I'm a biomedical and electrical engineer with interests in information theory, complexity, evolution, genetics, signal processing, IndieWeb, theoretical mathematics, and big history.
I'm also a talent manager-producer-publisher in the entertainment industry with expertise in representation, distribution, finance, production, content delivery, and new media.
The Golden Rule mandating that you treat others as you want them to treat you is simply a variation on tit-for-tat, one that emphasizes the benefit rather than the harm side. (The Christian principle of returning a favor for a harm in this respect is highly unusual and, one might note, more often than not unimplemented in Christian societies. No society I know of approves returning a harm for a favor as a general moral rule within the group.)
[recipe title=”Cream Scones” servings=”6-8″ time=”25-30mins” difficulty=”easy” image=”http://boffosocko.com/wp-content/uploads/2015/07/20150704_100549.jpg” description=”Light, flaky classic scones with full flavor”]
[recipe-ingredients]
– flour (all purpose generally yields better results than cake)
– sugar
– baking powder
– salt
– unsalted butter (cold)
– fruit: usually dried currants, raisins, chocolate chips, or other fruit
– egg
– heavy cream
– fruit zest (orange, lemon, grapefruit, other)
– cinnamon
[/recipe-ingredients]
[recipe-notes]
Other fats could be substituted for the butter, but butter generally tastes best here. For the small handful of health conscious non-professional home cooks, absolutely do not substitute milk for the cream, otherwise the fat ratio for the recipe will be thrown completely off and your results will be horrifying.
Ratio
5 parts flour : 1 part sugar : 1.5 parts butter : 1 parts egg : 2 parts cream : 1.5 parts fruit
Other ingredients (approximately per part)
1/2 teaspoon salt per part
1 tablespoon baking powder
1/4 oz zest
Professional kitchens scaling the recipe beyond 75 oz of flour, may wish to use 1.25 parts of sugar for more even results.
[/recipe-notes]
[recipe-directions]
1. Preheat oven to 425° F.
2. Whisk together the flour, sugar, baking powder and salt until mixed thoroughly.
3. Cut the cold butter into the flour mixture with a pastry blender until the lumps of butter are just larger than the size of a pea. Any smaller and the scones will be tougher and less flaky.
4. Mix together the cream, egg, (optional currants, raisins, fruit), and the zest, then mix into the flour/butter just until the dough comes together.
5. Do not overwork the scone dough or the resultant scones will not be light and flaky. You should preferably be able to still see small chunks of butter in the dough.
6. Roll the dough out into a disk about 1.5″ thick.
7. Brush a light layer of cream (or milk) onto the top of the disk and sprinkle on a nice layer of cinnamon and sugar.
8. Using a dough scraper cut the dough into eight equal wedges and place onto cooking sheet.
9. Put the sheet of scone dough into the oven at 450 for 12-15 minutes until golden brown, or until an inserted toothpick comes out clean.
10. Cool for a few minutes and then enjoy fresh with clotted cream and fresh fruit.
[/recipe-directions]
[/recipe]
Step-by-step photos
Follow the instructions in the captions below: Ingredients for making scones
Mise on place for scone ingredientsClose up of scone ingredientsWhisk together the flour, sugar, baking powder and saltPut the cold butter into the flour mixture.Cut in the butter with a pastry blender until the lumps of butter are just larger than the size of a pea. Any smaller and the scones will be tougher and less flaky.Mix together the cream, egg, (optional currants, raisins, fruit), and the zest, then mix into the flour/butter JUST until the dough comes together.Do not overwork the scone dough or the resultant scones will not be light and flaky.Roll the dough out into a disk about 1.5″ thick.Brush a light layer of cream (or milk) onto the top of the disk.Close up of the dough disk with cream. You should preferably be able to still see small chunks of butter in the dough.Sprinkle on a nice layer of cinnamon and sugar.Close up of the texture of the dough.
Using a dough scraper cut the dough into eight equal wedges and place onto cooking sheet.Put the sheet of scone dough into the oven at 450 for 12-15 minutes until golden brown, or until an inserted toothpick comes out clean.
Cool for a few minutes and then enjoy fresh with clotted cream and fresh fruit.
I have to imagine that once the conceptualization of language and some basic grammar existed, word generation was a much more common thing than it is now. It’s only been since the time of Noah Webster that humans have been actively standardizing things like spelling. If we can use Papua New Guinea as a model of pre-agrarian society and consider that almost 12% of extant languages on the Earth are spoken in an area about the size of Texas (and with about 1/5th the population of Texas too), then modern societies are actually severely limiting language (creation, growth, diversity, creativity, etc.) [cross reference: A World of Languages – and How Many Speak Them (Infographic)]
Consider that the current extinction of languages is about one every 14 weeks, which puts us on a course to loose about half of the 7,100 languages on the planet right now before the end of the century. Collective learning has potentially been growing at the expense of a shrinking body of diverse language! In the paper “Global distribution and drivers of language extinction risk” the authors indicate that of all the variables tested, economic growth was most strongly linked to language loss.
To help put this exercise into perspective, we can look at the corpus of extant written Latin (a technically dead language):
“It is a truly impressive fact that, simply by knowing that if one can memorize and master about 250 words in Latin, it will allow them to read and understand 50% of most written Latin. Further, knowledge of 1,500 Latin words will put one at the 80% level of vocabulary mastery for most texts. Mastering even a very small list of vocabulary allows one to read a large variety of texts very comfortably.”
These numbers become even smaller when considering ancient Greek texts.
Another interesting measurement is the vocabulary of a modern 2 year old who typically has a 50-75 word vocabulary while a 4 year old has 250-500 words, which is about the level of the exercise.
As a contrast, consider the message in this TED Youth Talk from last year by Erin McKean, which students should be able to relate to:
[ted id=2158]
And of course, there’s the dog Chaser, which 60 minutes recently reported has a vocabulary of over 1,000 words. (Are we now destroying variants of “dog language” for English too?!)
Hopefully the evolutionary value of the loss of the multiple languages will be more than balanced out by the power of collective learning in the long run.
“The Molecular Programming Project aims to develop computer science principles for programming information-bearing molecules like DNA and RNA to create artificial biomolecular programs of similar complexity. Our long-term vision is to establish molecular programming as a subdiscipline of computer science — one that will enable a yet-to-be imagined array of applications from chemical circuitry for interacting with biological molecules to nanoscale computing and molecular robotics.”
An infographic from the South China Morning Post has some interesting statistics about which many modern people don’t know (or remember). It’s very interesting to see the distribution of languages and where they’re spoken. Of particular note that most will miss, even from this infographic, is that 839 languages are spoken in Papua New Guinea (11.8% of all known languages on Earth). Given the effects of history and modernity, imagine how many languages there might have been without them.
I just ordered a copy of Why Information Grows: The Evolution of Order, from Atoms to Economies by Cesar Hidalgo. Although it seems more focused on economics, the base theory seems to fit right into some similar thoughts I’ve long held about biology.
Why Information Grows: The Evolutiion of Order from Atoms to Economies by Cesar Hidalgo
From the book description:
“What is economic growth? And why, historically, has it occurred in only a few places? Previous efforts to answer these questions have focused on institutions, geography, finances, and psychology. But according to MIT’s antidisciplinarian César Hidalgo, understanding the nature of economic growth demands transcending the social sciences and including the natural sciences of information, networks, and complexity. To understand the growth of economies, Hidalgo argues, we first need to understand the growth of order.
At first glance, the universe seems hostile to order. Thermodynamics dictates that over time, order–or information–will disappear. Whispers vanish in the wind just like the beauty of swirling cigarette smoke collapses into disorderly clouds. But thermodynamics also has loopholes that promote the growth of information in pockets. Our cities are pockets where information grows, but they are not all the same. For every Silicon Valley, Tokyo, and Paris, there are dozens of places with economies that accomplish little more than pulling rocks off the ground. So, why does the US economy outstrip Brazil’s, and Brazil’s that of Chad? Why did the technology corridor along Boston’s Route 128 languish while Silicon Valley blossomed? In each case, the key is how people, firms, and the networks they form make use of information.
Seen from Hidalgo’s vantage, economies become distributed computers, made of networks of people, and the problem of economic development becomes the problem of making these computers more powerful. By uncovering the mechanisms that enable the growth of information in nature and society, Why Information Grows lays bear the origins of physical order and economic growth. Situated at the nexus of information theory, physics, sociology, and economics, this book propounds a new theory of how economies can do, not just more, but more interesting things.”
