Notes, Highlights, and Marginalia: From E-books to Online

Notes on an outlined workflow for sharing notes, highlights, and annotations from ebooks online.

For several years now, I’ve been meaning to do something more interesting with the notes, highlights, and marginalia from the various books I read. In particular, I’ve specifically been meaning to do it for the non-fiction I read for research, and even more so for e-books, which tend to have slightly more extract-able notes given their electronic nature. This fits in to the way in which I use this site as a commonplace book as well as the IndieWeb philosophy to own all of one’s own data.[1]

Over the past month or so, I’ve been experimenting with some fiction to see what works and what doesn’t in terms of a workflow for status updates around reading books, writing book reviews, and then extracting and depositing notes, highlights, and marginalia online. I’ve now got a relatively quick and painless workflow for exporting the book related data from my Amazon Kindle and importing it into the site with some modest markup and CSS for display. I’m sure the workflow will continue to evolve (and further automate) somewhat over the coming months, but I’m reasonably happy with where things stand.

The fact that the Amazon Kindle allows for relatively easy highlighting and annotation in e-books is excellent, but having the ability to sync to a laptop and do a one click export of all of that data, is incredibly helpful. Adding some simple CSS to the pre-formatted output gives me a reasonable base upon which to build for future writing/thinking about the material. In experimenting, I’m also coming to realize that simply owning the data isn’t enough, but now I’m driven to help make that data more directly useful to me and potentially to others.

As part of my experimenting, I’ve just uploaded some notes, highlights, and annotations for David Christian’s excellent text Maps of Time: An Introduction to Big History[2] which I read back in 2011/12. While I’ve read several of the references which I marked up in that text, I’ll have to continue evolving a workflow for doing all the related follow up (and further thinking and writing) on the reading I’ve done in the past.

I’m still reminded me of Rick Kurtzman’s sage advice to me when I was a young pisher at CAA in 1999: “If you read a script and don’t tell anyone about it, you shouldn’t have wasted the time having read it in the first place.” His point was that if you don’t try to pass along the knowledge you found by reading, you may as well give up. Even if the thing was terrible, at least say that as a minimum. In a digitally connected era, we no longer need to rely on nearly illegible scrawl in the margins to pollinate the world at a snail’s pace.[4] Take those notes, marginalia, highlights, and meta data and release it into the world. The fact that this dovetails perfectly with Cesar Hidalgo’s thesis in Why Information Grows: The Evolution of Order, from Atoms to Economies,[3] furthers my belief in having a better process for what I’m attempting here.

Hopefully in the coming months, I’ll be able to add similar data to several other books I’ve read and reviewed here on the site.

If anyone has any thoughts, tips, tricks for creating/automating this type of workflow/presentation, I’d love to hear them in the comments!


“Own your data,” IndieWeb. [Online]. Available: [Accessed: 24-Oct-2016]
D. Christian and W. McNeill H., Maps of Time: An Introduction to Big History, 2nd ed. University of California Press, 2011.
C. Hidalgo, Why Information Grows: The Evolution of Order, from Atoms to Economies, 1st ed. Basic Books, 2015.
O. Gingerich, The Book Nobody Read: Chasing the Revolutions of Nicolaus Copernicus. Bloomsbury Publishing USA, 2004.
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Transplantation of spinal cord–derived neural stem cells for ALS

Transplantation of spinal cord–derived neural stem cells for ALS (
Analysis of phase 1 and 2 trials testing the safety of spinal cord transplantation of human stem cells in patients with amyotrophic lateral sclerosis (ALS) with escalating doses and expansion of the trial to multiple clinical centers.

I built the microinjectors used in these experiments for injecting stem cells into the first human patients.

CNN also has a general interest article talking about some of the results.

Links to some earlier articles:

Transplantation of spinal cord–derived neural stem cells for ALS

Analysis of phase 1 and 2 trials

Authors: Jonathan D. Glass, MD; Vicki S. Hertzberg, PhD; Nicholas M. Boulis, MD; Jonathan Riley, MD; Thais Federici, PhD; Meraida Polak, RN; Jane Bordeau, RN; Christina Fournier, MD; Karl Johe, PhD; Tom Hazel, PhD; Merit Cudkowicz, MD; Nazem Atassi, MD; Lawrence F. Borges, MD; Seward B. Rutkove, MD; Jayna Duell, RN; Parag G. Patil, MD; Stephen A. Goutman, MD; Eva L. Feldman, MD, PhD


Objective: To test the safety of spinal cord transplantation of human stem cells in patients with amyotrophic lateral sclerosis (ALS) with escalating doses and expansion of the trial to multiple clinical centers.

