Winter Q-BIO Quantitative Biology Meeting February 15-18, 2016

Bookmarked Winter Q-BIO Quantitative Biology Meeting February 15-18, 2016 (w-qbio.org)
The Winter Q-BIO Quantitative Biology Meeting is coming up at the Sheraton Waikiki in Oahu, HI, USA

A predictive understanding of living systems is a prerequisite for designed manipulation in bioengineering and informed intervention in medicine. Such an understanding requires quantitative measurements, mathematical analysis, and theoretical abstraction. The advent of powerful measurement technologies and computing capacity has positioned biology to drive the next scientific revolution. A defining goal of Quantitative Biology (qBIO) is the development of general principles that arise from networks of interacting elements that initially defy conceptual reasoning. The use of model organisms for the discovery of general principles has a rich tradition in biology, and at a fundamental level the philosophy of qBIO resonates with most molecular and cell biologists. New challenges arise from the complexity inherent in networks, which require mathematical modeling and computational simulation to develop conceptual “guideposts” that can be used to generate testable hypotheses, guide analyses, and organize “big data.”

The Winter q-bio meeting welcomes scientists and engineers who are interested in all areas of q-bio. For 2016, the meeting will be hosted at the Sheraton Waikiki, which is located in Honolulu, on the island of Oahu. The resort is known for its breathtaking oceanfront views, a first-of-its-kind recently opened “Superpool” and many award-winning dining venues. Registration and accommodation information can be found via the links at the top of the page.

Source: Winter Q-BIO Quantitative Biology Meeting

The Math That Connects Pluto to DNA — NOVA Next | PBS

Bookmarked The Math That Connects Pluto to DNA by Alex RileyAlex Riley (NOVA Next | PBS)
How a mathematical breakthrough from the 1960s now powers everything from spacecraft to cell phones.

Concurrent with the recent Pluto fly by, Alex Riley has a great popular science article on PBS that helps put the application of information theory and biology into perspective for the common person. Like a science version of “The Princess Bride”, this story has a little bit of everything that could be good and entertaining: information theory, biology, DNA, Reed-Solomon codes, fossils, interplanetary exploration, mathematics, music, genetics, computers, and even paleontology. Fans of Big History are sure to love the interconnections presented here.

Reed-Solomon codes correct for common transmission errors, including missing pixels (white), false signals (black), and paused transmissions (the white stripe).
Reed-Solomon codes correct for common transmission errors, including missing pixels (white), false signals (black), and paused transmissions (the white stripe).
Microscopic view of glass DNA storage beads

Molecular Programming Project

Bookmarked Molecular Programming Project (Molecular Programming Project)

 

“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.”

Source: MPP: Home

BIRS Workshop: Advances and Challenges in Protein-RNA: Recognition, Regulation and Prediction (15w5063)

Bookmarked 15w5063: Advances and Challenges in Protein-RNA: Recognition, Regulation and Prediction (Banff International Research Station | birs.ca)
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

The Information Universe Conference

"The Information Universe" Conference in The Netherlands in October hits several of the sweet spots for areas involving information theory, physics, the origin of life, complexity, computer science, and microbiology.

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
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.

The Information Universe Website

Additional details about the conference including the participants, program, venue, and registration can also be found at their website.

Videos from the NIMBioS Workshop on Information and Entropy in Biological Systems

Videos from the NIMBioS workshop on Information and Entropy in Biological Systems from April 8-10, 2015 are slowly starting to appear on YouTube.

Videos from the April 8-10, 2015, NIMBioS workshop on Information and Entropy in Biological Systems are slowly starting to appear on YouTube.

John Baez, one of the organizers of the workshop, is also going through them and adding some interesting background and links on his Azimuth blog as well for those who are looking for additional details and depth

Additonal resources from the Workshop:

 

Popular Science Books on Information Theory, Biology, and Complexity

The beginning of a four part series in which I provide a gradation of books and texts that lie in the intersection of the application of information theory, physics, and engineering practice to the area of biology.

Previously, I had made a large and somewhat random list of books which lie in the intersection of the application of information theory, physics, and engineering practice to the area of biology.  Below I’ll begin to do a somewhat better job of providing a finer gradation of technical level for both the hobbyist or the aspiring student who wishes to bring themselves to a higher level of understanding of these areas.  In future posts, I’ll try to begin classifying other texts into graduated strata as well.  The final list will be maintained here: Books at the Intersection of Information Theory and Biology.

Introductory / General Readership / Popular Science Books

These books are written on a generally non-technical level and give a broad overview of their topics with occasional forays into interesting or intriguing subtopics. They include little, if any, mathematical equations or conceptualization. Typically, any high school student should be able to read, follow, and understand the broad concepts behind these books.  Though often non-technical, these texts can give some useful insight into the topics at hand, even for the most advanced researchers.

Complexity: A Guided Tour by Melanie Mitchell (review)

Possibly one of the best places to start, this text gives a great overview of most of the major areas of study related to these fields.

Entropy Demystified: The Second Law Reduced to Plain Common Sense by Arieh Ben-Naim

One of the best books on the concept of entropy out there.  It can be read even by middle school students with no exposure to algebra and does a fantastic job of laying out the conceptualization of how entropy underlies large areas of the broader subject. Even those with Ph.D.’s in statistical thermodynamics can gain something useful from this lovely volume.

The Information: A History, a Theory, a Flood by James Gleick (review)

A relatively recent popular science volume covering various conceptualizations of what information is and how it’s been dealt with in science and engineering.  Though it has its flaws, its certainly a good introduction to the beginner, particularly with regard to history.

The Origin of Species by Charles Darwin

One of the most influential pieces of writing known to man, this classical text is the basis from which major strides in biology have been made as a result. A must read for everyone on the planet.

Information, Entropy, Life and the Universe: What We Know and What We Do Not Know by Arieh Ben-Naim

Information Theory and Evolution by John Avery

The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life by Werner R. Loewenstein (review)

Information Theory, Evolution, and the Origin of Life by Hubert P. Yockey

The four books above have a significant amount of overlap. Though one could read all of them, I recommend that those pressed for time choose Ben-Naim first. As I write this I’ll note that Ben-Naim’s book is scheduled for release on May 30, 2015, but he’s been kind enough to allow me to read an advance copy while it was in process; it gets my highest recommendation in its class. Loewenstein covers a bit more than Avery who also has a more basic presentation. Most who continue with the subject will later come across Yockey’s Information Theory and Molecular Biology which is similar to his text here but written at a slightly higher level of sophistication. Those who finish at this level of sophistication might want to try Yockey third instead.

The Red Queen: Sex and the Evolution of Human Nature by Matt Ridley

Grammatical Man: Information, Entropy, Language, and Life  by Jeremy Campbell

Life’s Ratchet: How Molecular Machines Extract Order from Chaos by Peter M. Hoffmann

Complexity: The Emerging Science at the Edge of Order and Chaos by M. Mitchell Waldrop

The Big Picture: On the Origins of Life, Meaning, and the Universe Itself (Dutton, May 10, 2016) 

In the coming weeks/months, I’ll try to continue putting recommended books on the remainder of the rest of the spectrum, the balance of which follows in outline form below. As always, I welcome suggestions and recommendations based on others’ experiences as well. If you’d like to suggest additional resources in any of the sections below, please do so via our suggestion box. For those interested in additional resources, please take a look at the ITBio Resources page which includes information about related research groups; references and journal articles; academic, research institutes, societies, groups, and organizations; and conferences, workshops, and symposia.

Lower Level Undergraduate

These books are written at a level that can be grasped and understood by most with a freshmen or sophomore university level. Coursework in math, science, and engineering will usually presume knowledge of calculus, basic probability theory, introductory physics, chemistry, and basic biology.

Upper Level Undergraduate

These books are written at a level that can be grasped and understood by those at a junior or senor university level. Coursework in math, science, and engineering may presume knowledge of probability theory, differential equations, linear algebra, complex analysis, abstract algebra, signal processing, organic chemistry, molecular biology, evolutionary theory, thermodynamics, advanced physics, and basic information theory.

Graduate Level

These books are written at a level that can be grasped and understood by most working at the level of a master’s level at most universities.  Coursework presumes all the previously mentioned classes, though may require a higher level of sub-specialization in one or more areas of mathematics, physics, biology, or engineering practice.  Because of the depth and breadth of disciplines covered here, many may feel the need to delve into areas outside of their particular specialization.

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.

Schools of Thought in the Hard and Soft Sciences

A framework for determining the difference between the hard and soft sciences.

A recent post in one of the blogs at Discover Magazine the other day had me thinking about the shape of science over time.

Neuroscientists don’t seem to disagree on the big issues. Why are there no big ideas in neuroscience?

Neuroskeptic, Where Are The Big Ideas in Neuroscience? (Part 1)

The article made me wonder about the divide between the ‘soft’ and ‘hard’ sciences, and how we might better define and delineate them. Perhaps in a particular field, the greater the proliferation of “schools of though,” the more likely something is to be a soft science? (Or mathematically speaking, there’s an inverse relationship in a field between how well supported it is and the number of schools of thought it has.) I consider a school of thought to be a hypothetical/theoretical proposed structure meant to potentially help advance the state of the art and adherents join one of many varying camps while evidence is built up (or not) until one side carries the day.

Firmness of Science vs. # of Schools of Thought
Simple linear approximation of the relationship, though honestly something more similar to y=1/x which is asymptotic to the x and y axes is far more realistic.

Theorem: The greater the proliferation of “schools of though,” the more likely something is to be a soft science.

Generally in most of the hard sciences like physics, biology, or microbiology, there don’t seem to be any opposing or differing schools of thought. While in areas like psychology or philosophy they abound, and often have long-running debates between schools without any hard data or evidence to truly allow one school to win out over another. Perhaps as the structure of a particular science becomes more sound, the concept of schools of thought become more difficult to establish?

For some of the hard sciences, it would seem that schools of thought only exist at the bleeding edge of the state-of-the-art where there isn’t yet enough evidence to swing the field one way or another to firmer ground.

Example: Evolutionary Biology

We might consider the area of evolutionary biology in which definitive evidence in the fossil record is difficult to come by, so there’s room for the opposing thoughts for gradualism versus punctuated equilibrium to be individual schools. Outside of this, most of evolutionary theory is so firmly grounded that there aren’t other schools.

Example: Theoretical Physics

The relatively new field of string theory might be considered a school of thought, though there don’t seem to be a lot of other opposing schools at the moment. If it does, such a school surely exists, in part, because there isn’t the ability to validate it with predictions and current data. However, because of the strong mathematical supporting structure, I’ve yet to hear anyone use the concept of school of thought to describe string theory, which sits in a community which seems to believe its a foregone conclusion that it or something very close to it represents reality. (Though for counterpoint, see Lee Smolin’s The Trouble with Physics.)

Example: Mathematics

To my knowledge, I can’t recall the concept of school of thought ever being applied to mathematics except in the case of the Pythagorean School which historically is considered to have been almost as much a religion as a science. Because of its theoretical footings, I suppose there may never be competing schools, for even in the case of problems like P vs. NP, individuals may have some gut reaction to which way things are leaning, everyone ultimately knows it’s going to be one or the other (P=NP or P \neq NP). Many mathematicians also know that it’s useful to try to prove a theorem during the day and then try to disprove it (or find a counterexample) by night, so even internally and individually they’re self-segregating against creating schools of thought right from the start.

Example: Religion

Looking at the furthest end of the other side of the spectrum, because there is no verifiable way to prove that God exists, there has been an efflorescence of religions of nearly every size and shape since the beginning of humankind. Might we then presume that this is the softest of the ‘sciences’?

What examples or counter examples can you think of?

Richard Dawkins Interview: This Is My Vision Of “Life” | Edge.org

Bookmarked This Is My Vision Of "Life" by John Brockman (edge.org)
The Edge.org's interview with Richard Dawkins.

Richard Dawkins [4.30.15]

“My vision of life is that everything extends from replicators, which are in practice DNA molecules on this planet. The replicators reach out into the world to influence their own probability of being passed on. Mostly they don’t reach further than the individual body in which they sit, but that’s a matter of practice, not a matter of principle. The individual organism can be defined as that set of phenotypic products which have a single route of exit of the genes into the future. That’s not true of the cuckoo/reed warbler case, but it is true of ordinary animal bodies. So the organism, the individual organism, is a deeply salient unit. It’s a unit of selection in the sense that I call a “vehicle”.  There are two kinds of unit of selection. The difference is a semantic one. They’re both units of selection, but one is the replicator, and what it does is get itself copied. So more and more copies of itself go into the world. The other kind of unit is the vehicle. It doesn’t get itself copied. What it does is work to copy the replicators which have come down to it through the generations, and which it’s going to pass on to future generations. So we have this individual replicator dichotomy. They’re both units of selection, but in different senses. It’s important to understand that they are different senses.”

Richard Dawkins
Richard Dawkins

RICHARD DAWKINS is an evolutionary biologist; Emeritus Charles Simonyi Professor of the Public Understanding of Science, Oxford; Author, The Selfish Gene; The Extended Phenotype; Climbing Mount Improbable; The God Delusion; An Appetite For Wonder; and (forthcoming) A Brief Candle In The Dark.

Watch the entire video interview and read the transcript at Edge.org.

NIMBioS Workshop: Information Theory and Entropy in Biological Systems

Web resources for participants in the NIMBioS Worshop on Information Theory and Entropy in Biological Systems.

Over the next few days, I’ll be maintaining a Storify story covering information related to and coming out of the Information Theory and Entropy Workshop being sponsored by NIMBios at the Unviersity of Tennessee, Knoxville.

For those in attendance or participating by watching the live streaming video (or even watching the video after-the-fact), please feel free to use the official hashtag , and I’ll do my best to include your tweets, posts, and material into the story stream for future reference.

For journal articles and papers mentioned in/at the workshop, I encourage everyone to join the Mendeley.com group ITBio: Information Theory, Microbiology, Evolution, and Complexity and add them to the group’s list of papers. Think of it as a collaborative online journal club of sorts.

Those participating in the workshop are also encouraged to take a look at a growing collection of researchers and materials I maintain here. If you have materials or resources you’d like to contribute to the list, please send me an email or include them via the suggestions/submission form or include them in the comments section below.

Resources for Information Theory and Biology

RSS Icon  RSS Feed for BoffoSocko posts tagged with

 

Probability Models for DNA Sequence Evolution

Bookmarked Probability Models for DNA Sequence Evolution (Springer, 2008, 2nd Edition) by Rick Durrett (math.duke.edu)

While browsing through some textbooks and researchers today, I came across a fantastic looking title: Probability Models for DNA Sequence Evolution by Rick Durrett (Springer, 2008). While searching his website at Duke, I noticed that he’s made a .pdf copy of a LaTeX version of the 2nd edition available for download.   I hope others find it as interesting and useful as I do.

I’ll also give him a shout out for being a mathematician with a fledgling blog: Rick’s Ramblings.

Book Cover of Probability Models for DNA Sequence Evolution by Richard Durrett
Probability Models for DNA Sequence Evolution by Richard Durrett

BIRS Workshop on Biological and Bio-Inspired Information Theory | Storify Stream

Over the span of the coming week, I'll be updating (and archiving) the stream of information coming out of the BIRS Workshop on Biological and Bio-Inspired Information Theory.

Over the span of the coming week, I’ll be updating (and archiving) the stream of information coming out of the BIRS Workshop on Biological and Bio-Inspired Information Theory.

Editor’s note: On 12/12/17 Storify announced they would be shutting down. As a result, I’m changing the embedded version of the original data served by Storify for an HTML copy which can be found below:

BIRS: Biological and Bio-Inspired Information Theory

A 5 Day workshop on Biology and Information Theory hosted by the Banff International Research Station

  1. Wishing I was at the Gene Regulation and Information Theory meeting starting tomorrow  http://bit.ly/XnHRZs  #ITBio
  2. Mathematical and Statistical Models for Genetic Coding starts today.  http://www.am.hs-mannheim.de/genetic_code_2013.php?id=1  @andreweckford might borrow attendees for BIRS
  3. Mathematical Foundations for Information Theory in Diffusion-Based Molecular Communications  http://bit.ly/1aTVR2c  #ITBio
  4. Bill Bialek giving plenary talk “Information flow & order in real biological networks” at Feb 2014 workshop  http://mnd.ly/19LQH8f  #ITBio
  5. #ITBio http://t.co/Ty8dEIXQUT"/>

    CECAM Workshop: “Entropy in Biomolecular Systems” starts May 14 in Vienna.  http://jhu.md/1faLR8t  #ITBio pic.twitter.com/Ty8dEIXQUT
  6. Last RT: wonder what the weather is going to be like at the end of October for my @BIRS_Math workshop
  7. @JoVanEvery I’m organizing a workshop in Banff in October … hopefully this isn’t a sign of weather to come!
  8. Banff takes its name from the town of Banff, Scotland, not to be confused with Bamff, also Scotland.
  9. Good morning from beautiful Banff. How can you not love the mountains? http://t.co/mxYBNz7yzl