For those who are intimidated by the thought of higher mathematics, but are still considering joining our Category Theory Summer Study Group, I’ve just come across a lovely new book by Eugenia Cheng entitled How to Bake Pi: An Edible Exploration of the Mathematics of Mathematics.
Eugenia Cheng’s book How to Bake Pi
It just came out in the U.S. market on May 5, 2015, so it’s very new in the market. My guess is that even those who aren’t intimidated will get a lot out of it as well. A brief description of the book follows:
“What is math? How exactly does it work? And what do three siblings trying to share a cake have to do with it? In How to Bake Pi, math professor Eugenia Cheng provides an accessible introduction to the logic and beauty of mathematics, powered, unexpectedly, by insights from the kitchen: we learn, for example, how the béchamel in a lasagna can be a lot like the number 5, and why making a good custard proves that math is easy but life is hard. Of course, it’s not all cooking; we’ll also run the New York and Chicago marathons, pay visits to Cinderella and Lewis Carroll, and even get to the bottom of a tomato’s identity as a vegetable. This is not the math of our high school classes: mathematics, Cheng shows us, is less about numbers and formulas and more about how we know, believe, and understand anything, including whether our brother took too much cake.
At the heart of How to Bake Pi is Cheng’s work on category theory—a cutting-edge “mathematics of mathematics.” Cheng combines her theory work with her enthusiasm for cooking both to shed new light on the fundamentals of mathematics and to give readers a tour of a vast territory no popular book on math has explored before. Lively, funny, and clear, How to Bake Pi will dazzle the initiated while amusing and enlightening even the most hardened math-phobe.”
Dr. Cheng recently appeared on NPR’s Science Friday with Ira Flatow to discuss her book. You can listen to the interview below. Most of the interview is about her new book. Specific discussion of category theory begins about 14 minutes into the conversation.
Top chefs and Harvard researchers explore how everyday cooking and haute cuisine can illuminate basic principles in physics and engineering, and vice versa.
I’ve made a few posts here [1][2] about a summer study group for category theory. In an effort to facilitate the growing number of people from various timezones and differing platforms (many have come to us from Google+, Tumblr, Twitter, GoodReads, and friends from Dr. Miller’s class in a private Google Group), I’ve decided it may be easiest to set up something completely separate from all of these so our notes, resources, and any other group contributions can live on to benefit others in the future. Thus I’ve built Category Theory: Summer Study Group 2015 on WordPress. It will live as a sub-domain of my personal site until I get around to buying a permanent home for it (any suggestions for permanent domain names are welcome).
Registration
We’ve actually had a few people already find the new site and register before I’ve announced it, but for those who haven’t done so yet, please go to our participant registration page and enter your preferred username and email address. We’ll email you a temporary password which you can change when you login for the first time. Those who want to use their pre-existing WordPress credentials are welcome to do so.
Once you’ve registered, be sure to update your profile (at least include your name) so that others will know a little bit more about you. If you’d like you can also link your WordPress.com account [or sign up for one and then link it] so that you can add a photo and additional details. To login later, there’s a link hidden in the main menu under “Participants.”
You can also add your details to the form at the bottom of the Participants page to let others know a bit more about you and where you can be reached. Naturally this is optional as I know some have privacy issues. In the notes, please leave your location/timezone so that we can better coordinate schedules/meetings.
Category Theory Blog
Your username/password will allow you to post content directly to the study group’s blog. This can be contributed notes, questions, resources, code, photos, thoughts, etc. related to category theory and related areas of mathematics we’ll be looking at. Initially your posts will be moderated (primarily only to prevent spam), and over time your status will be elevated to allow immediate posting and editing. If you have any questions or need administrative help, I’m easy to find and happy to help if you get into trouble. Most of the interface will hopefully be easy to understand.
For those with questions, please try to read posts as you’re able and feel free to comment with hints and/or solutions. I’ve created “categories” with the chapter titles from the text we’re using to facilitate sorting/searching. Depending on the need, we can granularize this further as we proceed. There is also the ability to tag posts with additional metadata or upload photos as well.
As appropriate, I’ll take material out of the blog/posts stream and place it into freestanding pages for easier reference in the future. As an example, I’ve already found some material on YouTube and MIT’s Open Course Ware site (Spivak posted his 2013 class using our same text, though it unfortunately doesn’t include video or audio) that may be relevant to many.
For those interested, WordPress supports most basic LaTeX, though I doubt it supports any of the bigger category theory diagramming packages, so feel free to draw out pictures/diagrams, photograph them, and upload them for others to see if necessary.
As an advocate of the open web and owning one’s own data, I highly recommend everyone publish/post their content here as well as to their favorite site/platform of choice as they see fit.
Textbook
In emails and chatter around the web, I haven’t heard any major objections to the proposed textbook so far, so unless there are, I’m assuming that it should serve most of us well. Hopefully everyone has a copy by now (remember there are free versions available) and has begun reading the introductory material. Those requiring a bit more mathematical rigor and challenge can supplement with additional texts as I’m sure I and many others will. If you’re posting questions to the site about problems/questions from other texts, please either state them explicitly or tag them with the author’s last name as well as the problem/exercise number. (I’ll try to make them all canonical on the back end as we progress, so don’t worry too much if you’re not sure how or what to tag them with.)
Conference Call Tool
At the moment, most people have been fairly open to the three big platforms, though a few on either Linux or Chromebooks don’t have access to be able to install/operate anything but Google Hangouts, so I’m presently proposing that we adopt it for our group. Nearly everyone in the group already has a gmail account, so I don’t expect it to be an undue burden. If you haven’t used it before, please download/install any plugins you may require for your platform in advance of our first “call.”
Meeting Times
I’ve only heard back from a small handful of people on availability so far, but it doesn’t look like it will be difficult to find an appropriate time. If you haven’t already done so, please fill out the “survey,” so we can determine a good call time for next week. If necessary, we can do additional times to help serve everyone’s needs. We don’t want to leave out any who sincerely want to participate.
Office Hours
As most of the participants are spread over the United States, Europe, and Asia, I’m suggesting that everyone carve out a standing block of time (we can call them “office hours”) that they can use to be available (via Google Hangouts or otherwise) to help out others having difficulty or who have questions. Since there isn’t a “professor” I’m hoping that we can all serve each other as unofficial teaching assistants to get through the process, and having standing office hours may be the easiest way to catch others for help in addition to the web site itself.
Questions? Comments? Snide Remarks?
If you have any questions, or I’ve managed to miss something, please don’t hesitate to make a comment below. I’m hoping to get enough responses by Friday/Saturday this week to post our first meeting time for next week.
With my studies in category theory trundling along, I thought I’d take moment to share some general resources for typesetting commutative diagrams in . I’ll outline below some of the better resources and recommendations I’ve found, most by much more dedicated and serious users than I. Following that I’ll list a few resources, articles, and writings on some of the more common packages that I’ve seen mentioned.
Naturally, just reading through some of the 20+ page user guides to some of these packages can be quite daunting, much less wading through the sheer number that exist. Hopefully this one-stop-shop meta-overview will help others save some time trying to figure out what they’re looking for.
Feruglio Summary
Gabriel Valiente Feruglio has a nice overview article naming all the primary packages with some compare/contrast information. One will notice it was from 1994, however, and misses a few of the more modern packages including TikZ. His list includes: AMS; Barr (diagxy); Borceux; Gurari; Reynolds; Rose (XY-pic); Smith (Arrow); Spivak; Svensson (kuvio); Taylor (diagrams); and Van Zandt (PSTricks). He lists them alphabetically and gives brief overviews of some of the functionality of each.
J.S. Milne has a fantastic one-page quick overview description of several available packages with some very good practical advise to users depending on the level of their needs. He also provides a nice list of eight of the most commonly used packages including: array (LaTeX); amscd (AMS); DCpic (Quaresma); diagrams (Taylor); kuvio (Svensson); tikz (Tantau); xymatrix (Rose); and diagxy (Barr). It’s far less formal than Feruglio, but is also much more modern. I also found it a bit more helpful for trying to narrow down one or more packages with which to play around.
David Spivak, the author of Category Theory for the Sciences, seems to prefer XY-pic, diagXY, and TikZ based on his website from which he links to guides to each of these.
Resources for some of the “Bigger” Packages
Based on the recommendations given in several of the resources above, I’ve narrowed the field a bit to some of the better sounding packages. I’ve provided links to the packages with some of the literature supporting them.