Methods: This open-label trial included 15 participants at 3 academic centers divided into 5 treatment groups receiving increasing doses of stem cells by increasing numbers of cells/injection and increasing numbers of injections. All participants received bilateral injections into the cervical spinal cord (C3-C5). The final group received injections into both the lumbar (L2-L4) and cervical cord through 2 separate surgical procedures. Participants were assessed for adverse events and progression of disease, as measured by the ALS Functional Rating Scale–Revised, forced vital capacity, and quantitative measures of strength. Statistical analysis focused on the slopes of decline of these phase 2 trial participants alone or in combination with the phase 1 participants (previously reported), comparing these groups to 3 separate historical control groups.

Results: Adverse events were mostly related to transient pain associated with surgery and to side effects of immunosuppressant medications. There was one incident of acute postoperative deterioration in neurologic function and another incident of a central pain syndrome. We could not discern differences in surgical outcomes between surgeons. Comparisons of the slopes of decline with the 3 separate historical control groups showed no differences in mean rates of progression.

Conclusions: Intraspinal transplantation of human spinal cord–derived neural stem cells can be safely accomplished at high doses, including successive lumbar and cervical procedures. The procedure can be expanded safely to multiple surgical centers.

Classification of evidence: This study provides Class IV evidence that for patients with ALS, spinal cord transplantation of human stem cells can be safely accomplished and does not accelerate the progression of the disease. This study lacks the precision to exclude important benefit or safety issues.

Source: Transplantation of spinal cord–derived neural stem cells for ALS

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Ten Simple Rules for Taking Advantage of Git and GitHub

Ten Simple Rules for Taking Advantage of Git and GitHub by Yasset Perez-Riverol , Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno (
Bioinformatics is a broad discipline in which one common denominator is the need to produce and/or use software that can be applied to biological data in different contexts. To enable and ensure the replicability and traceability of scientific claims, it is essential that the scientific publication, the corresponding datasets, and the data analysis are made publicly available [1,2]. All software used for the analysis should be either carefully documented (e.g., for commercial software) or, better yet, openly shared and directly accessible to others [3,4]. The rise of openly available software and source code alongside concomitant collaborative development is facilitated by the existence of several code repository services such as SourceForge, Bitbucket, GitLab, and GitHub, among others. These resources are also essential for collaborative software projects because they enable the organization and sharing of programming tasks between different remote contributors. Here, we introduce the main features of GitHub, a popular web-based platform that offers a free and integrated environment for hosting the source code, documentation, and project-related web content for open-source projects. GitHub also offers paid plans for private repositories (see Box 1) for individuals and businesses as well as free plans including private repositories for research and educational use.
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A new plugin helps to improve annotations on the internet

Last night I saw two great little articles about, a web-based annotation engine, written by a proponent of the IndieWeb: as a public research notebook Aggregator ― a WordPress plugin

As a researcher, I fully appreciate the pro-commonplace book conceptualization of the first post, and the second takes things amazingly further with a plugin that allows one to easily display one’s annotations on one’s own WordPress-based site in a dead-simple fashion.

This functionality is a great first step, though honestly, in keeping with IndieWeb principles of owning one’s own data, I think it would be easier/better if both accepted and sent webmentions. This would potentially allow me to physically own the data on my own site while still participating in the larger annotation community as well as give me notifications when someone either comments or augments on one of my annotations or even annotates one of my own pages (bits of which I’ve written about before.)

Either way, kudos to Kris Shaffer for moving the ball forward!


My Notebook

The plugin mentioned in the second article allows me to keep a running online “notebook” of all of my annotations on my own site.

My IndieWeb annotations

I can also easily embed my recent annotations about the IndieWeb below:

[ hypothesis user = 'chrisaldrich' tags = 'indieweb']

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Some Thoughts on Academic Publishing and “Who’s downloading pirated papers? Everyone” from Science | AAAS

Who's downloading pirated papers? Everyone by John Bohannon (Science | AAAS)
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:

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.

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How can we be sure old books were ever read? – University of Glasgow Library

How can we be sure old books were ever read? by Robert MacLean (University of Glasgow Library)
Owning a book isn’t the same as reading it; we need only look at our own bloated bookshelves for confirmation.

This is a great little overview for people reading the books of others. There are also lots of great links to other resources.

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Thoughts on “Some academics remain skeptical of” | University Affairs

Some academics remain skeptical of by Shawna Wagman (University Affairs)
They warn scholars to €œthink twice€ before sharing their work on the popular social network.

This morning I ran across a tweet from colleague Andrew Eckford:

His response was probably innocuous enough, but I thought the article should be put to task a bit more.

“35 million academics, independent scholars and graduate students as users, who collectively have uploaded some eight million texts”

35 million users is an okay number, but their engagement must be spectacularly bad if only 8 million texts are available. How many researchers do you know who’ve published only a quarter of an article anywhere, much less gotten tenure?

“the platform essentially bans access for academics who, for whatever reason, don’t have an account. It also shuts out non-academics.”

They must have changed this, as pretty much anyone with an email address (including non-academics) can create a free account and use the system. I’m fairly certain that the platform was always open to the public from the start, but the article doesn’t seem to question the statement at all. If we want to argue about shutting out non-academics or even academics in poorer countries, let’s instead take a look at “big publishing” and their $30+/paper paywalls and publishing models, shall we?

“I don’t trust”

Given his following discussion, I can only imagine what he thinks of big publishers in academia and that debate.

“McGill’s Dr. Sterne calls it “the gamification of research,”

Most research is too expensive to really gamify in such a simple manner. Many researchers are publishing to either get or keep their jobs and don’t have much time, information, or knowledge to try to game their reach in these ways. And if anything, the institutionalization of “publish or perish” has already accomplished far more “gamification”, is just helping to increase the reach of the publication. Given that research shows that most published research isn’t even read, much less cited, how bad can really be? [Cross reference: Reframing What Academic Freedom Means in the Digital Age]

If we look at Twitter and the blogging world as an analogy with and researchers, Twitter had a huge ramp up starting in 2008 and helped bloggers obtain eyeballs/readers, but where is it now? Twitter, even with a reasonable business plan is stagnant with growing grumblings that it may be failing. I suspect that without significant changes that (which is a much smaller niche audience than Twitter) will also eventually fall by the wayside.

The article rails against not knowing what the business model is or what’s happening with the data. I suspect that the platform itself doesn’t have a very solid business plan and they don’t know what to do with the data themselves except tout the numbers. I’d suspect they’re trying to build “critical mass” so that they can cash out by selling to one of the big publishers like Elsevier, who might actually be able to use such data. But this presupposes that they’re generating enough data; my guess is that they’re not. And on that subject, from a journalistic viewpoint, where’s the comparison to the rest of the competition including or, which in fact was purchased by Elsevier? As it stands, this simply looks like a “hit piece” on, and sadly not a very well researched or reasoned one.

In sum, the article sounds to me like a bunch of Luddites running around yelling “fire”, particularly when I’d imagine that most referred to in the piece feed into the more corporate side of publishing in major journals rather than publishing it themselves on their own websites. I’d further suspect they’re probably not even practicing academic samizdat. It feels to me like the author and some of those quoted aren’t actively participating in the social media space to be able to comment on it intelligently. If the paper wants to pick at the academy in this manner, why don’t they write an exposé on the fact that most academics still have websites that look like they’re from 1995 (if, in fact, they have anything beyond their University’s mandated business card placeholder) when there are a wealth of free and simple tools they could use? Let’s at least build a cart before we start whipping the horse.

For academics who really want to spend some time and thought on a potential solution to all of this, I’ll suggest that they start out by owning their own domain and own their own data and work. The #IndieWeb movement certainly has an interesting philosophy that’s a great start in fixing the problem; it can be found at

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Dr. Michael Miller Math Class Hints and Tips | UCLA Extension

An informal orientation for those taking math classes from Dr. Michael Miller through UCLA Extension.

Congratulations on your new math class, and welcome to the “family”!

Beginners Welcome!

Invariably the handful of new students every year eventually figure the logistics of campus out, but it’s easier and more fun to know some of the options available before you’re comfortable halfway through the class. To help get you over the initial hump, I’ll share a few of the common questions and tips to help get you oriented. Others are welcome to add comments and suggestions below. If you have any questions, feel free to ask anyone in the class, we’re all happy to help.

First things first, for those who’ve never visited UCLA before, here’s a map of campus to help you orient yourself. Using the Waze app on your smartphone can also be incredibly helpful in getting to campus more quickly through the tail end of rush hour traffic.

Whether you’re a professional mathematician, engineer, physicist, physician, or even a hobbyist interested in mathematics you’ll be sure to get something interesting out of Dr. Miller’s math courses, not to mention the camaraderie of 20-30 other “regulars” with widely varying backgrounds (from actors to surgeons and evolutionary theorists to engineers) who’ve been taking almost everything Mike has offered over the years (and yes, he’s THAT good — we’re sure you’ll be addicted too.) Whether you’ve been away from serious math for decades or use it every day or even if you’ve never gone past Calculus or Linear Algebra, this is bound to be the most entertaining thing you can do with your Tuesday nights in the Autumn and Winter. If you’re not sure what you’re getting into (or are scared a bit by the course description), I highly encourage to come and join us for at least the first class before you pass up on the opportunity. I’ll mention that the greater majority of new students to Mike’s classes join the ever-growing group of regulars who take almost everything he teaches subsequently.

Don’t be intimidated if you feel like everyone in the class knows each other fairly well — most of us do. Dr. Miller and mathematics can be addictive so many of us have been taking classes from him for 5-20+ years, and over time we’ve come to know each other.

Tone of Class

If you’ve never been to one of Dr. Miller’s classes before, they’re fairly informal and he’s very open to questions from those who don’t understand any of the concepts or follow his reasoning. He’s a retired mathematician from RAND and long-time math professor at UCLA. Students run the gamut from the very serious who read multiple textbooks and do every homework problem to hobbyists who enjoy listening to the lectures and don’t take the class for a grade of any sort (and nearly every stripe in between). He’ll often recommend a textbook that he intends to follow, but it’s never been a “requirement” and more often that not, the bookstore doesn’t list or carry his textbook until the week before class. (Class insiders will usually find out about the book months before class and post it to the Google Group – see below).

His class notes are more than sufficient for making it through the class and doing the assigned (optional) homework. He typically hands out homework in handout form, so the textbook is rarely, if ever, required to make it through the class. Many students will often be seen reading various other texts relating to the topic at hand as they desire. Usually he’ll spend an 45-60 minutes at the opening of each class after the first to go over homework problems or questions that anyone has.

For those taking the class for a grade or pass/fail, his usual policy is to assign a take home problem set around week 9 or 10 to be handed in at the penultimate class. [As a caveat, make sure you check his current policy on grading as things may change, but the preceding has been the usual policy for a decade or more.]

Parking Options

Lot 9 – Located at the northern terminus of Westwood Boulevard, one can purchase a parking pass for about $12 a day at the kiosk in the middle of the street just before Westwood Blvd. ends. The kiosk is also conveniently located right next to the parking structure. If there’s a basketball game or some other major event, Lot 8 is just across the street as well, though it’s just a tad further away from the Math Sciences Building. Since more of the class uses this as their parking structure of choice, there is always a fairly large group walking back there after class for the more security conscious.

Lot 2 – Located off of Hilgard Avenue, this is another common option for easy parking as well. While fairly close to class, not as many use it as it’s on the quieter/darker side of campus and can be a bit more of a security issue for the reticent.

Tip: For those opting for on-campus parking, one can usually purchase a quarter-long parking pass for a small discount at the beginning of the term.

Westwood Village and Neighborhood – Those looking for less expensive options street parking is available in the surrounding community, but use care to check signs and parking meters as you assuredly will get a ticket. Most meters in the surrounding neighborhoods end at either 6pm or 8pm making parking virtually free (assuming you’re willing to circle the neighborhood to find one of the few open spots.)

There are a huge variety of lots available in the Village for a range of prices, but the two most common, inexpensive, and closer options seem to be:

  • Broxton Avenue Public Parking at 1036 Broxton Avenue just across from the Fox Village and Bruin Theaters – $3 for entering after 6pm / $9 max for the day
  • Geffen Playhouse Parking at 10928 Le Conte Ave. between Broxton and Westwood – price varies based on the time of day and potential events (screenings/plays in Westwood Village) but is usually $5 in the afternoon and throughout the evening

Dining Options

More often than not a group of between 4 and 15 students will get together every evening before class for a quick bit to eat and to catch up and chat. This has always been an informal group and anyone from class is more than welcome to join. Typically we’ll all meet in the main dining hall of Ackerman Union (Terrace Foodcourt, Ackerman Level 1) between 6 and 6:30 (some with longer commutes will arrive as early as 3-4pm, but this can vary) and dine until about 6:55pm at which time we walk over to class.

The food options on Ackerman Level 1 include Panda Express, Rubio’s Tacos, Sbarro, Wolfgang Puck, and Greenhouse along with some snack options including Wetzel’s Pretzels and a candy store. One level down on Ackerman A-level is a Taco Bell, Carl’s Jr., Jamba Juice, Kikka, Buzz, and Curbside, though one could get takeout and meet the rest of the “gang” upstairs.

There are also a number of other on-campus options as well though many are a reasonable hike from the class location. The second-closest to class is the Court of Sciences Student Center with a Subway, Yoshinoya, Bombshelter Bistro, and Fusion.

Naturally, for those walking up from Westwood Village, there are additional fast food options like In-N-Out, Chick-fil-A, Subway, and many others.

Killing Time

For those who’ve already eaten or aren’t hungry, you’ll often find one or more of us browsing the math and science sections of the campus bookstore on the ground level of Ackerman Union to kill time before class. Otherwise there are usually a handful of us who arrive a half an hour early and camp out in the classroom itself (though this can often be dauntingly quiet as most use the chance to catch up on reading here.) If you arrive really early, there are a number of libraries and study places on campus. Boelter Hall has a nice math/science library on the 8th Floor.

Mid-class Break Options

Usually about halfway through class we’ll take a 10-12 minute coffee break. For those with a caffeine habit or snacking urges, there are a few options:

Kerckhoff Hall Coffee Shop is just a building or two over and is open late as snack stop and study location. They offer coffee and various beverages as well as snacks, bagels, pastries, and ice cream. Usually 5-10 people will wander over as a group to pick up something quick.

The Math Sciences Breezeway, just outside of class, has a variety of soda, coffee, and vending machines with a range of beverages and snacks. Just a short walk around the corner will reveal another bank of vending machines if your vice isn’t covered. The majority of class will congregate in the breezeway to chat informally during the break.

The Court of Sciences Student Center, a four minute walk South, with the restaurant options noted above if you need something quick and more substantial, though few students use this option at the break.

Bathrooms – The closest bathrooms to class are typically on the 5th floor of the Math Sciences Building. The women’s is just inside the breezeway doors and slightly to the left. The men’s rooms are a bit further and are either upstairs on the 6th floor (above the women’s), or a hike down the hall to the left and into Boelter hall. I’m sure the adventurous may find others, but take care not to get lost.

Informal Class Resources

Google Group

Over the years, as an informal resource, members of the class have created and joined a private Google Group (essentially an email list-serv) to share thoughts, ideas, events, and ask questions of each other. There are over 50 people in the group, most of whom are past Miller students, though there are a few other various mathematicians, physicists, engineers, and even professors. You can request to join the private group to see the resources available there. We only ask that you keep things professional and civil and remember that replying to all reaches a fairly large group of friends. Browsing through past messages will give you an idea of the types of posts you can expect. The interface allows you to set your receipt preferences to one email per message posted, daily digest, weekly digest, or no email (you’re responsible for checking the web yourself), so be sure you have the setting you require as some messages are more timely than others. There are usually only 1-2 posts per week, so don’t expect to be inundated.

Study Groups

Depending on students’ moods, time requirements, and interests, we’ve arranged informal study groups for class through the Google Group above. Additionally, since Dr. Miller only teaches during the Fall and Winter quarters, some of us also take the opportunity to set up informal courses during the Spring/Summer depending on interests. In the past, we’ve informally studied Lie Groups, Quantum Mechanics, Algebraic Geometry, and Category Theory in smaller groups on the side.


As a class resource, some of us share a document repository via Dropbox. If you’d like access, please make a post to the Google Group.

Class Notes

Many people within the class use digital pens to capture not only the written notes but the audio discussion that occurred in class as well (the technology also links the two together to make it easier to jump around within a particular lecture). If it helps to have a copy of these notes, please let one of the users know you’d like them – we’re usually pretty happy to share. If you miss a class (sick, traveling, etc.) please let one of us know as the notes are so unique that it will be almost like you didn’t miss anything at all.

You can typically receive a link to the downloadable version of the notes in Livescribe’s Pencast .pdf format. This is a special .pdf file but it’s a bit larger in size because it has an embedded audio file in it that is playable with the more recent version of Adobe Reader X (or above) installed. (This means to get the most out of the file you have to download the file and open it in Reader X to get the audio portion. You can view the written portion in most clients, you’ll just be missing out on all the real fun and value of the full file.) With the notes, you should be able to toggle the settings in the file to read and listen to the notes almost as if you were attending the class live.

Viewing and Playing a Pencast PDF

Pencast PDF is a new format of notes and audio that can play in Adobe Reader X or above.

You can open a Pencast PDF as you would other PDF files in Adobe Reader X. The main difference is that a Pencast PDF can contain ink that has associated audio—called “active ink”. Click active ink to play its audio. This is just like playing a Pencast from Livescribe Online or in Livescribe Desktop. When you first view a notebook page, active ink appears in green type. When you click active ink, it turns gray and the audio starts playing. As audio playback continues, the gray ink turns green in synchronization with the audio. Non-active ink (ink without audio) is black and does not change appearance.

Audio Control Bar

Pencast PDFs have an audio control bar for playing, pausing, and stopping audio playback. The control bar also has jump controls, bookmarks (stars), and an audio timeline control.

Active Ink View Button

There is also an active ink view button. Click this button to toggle the “unwritten” color of active ink from gray to invisible. In the default (gray) setting, the gray words turn green as the audio plays. In the invisible setting, green words seem to write themselves on blank paper as the audio plays.


For those interested in past years’ topics, here’s the list I’ve been able to put together thus far:

Fall 2006: Complex Analysis
Winter 2007: Field Theory
Fall 2007: Algebraic Topology
Winter 2008: Integer Partitions
Fall 2008: Calculus on Manifolds
Winter 2009: Calculus on Manifolds: The Sequel
Fall 2009: Group Theory
Winter 2010: Galois Theory
Fall 2010: Differential Geometry
Winter 2011: Differential Geometry II
Fall 2011: p-Adic Analysis
Winter 2012: Group Representations
Fall 2012: Set Theory
Winter 2013: Functional Analysis
Fall 2013: Number Theory (Skipped)
Winter 2014: Measure Theory
Fall 2014: Introduction to Lie Groups and Lie Algebras Part I
Winter 2015: Introduction to Lie Groups and Lie Algebras Part II
Fall 2015: Algebraic Number Theory
Winter 2016: Algebraic Number Theory: The Sequel
Fall 2016: Introduction to Complex Analysis, Part I
Winter 2017: Introduction to Complex Analysis, Part II

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Is Flaxseed Oil The Ultimate Way to Season Cast Iron?

Quick literature review for seasoning cast iron for some pending research.

There are thousands of websites out there with details and instructions on how to properly season your cast iron cooking implements. Sadly, very few, if any, actually discuss the science behind what is going on or why one method is better than another. All of them typically reference dozens of oils and fats that should or shouldn’t be used with little or no justification for their choices other than the culinary equivalent of old wives tales.

Flaxseed Oil for Seasoning Cast Iron

About two seasonings ago, I had come across an interesting concept surrounding flaxseed oil and have always meant to try it, but wanted to do some tests and comparisons of my own.  After some research, I’ve found Sheryl Canter’s original article which now seems to be referenced by most serious food blogs and sites. I’ll try some tests with in the coming weeks and hopefully get around to reporting some of the results. Time to get the trusty microscope out for some photomicrography!

In the meanwhile, here are some links to what appear to be the forefront of material out there on the subject.

Supporting Ideas and Criticism:

Harold McGee on Cast Iron

The inimitable McGee has relatively little to say on the subject, so I’ll quote it briefly below:


Iron was a relatively late discovery because it exists in the earth’s crust primarily in the form of oxides, and had to be encountered in it’s pure form by accident, perhaps when a fire was built on an outcropping of ore. Iron artifacts have been found that date from 3000 BCE, though the Iron Age, when the metal came into regular use without replacing copper and bronze (a copper-tin alloy) in preeminence, is said to begin around 1200 BCE. Cast iron is alloyed with about 3% carbon to harden the metal, and also contains some silicon; carbon steel contains less carbon, and is heat-treated to obtain a less brittle, tougher alloy that can be formed into thinner pans.  The chief attractions of cast iron and carbon steel in kitchen work are their cheapness and safety.  Excess iron is readily eliminated from the body, and most people can actually benefit from additional dietary iron.  Their greatest disadvantage is a tendency to corrode, though this can be avoided by regular seasoning (below) and gentle cleaning. Like aluminum, iron and carbon steel can discolor foods. And iron turns out to be a poorer conductor of heat than copper or aluminum. But exactly for this reason, and because it’s denser than aluminum, a cast iron pan will absorb more heat and hold it longer than a similar aluminum pan. Thick cast iron pans provide steady, even heat.

“Seasoning” Cast Iron and Carbon Steel Cooks who appreciate cast iron and carbon steel pans improve their easily corroded surface by building up an artificial protective layer.  They “season” them by coating them with cooking oil and heating them for several hours. The oil penetrates into the pores and fissures of the metal, sealing it from the attack of air and water. And the combination of heat, metal, and air oxidizes the fatty acid chains and enourages them to bond to each other (“polymerize”) to form a dense, hard, dry layer (just as linseed and other “drying oils” do on wood and on painintgs).  Highly unsaturated oils — soy oil, corn oil — are expecially prone to oxidation and polymerizing. To avoid removing the protective oil layer, cooks carefully clean seasoned cast iron pans with mild soaps and dissolving abrassive like salt, rather than with detergents and scouring pads.

Harold McGee (1951- ), food science writer
in On Food and Cooking: The Science and Lore of the Kitchen (Scribner, revised edition 2004)

It’s almost immediately apparent that Canter was inspired to use flaxseed oil by the standard go-to reference which mentions “linseed and other ‘drying oils'”.  Since it’s somewhat illustrative of cast iron pans in general, though it doesn’t reference seasoning, I’ll also direct the reader to McGee’s article What’s Hot, What’s Not, in Pots and Pans (New York Times, October 7, 2008) as well as Dave Arnold’s article Heavy Metal: the Science of Cast Iron Cooking.

I’ll note that the Culinary Institute of America’s The Professional Chef (Wiley, 7th edition, 2001) only mentions cast iron in passing on page 91 and doesn’t even use the word seasoning. (There is a more recent 9th edition, which I don’t own, but I doubt it has additional information given the scant nature found in the 7th edition.) Similarly “Iron Chef” Alton Brown’s I’m Just Here for the Food (Stewart, Tabori & Chang, 2011) has some generally fine directions for the beginning chef interested in science, but it doesn’t go past either McGee or the bulk of the online blogs with the common wisdom for cast iron.

cast iorn pan
A well-seasoned (manteca) cast iron pan cooking hashbrowns

In the coming research, I’ll delve into some of the journal literature to see what else I come up with, though I expect that it will be scant at best and not much more than the often cited July 1986 study in the Journal of the American Dietetic Association which discusses iron leaching out of pans into food substances.

Anyone with serious thoughts and ideas in this area is encouraged to share them in the comments.


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Nicolas Perony: Puppies! Now that I’ve got your attention, complexity theory | TED

Animal behavior isn't complicated, but it is complex. Nicolas Perony studies how individual animals — be they Scottish Terriers, bats or meerkats — follow simple rules that, collectively, create larger patterns of behavior. And how this complexity born of simplicity can help them adapt to new circumstances, as they arise.

For those who are looking for a good, simple, and entertaining explanation of the concept of emergent properties and behavior within complexity theory (or Big History), I just came across a nice TED talk that simplifies complexity using a few animal examples including a cute puppy video as well as a bat and a meerkat example. The latter two also have implications for evolution and survival which are lovely examples as well.

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The Postdoctoral Experience (Revisited)

The Postdoctoral Experience Revisited (2014) (The National Academies Press)
The Postdoctoral Experience Revisited builds on the 2000 report Enhancing the Postdoctoral Experience for Scientists and Engineers. That ground-breaking report assessed the postdoctoral experience and provided principles, action points, and recommendations to enhance that experience. Since the publication of the 2000 report, the postdoctoral landscape has changed considerably. The percentage of PhDs who pursue postdoctoral training is growing steadily and spreading from the biomedical and physical sciences to engineering and the social sciences. The average length of time spent in postdoctoral positions seems to be increasing. The Postdoctoral Experience Revisited reexamines postdoctoral programs in the United States, focusing on how postdocs are being guided and managed, how institutional practices have changed, and what happens to postdocs after they complete their programs. This book explores important changes that have occurred in postdoctoral practices and the research ecosystem and assesses how well current practices meet the needs of these fledgling scientists and engineers and of the research enterprise. The Postdoctoral Experience Revisited takes a fresh look at current postdoctoral fellows - how many there are, where they are working, in what fields, and for how many years. This book makes recommendations to improve aspects of programs - postdoctoral period of service, title and role, career development, compensation and benefits, and mentoring. Current data on demographics, career aspirations, and career outcomes for postdocs are limited. This report makes the case for better data collection by research institution and data sharing. A larger goal of this study is not only to propose ways to make the postdoctoral system better for the postdoctoral researchers themselves but also to better understand the role that postdoctoral training plays in the research enterprise. It is also to ask whether there are alternative ways to satisfy some of the research and career development needs of postdoctoral researchers that are now being met with several years of advanced training. Postdoctoral researchers are the future of the research enterprise. The discussion and recommendations of The Postdoctoral Experience Revisited will stimulate action toward clarifying the role of postdoctoral researchers and improving their status and experience.

The National Academy of Sciences has published a (free) book: The Postdoctoral Experience (Revisited) discussing where we’re at and some ideas for a way forward.