    Good morning from beautiful Banff. How can you not love the mountains? pic.twitter.com/mxYBNz7yzl
  10. “Not an obvious connection between utility and information, just as there is no obvious connection between energy and entropy” @BIRS_Math
  11. Last RT: a lot of discussion of my signal transduction work with Peter Thomas.
  12. Live now: Nicolo Michelusi of @USCViterbi on Stochastic Model for Electron Transfer in Bacterial Cables  http://www.birs.ca/live  #ITBio
  13. Nicolo Michelusi (University of Southern California), A Stochastic Model for Electron Transfer in Bacterial Cables  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410271450-Michelusi.mp4 
  14. Listening to the always awesome @cnmirose talk about the ultimate limits of molecular communication.
  15. “Timing is fundamental … subsumes time-varying concentration channel” @cnmirose @BIRS_Math
  16. Standard opening quote of these talks: “I’m not a biologist, but …” @BIRS_Math
  17. Stefan Moser (ETH Zurich), Capacity Bounds of the Memoryless AIGN Channel – a Toy-Model for Molecular Communicat…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410271610-Moser.mp4 
  18. Weisi Guo (University of Warwick), Communication Envelopes for Molecular Diffusion and Electromagnetic Wave Propag…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410271643-Guo.mp4 
  19. .@ChrisAldrich @andreweckford @Storify @BIRS_Math Sounds like a fascinating workshop on bioinformation theory in Banff.
  20. Toby Berger, winner of the 2002 Shannon award, speaking right now. @BIRS_Math
  21. Naftali Tishby (Hebrew University of Jerusalem), Sensing and acting under information constraints – a principled a…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281032-Tishby.mp4 
  22. “…places such as BIRS and the Banff Centre exist to facilitate the exchange and pursuit of knowledge.” S. Sundaram  http://www.birs.ca/testimonials/#testimonial-1454 
  23. We’re going for a hike tomorrow. Many thanks to Lukas at the @ParksCanada info centre in Banff for helpful advice! @BIRS_Math
  24. Alexander Dimitrov (Washington State University), Invariant signal processing in auditory biological systems  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281416-Dimitrov.mp4 
  25. Joel Zylberberg (University of Washington), Communicating with noisy signals: lessons learned from the mammalian v…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281450-Zylberberg.mp4 
  26. Robert Schober (Universitat Erlangen-Nurnberg), Intersymbol interference mitigation in diffusive molecular communi…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281549-Schober.mp4 
  27. Rudolf Rabenstein (Friedrich-Alexander-Universitat Erlangen-Nurnberg (FAU)), Modelling Molecular Communication Cha…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410281627-Rabenstein.mp4 
  28. THis week @BIRS_Math ” Biological and Bio-Inspired Information Theory ” @thebanffcentre #biology #math @NSF
  29. “Your theory might match the data, but the data might be wrong” – Crick @BIRS_Math
  30. So information theory seems to be a big deal in ecology. @BIRS_Math
  31. Tom Schneider (National Institutes of Health), Three Principles of Biological States: Ecology and Cancer  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410290904-Schneider.mp4 
  32. “In biodiversity, the entropy of an ecosystem is the expected … information we gain about an organism by learning its species” @BIRS_Math
  33. Seriously, I’m blown away by this work in information theory in ecology. Huge body of work; I had no idea. @BIRS_Math
  34. I encourage @BIRS_Math attendees at Biological & Bio-Inspired Information Theory to contribute references here:  http://bit.ly/1jQwObk 
  35. Christoph Adami (Michigan State University), Some Information-Theoretic Musings Concerning the Origin and Evolutio…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410291114-Adami.mp4 
  36. #ITBio http://t.co/VA8komuuSW"/>

    .@ChristophAdami talk Some Information-Theoretic Musings Concerning the Origin of Life @BIRS_Math this morning #ITBio pic.twitter.com/VA8komuuSW
  37. ICYMI @ChristophAdami had great paper: Information-theoretic Considerations on Origin of Life on arXiv  http://bit.ly/1yIhK2Q  @BIRS_Math
  38. Baez has a post on Tishby's talk "Sensing &  Acting Under Information Constraints" http://t.co/t1nPVI1pxa @BIRS_Math http://t.co/dFuiVLFSGC

    Baez has a post on Tishby’s talk “Sensing & Acting Under Information Constraints”  http://bit.ly/1yIDonR  @BIRS_Math pic.twitter.com/dFuiVLFSGC
  39. INFORMATION THEORY is the new central ...