Below is a handful of suggestions and thoughts relating to the study group in terms of platforms to assist us in communicating as well as a general outline for the summer. I’m only “leading” this in the sense that I put my foot forward first, but I expect and sincerely hope that others will be active leaders and participants as well, so please take the following only as a suggestion, and feel free to add additional thoughts and commentary you feel might help the group.
Primary resources:
General Communication
Since many within the group are already members of the Google Group “Advanced Physics & Math – Los Angeles.” I suggest we use the email list here as a base of communication. I believe the group is still “private” but am happy to invite the handful of participants who aren’t already members. Those actively participating are encouraged to change their settings so that they receive emails from the group either as they’re posted, or in batches once a day. Those subscribed only once a week or less frequently are likely to miss out on questions, comments, and other matters.
Alternately we might also use the GoodReads.com discussion group within the “Mathematics Students” group. I believe only about three of us so far may already be goodreads members, so this may require more effort for others to join.
If anyone has an alternate platform suggestion for communicating and maintaining resources, I’m happy to entertain it.
I wouldn’t be opposed to setting up a multi-user WordPress site that we could all access and post/cross-post to. Doing this could also allow for use of as well, which may be useful down the line. This would also have the benefit of being open to the public and potentially assisting future students. It also has built-in functionality of notifying everyone of individual posts and updates as they’re entered.
Meetings
I’ll propose a general weekly meeting online via Google Hangouts on a day and time to be determined. It looks like the majority of respondents are in the Pacific timezone, so perhaps we could shoot for something around 7pm for an hour or so if we do something during weekdays so that East coasters can join without us running too late. If we decide to do something during the weekend, we obviously have a good bit more flexibility.
If we could have everyone start by indicating which days/times absolutely won’t work for them and follow up with their three to four preferred days/times, then we might be able to build a consensus for getting together.
Alternate videoconference options could include Skype, ooVoo, or others, in some part because I know that most participants are already part of the Google ecosystem and know that one or more potential participants is using Google Chromebooks and thus may not be able to use other platforms. Is anyone not able to use Google Hangouts? If we opt for something else, we want something that is ubiquitous for platform, allows screen sharing, and preferably the ability to record the sessions for those who aren’t present.
Ideally the videoconference meetings will be geared toward an inverted classroom style of work in which it would be supposed that everyone has read the week’s material and made an attempt at a number of problems. We can then bring forward any general or specific conceptual problems people may be having and then work as a group toward solving any problems that anyone in the group may be having difficulty with.
I’ll also suggest that even if we can’t all make a specific date and time, that we might get together in smaller groups to help each other out. Perhaps everyone could post one or two regular hours during the week as open “office hours” so that smaller groups can discuss problems and help each other out so that we can continue to all make progress as a group.
Given the diversity of people in the group and their backgrounds, I’ll suggest Spivak’s text which has a gentle beginning and is geared more toward scientists and non-professional mathematicians, though it seems to come up to speed fairly quickly without requiring a large number of prerequisites. It also has the benefit of being free as noted below.
The textbook can be purchased directly through most book retailers. Those looking for cheaper alternatives might find these two versions useful. The HTML version should be exactly in line with the printed one, while the “old version” may not be exactly the same.
Following this, I might suggest we use something like Awody’s text or Leinster’s which are slightly more technical, but still fairly introductory. Those who’d like a more advanced text can certainly supplement by reading portions of those texts as we work our way through the material in Spivak. If all of the group wants a more advanced text, we can certainly do it, but I’d prefer not to scare away any who don’t have a more sophisticated background.
The following schedule takes us from now through the end of the summer and covers the entirety of the book. Hopefully everyone will be able to participate through the end, though some may have additional pressures as the beginning of the Fall sees the start of other courses. Without much prior experience in the field myself, I’ve generally broken things up to cover about 35 pages a week, though some have slightly more or less. Many, like me, may feel like the text really doesn’t begin until week three or four as the early chapters provide an introduction and cover basic concepts like sets and functions which I have a feeling most have at least some experience with. I’ve read through chapter two fairly quickly already myself. This first easy two week stretch will also give everyone the ability to settle in as well as allow others to continue to join the group before we make significant headway.