Most might agree that our educational system is far less than ideal, but few pay attention to significant problems at the highest levels of academia which are holding back a great deal of our national “innovation machinery”. The National Academy of Sciences has published a (free) book: The Postdoctoral Experience (Revisited) discussing where we’re at and some ideas for a way forward. There are some interesting ideas here, but we’ve still got a long way to go.

Book cover of The Postdoctoral Experience Revisited (2014)
The Postdoctoral Experience Revisited (2014) | National Academies Press

Uri Alon: Why Truly Innovative Science Demands a Leap into the Unknown

I recently ran across this TED talk and felt compelled to share it. It really highlights some of my own personal thoughts on how science should be taught and done in the modern world.  It also overlaps much of the reading I’ve been doing lately on innovation and creativity. If these don’t get you to watch, then perhaps mentioning that Alon manages to apply comedy and improvisation techniques to science will.

Uri Alon was already one of my scientific heroes, but this adds a lovely garnish.



2014 Andrew J. Viterbi Distinguished Lecture in Communication: Abbas El Gamal

The USC Viterbi School has recently announced Professor Abbas El Gamal of Stanford University will present the 2014 Andrew J. Viterbi Distinguished Lecture in Communication. The 12th annual lecture entitled “Common Information” will be given on Thursday, April 17, 2014 at 4:00 PM at the University of Southern California in the Seeley Wintersmith Mudd Memorial Hall of Philosophy (MHP) room 101. A reception will precede the lecture at 3:00 PM.

USC’s Viterbi School of Engineering has provided the following abstract for the talk:

Entropy, introduced by Shannon in 1948, arises naturally as a universal measure of information in single-source compression, randomness extraction, and random number generation. In distributed systems, such as communication networks, multiprocessors, distributed storage, and sensor networks, there are multiple correlated sources to be processed jointly. The information that is common between these sources can be utilized, for example, to reduce the amount of communication needed for compression, computing, simulation, and secret key generation. My talk will focus on the question of how such common information should be measured. While our understanding of common information is far from complete, I will aim to demonstrate the richness of this question through the lens of network information theory. I will show that, depending on the distributed information processing task considered, there can be several well-motivated measures of common information. Along the way, I will present some of the key models, ideas, and tools of information theory, which invite further investigation into this intriguing subject. Some parts of this talk are based on recent joint work with Gowtham Kumar and Cheuk Ting Li and on discussions with Young-Han Kim.

Headshot of Abbas El GamalBiography: Abbas El Gamal is the Hitachi America Professor in the School of Engineering and Chair of the Department of Electrical Engineering at Stanford University. He received his Ph.D. degree in electrical engineering from Stanford University in 1978. He was an Assistant Professor in the Department of Electrical Engineering at the University of Southern California (USC) from 1978 to 1980. His research interests and contributions have spanned the areas of information theory, wireless networks, CMOS imaging sensors and systems, and integrated circuit design and design automation. He has authored or coauthored over 200 papers and 30 patents in these areas. He is coauthor of the book Network Information Theory (Cambridge Press 2011). He has won several honors and awards, including the 2012 Claude E. Shannon Award, and the 2004 Infocom best paper award. He is a member of the National Academy of Engineering and a Fellow of the IEEE. He has been active in several IEEE societies, including serving on the Board on Governors of the IT society where he is currently its President. He cofounded and/or served in various leadership roles at several semiconductor, EDA, and biotechnology companies.

Audiences: Everyone Is Invited

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Bill Davenhall at TEDMED 2009 on Geomedicine: How Your Environment May Affect Your Health

TEDMED 2009 on Geomedicine: How Your Environment May Affect Your Health by Bill Davenhall from TEDMED
Does where you live have an impact on your overhall health? Bill Davenhall believes that the location of our homes is critical to our medical history.


This is a great thing to think about the next time your doctor asks for your medical history. Perhaps with more data and a better visualization of it, it may bring home the messages of pollution and global warming.

The Decline Effect and the Scientific Method | The New Yorker

The Truth Wears Off: Is there something wrong with the scientific method? by Jonah Lehrer (The New Yorker)

Jonah Lehrer’s New Yorker article “The Truth Wears Off: Is there something wrong with the scientific method?” is an interesting must-read article. In it he discusses the “Decline Effect” and outlier statistical effects within scientific research.

Among other interesting observations in it, he calls attention to the fact that, “according to the journal Nature, a third of all studies never even get cited, let alone repeated.”

For scholars of Fisher, Popper, and Kuhn, some of this discussion won’t be quite so novel, but for anyone designing scientific experiments, the effects discussed here are certainly worthy of notice and further study and scrutiny.