Category: Science

👓 Welcome to Voldemorting, the Ultimate SEO Dis | Wired

Read Welcome to Voldemorting, the Ultimate SEO Dis by Gretchen McCulloch (WIRED)
When writers swap Trump for Cheeto and 45, it's not just a put-down. Removing a keyword is the anti-SEO—transforming your subject into a slippery, ungraspable, swarm.
Surprised she didn’t mention the phenomena of subtweeting, snitch tagging, or dunking which are also closely related to voldemorting.

To my experience, the phrase “bird site” was generally used as a derogatory phrase on Mastodon (represented by a Mastodon character instead of a bird), by people who were fed up by Twitter and the interactions they found there. I recall instances of it as early as April 2017.

In addition to potential SEO implications, this phenomenon is also interesting for its information theoretic implications.

I particularly like the reference in the van der Nagle paper

[…] screenshotting, or making content visible without sending its website traffic – to demonstrate users’ understandings of the algorithms that seek to connect individuals to other people, platforms, content and advertisers, and their efforts to wrest back control.

This seems like an awesome way to skirt around algorithms in social sites as well as not rewarding negative sites with clicks.

📕 Read pages 177-231 of 288 of Linked: The New Science Of Networks by Albert-László Barabási

📕 Read pages 177-231 of 288 to finish Linked: The New Science Of Networks by Albert-László Barabási

Some generally solid overview of the earlier days of network science. Barabasi is a pretty solid general science writer and makes most of his ideas relatively clear. I’m hoping this is a good intro to some of the background for his new textbook on network science.

While some pieces and ideas seem dated, this was generally enjoyable without getting too deep into the weeds. Naturally there are many sections that could stand for updates, even just a decade or more later.

Rating:

🔖 Collaborative Workshop for Women in Mathematical Biology | IPAM

Bookmarked Collaborative Workshop for Women in Mathematical Biology (IPAM)

June 17-21, 2019

This workshop will tackle a variety of biological and medical questions using mathematical models to understand complex system dynamics. Working in collaborative teams of 6, each with a senior research mentor, participants will spend a week making significant progress with a research project and foster innovation in the application of mathematical, statistical, and computational methods in the resolution of problems in the biosciences. By matching senior research mentors with junior mathematicians, the workshop will expand and support the community of scholars in mathematical biosciences. In addition to the modeling goals, an aim of this workshop is to foster research collaboration among women in mathematical biology. Results from the workshop will be published in a peer-reviewed volume, highlighting the contributions of the newly-formed groups. Previous workshops in this series have occurred at IMA, NIMBioS, and MBI.

This workshop will have a special format designed to facilitate effective collaborations.

  • Each senior group leader will present a problem and lead a research group.
  • Group leaders will work with a more junior co-leader, someone with whom they do not have a long-standing collaboration, but who has enough experience to take on a leadership role.
  • Additional team members will be chosen from applicants and invitees. We anticipate a total of five or six people per group.

It is expected that each group will continue to work on their project together after the workshop, and that they will submit results to the Proceedings volume for the workshop.

The benefit of such a structured program with leaders, projects and working groups planned in advance is based on the successful WIN, Women In Numbers, conferences and is intended to provide vertically integrated mentoring: senior women will meet, mentor, and collaborate with the brightest young women in their field on a part of their research agenda of their choosing, and junior women and graduate students will develop their network of colleagues and supporters and encounter important new research areas to work in, thereby fostering a successful research career. This workshop is partially supported by NSF-HRD 1500481 – AWM ADVANCE grant.

ORGANIZING COMMITTEE

Rebecca Segal (Virginia Commonwealth University)
Blerta Shtylla (Pomona College)
Suzanne Sindi (University of California, Merced)

Reply to Andy Gonzalez about NIMBIOS Workshop

Replied to a tweet by Andy GonzalezAndy Gonzalez (Twitter)
Andrew Eckford et al. hosted a related conference a few months prior at BIRS which also has some great videos:

Biological and Bio-Inspired Information Theory(14w5170)

Perhaps it’s time for a follow up conference?

👓 Mathematics matters | Bits of DNA

Read Mathematics matters by Lior PachterLior Pachter (Bits of DNA)
Six years ago I received an email from a colleague in the mathematics department at UC Berkeley asking me whether he should participate in a study that involved “collecting DNA from the brigh…
Not sure how I had missed this in the brouhaha a few weeks back, but it’s one of the more sober accounts from someone who’s actually got some math background and some reasonable idea about the evolutionary theory involved. It had struck me quite significantly that both Gowers and Tao weighed in as they did given their areas of expertise (or not). Perhaps it was worthwhile simply for the attention they brought? Gowers did specifically at least call out his lack of experience and asked for corrections, though I didn’t have the fortitude to wade through his hundreds of comments–perhaps this stands in part because there was little, if any indication of the background and direct identity of any of the respondents within the thread. As an simple example, while reading the comments on Dr. Pachter’s site, I’m surprised there is very little indication of Nicholas Bray’s standing there as he’s one of Pachter’s students. It would be much nicer if, in fact, Bray had a more fully formed and fleshed out identity there or on his linked Gravatar page which has no detail at all, much less an actual avatar!

This post, Gowers’, and Tao’s are all excellent reasons for a more IndieWeb philosophical approach in academic blogging (and other scientific communication). Many of the respondents/commenters have little, if any, indication of their identities or backgrounds which makes it imminently harder to judge or trust their bonafides within the discussion. Some even chose to remain anonymous and throw bombs. If each of the respondents were commenting (preferably using their real names) on their own websites and using the Webmention protocol, I suspect the discussion would have been richer and more worthwhile by an order of magnitude. Rivin at least had a linked Twitter account with an avatar, though I find it less than useful that his Twitter account is protected, a fact that makes me wonder if he’s only done so recently as a result of fallout from this incident? I do note that it at least appears his Twitter account links to his university website and vice-versa, so there’s a high likelihood that they’re at least the same person.

I’ll also note that a commenter noted that they felt that their reply had been moderated out of existence, something which Lior Pachter certainly has the ability and right to do on his own website, but which could have been mitigated had the commenter posted their reply on their own website and syndicated it to Pachter’s.

Hiding in the comments, which are generally civil and even-tempered, there’s an interesting discussion about academic publishing that could have been its own standalone post. Beyond the science involved (or not) in this entire saga, a lot of the background for the real story is one of process, so this comment was one of my favorite parts.

👓 Tenured Faculty Position at Princeton University | IEEE Information Theory Society

Read Tenured Faculty Position at Princeton University (itsoc.org)
The Department of Electrical Engineering at Princeton University seeks outstanding applicants for a tenured appointment at the Associate or Full Professor level, effective as early as September 1, 2019. The search is open to candidates specializing in areas related to information sciences and systems, with strength in core fundamentals and an interest in applications areas such as networks, machine learning, energy systems, cyber-physical systems, robotics and control, wireless communications, biology, etc. The successful candidate should have a Ph.D. in Electrical Engineering or a related field, demonstrated excellence in academic research, and a proven track record of teaching and advising undergraduate and graduate students (if currently holding an academic appointment). We seek faculty members who will create a climate that embraces excellence and diversity, with a strong commitment to teaching and mentoring that will enhance the work of the department and attract and retain a diverse student body. Candidates must complete an online faculty application at: https://www.princeton.edu/acad-positions/position/4801; a detailed curriculum vitae, descriptions of teaching and research interests, reprints of selected publications, and the names and addresses of three references should be uploaded as .pdf documents via the on-line application. This position is subject to Princeton University's background check policy. To ensure full consideration, applications should be received by November 15, 2018, but the search will remain open until the position is filled.
Wow! Verdu hasn’t even started experiencing entropy yet…

👓 U. confirms Verdu’s dismissal following misconduct investigation | The Princetonian

Read U. confirms Verdu's dismissal following misconduct investigation (The Princetonian)
On Friday night, Assistant Vice President for Communications Dan Day confirmed that professor Sergio Verdú was dismissed from the faculty as of Sept. 24 following a University investigation into his conduct in relation to University policies that prohibit consensual relations with students and require honesty and cooperation in University matters.