If anyone has more experience in the subject and wishes to comment on which sections we may all have more conceptual issues with, please let us know so we can adjust the schedule as necessary. I suppose we may modify the schedule as needed going forward, though like many of you, I’d like to try to cover as much as we can before the end of the summer.
Week One: May 24 (24 pages)
Administrative tasks
Purchase Textbook
Decide on best day/time for meeting
Decide on platform for meetings: Google Hangouts /Skype /ooVoo /Other
1 A brief history of category theory
1.2 Intention of this book
1.3 What is requested from the student
1.4 Category theory references
2 The Category of Sets 9
2.1 Sets and functions
2.2 Commutative diagrams
Week Two: May 31 (50 pages)
2.3 Ologs
3 Fundamental Considerations in Set 41
3.1 Products and coproducts
3.2 Finite limits in Set
Week Three: June 7 (40 pages)
3.3 Finite colimits in Set
3.4 Other notions in Set
Week Four: June 14 (31 pages)
4 Categories and Functors, Without Admitting It 115
4.1 Monoids
4.2 Groups
Week Five: June 21 (38 pages)
4.3 Graphs
4.4 Orders
Week Six: June 28 (19 pages)
4.5 Databases: schemas and instances
Week Seven: July 5 (36 pages)
5 Basic Category Theory 203
5.1 Categories and functors
Week Eight: July 12 (28 pages)
5.2 Common categories and functors from pure math
Week Nine: July 19 (48 pages)
5.3 Natural transformations
5.4 Categories and schemas are equivalent, Cat » Sch
August 10-13, 2015 – UC San Diego, La Jolla, California
Application deadline: June 7, 2015
The School of Information Theory will bring together over 100 graduate students, postdoctoral scholars, and leading researchers for four action-packed days of learning, stimulating discussions, professional networking and fun activities, all on the beautiful campus of the University of California, San Diego (UCSD) and in the nearby beach town of La Jolla.
Tutorials by some of the best known researchers in information theory and related fields
Poster presentations by student participants with feedback and discussion
Panel discussion on “IT: Academia vs. Industry Perspectives”
BIRS 5 day worksop, arriving in Banff, Alberta Sunday, June 7 and departing Friday, June 12, 2015
In the years since the first assembly of the human genome, the complex and vital role of RNA and RNA binding proteins in regulation of the genome expression has expanded through the discovery of RNA-binding proteins and large classes of non-coding RNA that control many developmental decisions as part of protein- RNA complexes. Our molecular level understanding of RNA regulation has dramatically improved as many new structures of RNA–protein complexes have been determined and new sophisticated experimental technologies and dedicated computational modeling have emerged to investigate these interactions at the whole-genome level. Further deep insight on the molecular mechanisms that underline genome expression regulation is critical for understanding fundamental biology and disease progression towards the discovery of new approaches to interfere with disease progression.
The proposed workshop will bring together experts in RNA biology with structural biologists that focus on RNA-protein complexes, as well as computational biologists who seek to model and develop predictive tools based on the confluence of these experimental advances. The workshop intends to foster new collaborations between experimental and computational biologists and catalyze the development of new and improved technologies (such as single cell binding methods) that merge experimental analysis with novel mathematical and computational techniques to better understand the rules of protein-RNA recognition and RNA-based biological regulation.
The organizers of the workshop are both leaders in the field of protein-RNA recognition and interactions: Yael Mandel-Gutfreund has been working in the field of protein-Nucleic Acids interactions since 1994. Her main research interest is protein-RNA recognition and regulation. She has developed several tools and web servers for predicting RNA binding proteins and RNA binding motifs. Yael is the head to the computational molecular laboratory at the Technion and the president of the Israeli society of Bioinformatics and Computational Biology. Gabriele Varani has been working in the field of RNA structure and protein-RNA interactions since 1987. His main research interest is the structural basis for protein-RNA recognition and the prediction and design of RNA-binding proteins. He determined some of the first few structures of protein-RNA complexes and developed computational tools to analyze and predict the specificity of RNA -binding proteins. His group applies these tools to design RNA-binding proteins with new specificity to control gene expression. Our invitation to participate in the workshop has been met with great enthusiasm by the researchers. More than 20 principle investigators have already confirmed their interest in attending. Six of the confirmed participants are female scientists including the organizer Yael Mandel-Gutfreund as well as Traci Hall, Lynne Maquat, Elena Conti, Susan Jones, Drena Dobbs. We also have invited and confirmed the participation of young and promising researchers including Markus Landthaler, Gene Yeo, Jernej Ule, Uwe Ohler and others. Our confirmed participants come from many different countries: US, Canada, UK, Scotland, Germany, Spain, Switzerland, Poland and Israel. Two confirmed participants as well as the organizer have attended the BIRS workshops in the past.
A key objective of the workshop is to bring together researchers with experimental, mathematical and computational background to share results and discuss the main advances and challenges in the prediction, analysis and control of RNA-protein recognition and RNA-based regulation of gene expression. Towards this aim, we plan to adopt the format of previous BIRS meetings in which invited participants (including selected students) will present relatively short presentations of 20 minutes plus 10 minutes of active discussions. This format will leave aside ample time for informal discussions to foster exchanges between participants. To stress the collaborative, multidisciplinary nature of the workshop, we plan to dedicate each of the workshop sessions to a specific topic that will comprise presentations of structural, experimental and computational approaches, rather than create session focused on a particular approach. Each session we will include at least one lecture from a young scientist/postdoctoral fellow/student to be chosen among attendees by the organizers.
Suggested preliminary schedule:
Day 1: Modeling and high throughput approaches to genome-wide analysis of protein-RNA interactions
Day 2: Predicting and designing new RNA binding proteins
Day 3: Generating and modeling RNA-based regulatory networks
Day 4: Principles of RNA regulation by RNA binding proteins
Day 5: Conclusion round table discussion on the present and future challenges of the field
Yesterday, via a notification from Lanyard, I came across a notice for the upcoming conference “The Information Universe” which hits several of the sweet spots for areas involving information theory, physics, the origin of life, complexity, computer science, and microbiology. It is scheduled to occur from October 7-9, 2015 at the Infoversum Theater in Groningen, The Netherlands.
I’ll let their site speak for itself below, but they already have an interesting line up of speakers including:
Keynote speakers
Erik Verlinde, Professor Theoretical Physics, University of Amsterdam, Netherlands
Alex Szalay, Alumni Centennial Professor of Astronomy, The Johns Hopkins University, USA
Gerard ‘t Hooft, Professor Theoretical Physics, University of Utrecht, Netherlands
Gregory Chaitin, Professor Mathematics and Computer Science, Federal University of Rio de Janeiro, Brasil
Charley Lineweaver, Professor Astronomy and Astrophysics, Australian National University, Australia
Lude Franke, Professor System Genetics, University Medical Center Groningen, Netherlands
Infoversum Theater, The Netherlands
Conference synopsis from their homepage:
The main ambition of this conference is to explore the question “What is the role of information in the physics of our Universe?”. This intellectual pursuit may have a key role in improving our understanding of the Universe at a time when we “build technology to acquire and manage Big Data”, “discover highly organized information systems in nature” and “attempt to solve outstanding issues on the role of information in physics”. The conference intends to address the “in vivo” (role of information in nature) and “in vitro” (theory and models) aspects of the Information Universe.
The discussions about the role of information will include the views and thoughts of several disciplines: astronomy, physics, computer science, mathematics, life sciences, quantum computing, and neuroscience. Different scientific communities hold various and sometimes distinct formulations of the role of information in the Universe indicating we still lack understanding of its intrinsic nature. During this conference we will try to identify the right questions, which may lead us towards an answer.
Is the universe one big information processing machine?
Is there a deeper layer in quantum mechanics?
Is the universe a hologram?
Is there a deeper physical description of the world based on information?
How close/far are we from solving the black hole information paradox?
What is the role of information in highly organized complex life systems?
The Big Data Universe and the Universe : are our numerical simulations and Big Data repositories (in vitro) different from real natural system (in vivo)?
Is this the road to understanding dark matter, dark energy?
The conference will be held in the new 260 seats planetarium theatre in Groningen, which provides an inspiring immersive 3D full dome display, e.g. numerical simulations of the formation of our Universe, and anything else our presenters wish to bring in. The digital planetarium setting will be used to visualize the theme with modern media.
. I’ll outline below some of the better resources and recommendations I’ve found, most by much more dedicated and serious users than I. Following that I’ll list a few resources, articles, and writings on some of the more common packages that I’ve seen mentioned.