    INFORMATION THEORY is the new central …
  40. I’m listening to a talk on the origin of life at a workshop on Biological and Bio-Inspired Information Theory. …  https://plus.google.com/117562920675666983007/posts/gqFL7XY3quF 
  41. Now accepting applications for the #Research Collaboration Workshop for Women in #MathBio at NIMBioS  http://ow.ly/DzeZ7 
  42. We removed a faulty microphone from our lecture room this morning. We’re now fixing the audio buzz in this week’s videos, and reposting.
  43. Didn’t get enough information theory & biology this week @BIRS_Math? Apply for NIMBioS workshop in April 2015  http://bit.ly/1yIeiWe  #ITBio
  44. Amin Emad (University of Illinois at Urbana-Champaign), Applications of Discrete Mathematics in Bioinformatics  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410301329-Emad.mp4 
  45. Paul Bogdan (University of Southern California), Multiscale Analysis Reveals Complex Behavior in Bacteria Populati…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410301401-Bogdan.mp4 
  46. Lubomir Kostal (Institute of Physiology, Academy of Sciences of the Czech Republic), Efficient information transmi…  http://www.birs.ca/events/2014/5-day-workshops/14w5170/videos/watch/201410301534-Kostal.mp4 
  47. Banff ☀️❄️🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲🌲❤️
  48. @conservativelez I’m a big fan of your dad’s research & was reminded of much of it via a workshop on Biological Information Theory
  49. @conservativelez Though he may not have been able to attend, he can catch most of the talks online if he’d like  https://www.birs.ca/events/2014/5-day-workshops/14w5170 
  50. Depressed that @BIRS_Math Workshop on Biological & Bio-Inspired Information Theory is over? Relive it here:  http://bit.ly/1rF3G4B  #ITBio
  51. A few thoughts about that workshop while I wait for my flight back to Toronto.
  52. 1/ Everyone I talked to said it was the best workshop they’d ever been to, and they’d like to do a follow-up workshop @BIRS_Math
  53. 2/ There is an amazing diversity of work under the umbrella of “information theory”. @BIRS_Math
  54. 3/ Much of this work is outside the IT mainstream, and an issue is that people use different terms for related concepts. @BIRS_Math
  55. 4/ Some community building is in order. I think this workshop was a good first step. @BIRS_Math
  56. 5/ Many many thanks to @BIRS_Math and huge kudos to @NGhoussoub for excellent service to the Canadian scientific community. BIRS is a gem.
  57. 6/ Also many thanks to the participants for their excellent talks, and to @ChrisAldrich for maintaining a Storify.


Information Theory is the New Central Discipline

Replied to Information Theory is the new central discipline. by Nassim Nicholas Taleb (facebook.com)

INFORMATION THEORY is the new central discipline. This graph was from 20y ago in the seminal book Cover and Thomas, as the field was starting to be defined. Now Information Theory has been expanded to swallow even more fields.

Born in, of all disciplines, Electrical Engineering, the field has progressively infiltrating probability theory, computer science, statistical physics, data science, gambling theory, ruin problems, complexity, even how one deals with knowledge, epistemology. It defines noise/signal, order/disorder, etc. It studies cellular automata. You can use it in theology (FREE WILL & algorithmic complexity). As I said, it is the MOTHER discipline.

I am certain much of Medicine will naturally grow to be a subset of it, both operationally, and in studying how the human body works: the latter is an information machine. Same with linguistics. Same with political “science”, same with… everything.

I am saying this because I figured out what the long 5th volume of the INCERTO will be. Cannot say now with any precision but it has to do with a variant of entropy as the core natural generator of Antifragility.

[Revised to explain that it is not *replacing* other disciplines, just infiltrating them as the point was initially misunderstood…]

Nassim Nicholas Taleb via Facebook

[My comments posted to the original Facebook post follow below.]

I’m coming to this post a bit late as I’m playing a bit of catch up, but agree with it wholeheartedly.

In particular, applications to molecular biology and medicine are really beginning to come to a heavy boil in just the past five years. This particular year is the progenitor of what appears to be the biggest renaissance for the application of information theory to the area of biology since Hubert Yockey, Henry Quastler, and Robert L. Platzman’s “Symposium on Information Theory in Biology at Gatlinburg, Tennessee” in 1956.

Upcoming/recent conferences/workshops on information theory in biology include:

At the beginning of September, Christoph Adami posted an awesome and very sound paper on arXiv entitled “Information-theoretic considerations concerning the origin of life”  which truly portends to turn the science of the origin of life on its head.

I’ll note in passing, for those interested, that Claude Shannon’s infamous master’s thesis at MIT (in which he applied Boolean Algebra to electric circuits allowing the digital revolution to occur) and his subsequent “The Theory of Mathematical Communication” were so revolutionary, nearly everyone forgets his MIT Ph.D. Thesis “An Algebra for Theoretical Genetics” which presaged the areas of cybernetics and the current applications of information theory to microbiology and are probably as seminal as Sir R.A Fisher’s applications of statistics to science in general and biology in particular.

For those commenting on the post who were interested in a layman’s introduction to information theory, I recommend John Robinson Pierce’s An Introduction to Information Theory: Symbols, Signals and Noise (Dover has a very inexpensive edition.) After this, one should take a look at Claude Shannon’s original paper. (The MIT Press printing includes some excellent overview by Warren Weaver along with the paper itself.) The mathematics in the paper really aren’t too technical, and most of it should be comprehensible by most advanced high school students.

For those that don’t understand the concept of entropy, I HIGHLY recommend Arieh Ben-Naim’s book Entropy Demystified The Second Law Reduced to Plain Common Sense with Seven Simulated Games. He really does tear the concept down into its most basic form in a way I haven’t seen others come remotely close to and which even my mother can comprehend (with no mathematics at all).  (I recommend this presentation to even those with Ph.D.’s in physics because it is so truly fundamental.)

For the more advanced mathematicians, physicists, and engineers Arieh Ben-Naim does a truly spectacular job of extending ET Jaynes’ work on information theory and statistical mechanics and comes up with a more coherent mathematical theory to conjoin the entropy of physics/statistical mechanics with that of Shannon’s information theory in A Farewell to Entropy: Statistical Thermodynamics Based on Information.

For the advanced readers/researchers interested in more at the intersection of information theory and biology, I’ll also mention that I maintain a list of references, books, and journal articles in a Mendeley group entitled “ITBio: Information Theory, Microbiology, Evolution, and Complexity.”

Venn Diagram of how information theory relates to other fields.
Figure 1.1 [page 2] from
Thomas M. Cover and Joy Thomas’s textbook Elements of Information Theory, Second Edition
(John Wiley & Sons, Inc., 2006) [First Edition, 1991]

CECAM Workshop: “Entropy in Biomolecular Systems”

On Friday, I had an excellent and stimulating conversation with Arieh Ben-Naim about his recent writing and work, and he mentioned in passing that he had been invited to a conference relating to entropy and biology in Vienna.  A quick websearch found it quickly, and not having heard about it myself yet, I thought I’d pass it along to others who are regular readers and interested in the area.

The workshop on “Entropy in Biomolecular Systems” is being hosted by the Centre Européen de Calcul Atomique et Moléculaire (CECAM)

Logo for the Centre Européen de Calcul Atomique et Moléculaire (CECAM)

Location: DACAM, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030, Vienna, Austria
Dates: May 14, 2014 to May 17, 2014

The workshop is being organized by:

  • Richard Henchman (University of Manchester, United Kingdom)
  • Bojan Zagrovic (University of Vienna, Austria)
  • Michel Cuendet (Swiss Institute of Bioinformatics, Lausanne, Switzerland and Weill Cornell Medical College, New York, USA)
  • Chris Oostenbrink (University of Natural Resources and Life Sciences, Austria)

It’s being supported by CECAM, the European Research Council, and the Royal Society of Chemistry’s Statistical Mechanics and Thermodynamics Group.

I’ll note that the registration deadline is on April 21 with a payment deadline of April 30, so check in quickly if you haven’t already.

The summary from the workshop website states:

This workshop brings together the world’s experts to address the challenges of determining the entropy of biomolecular systems, either by experiment or computer simulation. Entropy is one the main driving forces for any biological process such as binding, folding, partitioning and reacting. Our deficient understandng of entropy, however, means that such important processes remain controversial and only partially understood. Contributions of water, ions, cofactors, and biomolecular flexibility are actively examined but yet to be resolved. The state-of-the-art of each entropy method will be presented and explained, highlighting its capabilities and deficiencies. This will be followed by intensive discussion on the main areas that need improving, leading suitable actions and collaborations to address the main biological and industrial questions.

Further details on the workshop can be found on the CECAM website.

 

As always, details on other upcoming workshops and conferences relating to information theory and biology can be found on our ITBio Conferences/Workshops page.