👓 Nobel Prize for Medicine Goes to Cancer Immune Therapy Pioneers | Scientific American

Read Nobel Prize for Medicine Goes to Cancer Immune Therapy Pioneers by Karen WeintraubKaren Weintraub (Scientific American)
Two men are recognized for basic research that unleashed the immune system against cancer, becoming a new pillar of therapy
A nice quick overview of some basic cancer immune therapy.

🔖 Categorical informatics

Bookmarked Categorical informatics by David Spivak (math.mit.edu)

"Category theory is a universal modeling language."

Background.

Success is founded on information. A tight connection between success (in anything) and information. It follows that we should (if we want to be more successful) study what information is.

Grant proposals. These are several grant proposals, some funded, some in the pipeline, others not funded, that explain various facets of my research project.

Introductory talk (video, slides).

Blog post, on John Baez's blog Azimuth, about my motivations for studying this subject. (Here's a .pdf version.)

👓 Discovery of Galileo’s long-lost letter shows he edited his heretical ideas to fool the Inquisition | Nature

Read Discovery of Galileo’s long-lost letter shows he edited his heretical ideas to fool the Inquisition by Alison Abbott (Nature)
Exclusive: Document shows that the astronomer toned down the claims that triggered science history’s most infamous battle — then lied about his edits.

👓 Scientists Gave MDMA to Octopuses—and What Happened Was Profound | Gizmodo

Read Scientists Gave MDMA to Octopuses—and What Happened Was Profound (Gizmodo)
When humans take the drug MDMA, versions of which are known as molly or ecstasy, they commonly feel very happy, extraverted, and particularly interested in physical touch. A group of scientists recently wondered whether this drug might have a similar effect on other species—specifically, octopuses, which are seemingly as different from humans as an animal can be. The results of their experiment, in which seven octopuses took MDMA, were “unbelievable.”

🔖 A New Factor in Evolution by James Mark Baldwin | The American Naturalist: Vol 30, No 354

Bookmarked A New Factor in Evolution by James Mark Baldwin (The American Naturalist: Vol 30, No 354 )

In several recent publications I have developed, from different points of view, some considerations which tend to bring out a certain influence at work in organic evolution which I venture to call "a new factor". I give below the list of references [1] to these publications and shall refer to them by number as this paper proceeds. The object of the present paper is to gather into one sketch an outline of the view of the process of development which these different publications have hinged upon.

The problems involved in a theory of organic development may be gathered up under three great heads: Ontogeny, Phylogeny, Heredity. The general consideration, the " factor " which I propose to bring out, is operative in the first instance, in the field of Ontogeny; I shall consequently speak first of the problem of Ontogeny, then of that of Phylogeny, in so far as the topic dealt with makes it necessary, then of that of Heredity, under the same limitation, and finally, give some definitions and conclusions.

👓 Baldwin effect | Wikipedia

Read Baldwin effect (Wikipedia)
In evolutionary biology, the Baldwin effect describes the effect of learned behavior on evolution. In brief, James Mark Baldwin and others suggested during the eclipse of Darwinism in the late 19th century that an organism's ability to learn new behaviors (e.g. to acclimatise to a new stressor) will affect its reproductive success and will therefore have an effect on the genetic makeup of its species through natural selection. Though this process appears similar to Lamarckian evolution, Lamarck proposed that living things inherited their parents' acquired characteristics. The Baldwin effect has been independently proposed several times, and today it is generally recognized as part of the modern synthesis.
Reminded about this by the lizard article I saw the other day. Worth digging back into again…

👓 Curve-Fitting | xkcd

Read Curve-Fitting (xkcd.com)
Cauchy-Lorentz: "Something alarmingly mathematical is happening, and you should probably pause to Google my name and check what field I originally worked in."
I love that it’s all the exact same data points…