on the planet.
The four books above have a significant amount of overlap. Though one could read all of them, I recommend that those pressed for time choose Ben-Naim first. As I write this I’ll note that Ben-Naim’s book is scheduled for release on May 30, 2015, but he’s been kind enough to allow me to read an advance copy while it was in process; it gets my highest recommendation in its class. Loewenstein covers a bit more than Avery who also has a more basic presentation. Most who continue with the subject will later come across Yockey’s Information Theory and Molecular Biology which is similar to his text here but written at a slightly higher level of sophistication. Those who finish at this level of sophistication might want to try Yockey third instead.
In the coming weeks/months, I’ll try to continue putting recommended books on the remainder of the rest of the spectrum, the balance of which follows in outline form below. As always, I welcome suggestions and recommendations based on others’ experiences as well. If you’d like to suggest additional resources in any of the sections below, please do so via our suggestion box. For those interested in additional resources, please take a look at the ITBio Resources page which includes information about related research groups; references and journal articles; academic, research institutes, societies, groups, and organizations; and conferences, workshops, and symposia.
These books are written at a level that can be grasped and understood by most with a freshmen or sophomore university level. Coursework in math, science, and engineering will usually presume knowledge of calculus, basic probability theory, introductory physics, chemistry, and basic biology.
These books are written at a level that can be grasped and understood by those at a junior or senor university level. Coursework in math, science, and engineering may presume knowledge of probability theory, differential equations, linear algebra, complex analysis, abstract algebra, signal processing, organic chemistry, molecular biology, evolutionary theory, thermodynamics, advanced physics, and basic information theory.
These books are written at a level that can be grasped and understood by most working at the level of a master’s level at most universities. Coursework presumes all the previously mentioned classes, though may require a higher level of sub-specialization in one or more areas of mathematics, physics, biology, or engineering practice. Because of the depth and breadth of disciplines covered here, many may feel the need to delve into areas outside of their particular specialization.Syndicated copies to: