Network Science by Albert-László Barabási

Network Science by Albert-László BarabásiAlbert-László Barabási (Cambridge University Press)

I ran across a link to this textbook by way of a standing Google alert, and was excited to check it out. I was immediately disappointed to think that I would have to wait another month and change for the physical textbook to be released, but made my pre-order directly. Then with a bit of digging around, I realized that individual chapters are available immediately to quench my thirst until the physical text is printed next month.

The power of network science, the beauty of network visualization.

Network Science, a textbook for network science, is freely available under the Creative Commons licence. Follow its development on Facebook, Twitter or by signing up to our mailing list, so that we can notify you of new chapters and developments.

The book is the result of a collaboration between a number of individuals, shaping everything, from content (Albert-László Barabási), to visualizations and interactive tools (Gabriele Musella, Mauro Martino, Nicole Samay, Kim Albrecht), simulations and data analysis (Márton Pósfai). The printed version of the book will be published by Cambridge University Press in 2016. In the coming months the website will be expanded with an interactive version of the text, datasets, and slides to teach the material.

Book Contents

Personal Introduction
1. Introduction
2. Graph Theory
3. Random Networks
4. The Scale-Free Property
5. The Barabási-Albert Model
6. Evolving Networks
7. Degree Correlations
8. Network Robustness
9. Communities
10. Spreading Phenomena
Usage & Acknowledgements
About

Albert-László Barabási
on Network Science (book website)

Networks are everywhere, from the Internet, to social networks, and the genetic networks that determine our biological existence. Illustrated throughout in full colour, this pioneering textbook, spanning a wide range of topics from physics to computer science, engineering, economics and the social sciences, introduces network science to an interdisciplinary audience. From the origins of the six degrees of separation to explaining why networks are robust to random failures, the author explores how viruses like Ebola and H1N1 spread, and why it is that our friends have more friends than we do. Using numerous real-world examples, this innovatively designed text includes clear delineation between undergraduate and graduate level material. The mathematical formulas and derivations are included within Advanced Topics sections, enabling use at a range of levels. Extensive online resources, including films and software for network analysis, make this a multifaceted companion for anyone with an interest in network science.

Source: Cambridge University Press

The textbook is available for purchase in September 2016 from Cambridge University Press. Pre-order now on Amazon.com.

If you’re not already doing so, you should follow Barabási on Twitter.

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Matter, energy… knowledge: How to harness physics’ demonic power | New Scientist

Matter, energy… knowledge: How to harness physics' demonic power by Stephen Battersby (New Scientist)
Running a brain-twisting thought experiment for real shows that information is a physical thing – so can we now harness the most elusive entity in the cosmos?

This is a nice little overview article of some of the history of thermodynamics relating to information in physics and includes some recent physics advances as well. There are a few references to applications in biology at the micro level as well.

References

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Nick Lane and Philip Ball Discuss Mitochondria, Sex, and How to Live Longer

Nick Lane and Philip Ball Discuss Mitochondria, Sex, and How to Live Longer by Philip Ball (Nautil.us)
In his 2010 book, Life Ascending: The Ten Great Inventions of Evolution, Nick Lane, a biochemist at University College London, explores with eloquence and clarity the big questions of life: how it began, why we age and die, and why we have sex. Lane been steadily constructing an alternative view of evolution to the one in which genes explain it all. He argues that some of the major events during evolutionary history, including the origin of life itself, are best understood by considering where the energy comes from and how it is used. Lane describes these ideas in his 2015 book, The Vital Question: Why Is Life the Way It Is?. Recently Bill Gates called it “an amazing inquiry into the origins of life,” adding, Lane “is one of those original thinkers who make you say: More people should know about this guy’s work.” Nautilus caught up with Lane in his laboratory in London and asked him about his ideas on aging, sex, and death.

Biochemist Nick Lane explains the elements of life, sex, and aging in an engaging popular science interview.

Read more

Books by Nick Lane

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How Can We Apply Physics to Biology?

How Can We Apply Physics to Biology? by Philip Ball (nautil.us)
We don’t yet know quite what a physics of biology will consist of. But we won’t understand life without it.

This is an awesome little article with some interesting thought and philosophy on the current state of physics within biology and other related areas of study. It’s also got some snippets of history which aren’t frequently discussed in longer form texts.

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Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae”

A review of Summa Technologiae by Stanislaw Lem by David Auerbach from the Los Angeles Review of Books.

Summa Technologiae

AT LAST WE have it in English. Summa Technologiae, originally published in Polish in 1964, is the cornerstone of Stanislaw Lem’s oeuvre, his consummate work of speculative nonfiction. Trained in medicine and biology, Lem synthesizes the current science of the day in ways far ahead of most science fiction of the time.

His subjects, among others, include:

  • Virtual reality
  • Artificial intelligence
  • Nanotechnology and biotechnology
  • Evolutionary biology and evolutionary psychology
  • Artificial life
  • Information theory
  • Entropy and thermodynamics
  • Complexity theory, probability, and chaos
  • Population and ecological catastrophe
  • The “singularity” and “transhumanism”

Source: Devourer of Encyclopedias: Stanislaw Lem’s “Summa Technologiae” – The Los Angeles Review of Books

I came across this book review quite serendipitously today via an Auerbach article in Slate, which I’ve bookmarked. I found a copy of the book and have added it to the top of my reading pile. As I’m currently reading an advance reader edition of Sean Carroll’s The Big Picture, I can only imagine how well the two may go together despite being written nearly 60 years apart.

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What is Information? by Christoph Adami

What is Information? [1601.06176] by Christoph Adami (arxiv.org)
Information is a precise concept that can be defined mathematically, but its relationship to what we call "knowledge" is not always made clear. Furthermore, the concepts "entropy" and "information", while deeply related, are distinct and must be used with care, something that is not always achieved in the literature. In this elementary introduction, the concepts of entropy and information are laid out one by one, explained intuitively, but defined rigorously. I argue that a proper understanding of information in terms of prediction is key to a number of disciplines beyond engineering, such as physics and biology.

A proper understanding of information in terms of prediction is key to a number of disciplines beyond engineering, such as physics and biology.

Comments: 19 pages, 2 figures. To appear in Philosophical Transaction of the Royal Society A
Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Information Theory (cs.IT); Biological Physics (physics.bio-ph); Quantitative Methods (q-bio.QM)
Cite as:arXiv:1601.06176 [nlin.AO] (or arXiv:1601.06176v1 [nlin.AO] for this version)

From: Christoph Adami
[v1] Fri, 22 Jan 2016 21:35:44 GMT (151kb,D) [.pdf]

Source: Christoph Adami [1601.06176] What is Information? on arXiv

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Donald Forsdyke Indicates the Concept of Information in Biology Predates Claude Shannon

In the 1870s Ewald Hering in Prague and Samuel Butler in London laid the foundations. Butler's work was later taken up by Richard Semon in Munich, whose writings inspired the young Erwin Schrodinger in the early decades of the 20th century.

As it was published, I had read Kevin Hartnett’s article and interview with Christoph Adami The Information Theory of Life in Quanta Magazine. I recently revisited it and read through the commentary and stumbled upon an interesting quote relating to the history of information in biology:

Polymath Adami has ‘looked at so many fields of science’ and has correctly indicated the underlying importance of information theory, to which he has made important contributions. However, perhaps because the interview was concerned with the origin of life and was edited and condensed, many readers may get the impression that IT is only a few decades old. However, information ideas in biology can be traced back to at least 19th century sources. In the 1870s Ewald Hering in Prague and Samuel Butler in London laid the foundations. Butler’s work was later taken up by Richard Semon in Munich, whose writings inspired the young Erwin Schrodinger in the early decades of the 20th century. The emergence of his text – “What is Life” – from Dublin in the 1940s, inspired those who gave us DNA structure and the associated information concepts in “the classic period” of molecular biology. For more please see: Forsdyke, D. R. (2015) History of Psychiatry 26 (3), 270-287.

Donald Forsdyke, bioinformatician and theoretical biologist
in response to The Information Theory of Life in Quanta Magazine on

These two historical references predate Claude Shannon’s mathematical formalization of information in A Mathematical Theory of Communication (The Bell System Technical Journal, 1948) and even Erwin Schrödinger‘s lecture (1943) and subsequent book What is Life (1944).

For those interested in reading more on this historical tidbit, I’ve dug up a copy of the primary Forsdyke reference which first appeared on arXiv (prior to its ultimate publication in History of Psychiatry [.pdf]):

🔖 [1406.1391] ‘A Vehicle of Symbols and Nothing More.’ George Romanes, Theory of Mind, Information, and Samuel Butler by Donald R. Forsdyke  [1]
Submitted on 4 Jun 2014 (v1), last revised 13 Nov 2014 (this version, v2)

Abstract: Today’s ‘theory of mind’ (ToM) concept is rooted in the distinction of nineteenth century philosopher William Clifford between ‘objects’ that can be directly perceived, and ‘ejects,’ such as the mind of another person, which are inferred from one’s subjective knowledge of one’s own mind. A founder, with Charles Darwin, of the discipline of comparative psychology, George Romanes considered the minds of animals as ejects, an idea that could be generalized to ‘society as eject’ and, ultimately, ‘the world as an eject’ – mind in the universe. Yet, Romanes and Clifford only vaguely connected mind with the abstraction we call ‘information,’ which needs ‘a vehicle of symbols’ – a material transporting medium. However, Samuel Butler was able to address, in informational terms depleted of theological trappings, both organic evolution and mind in the universe. This view harmonizes with insights arising from modern DNA research, the relative immortality of ‘selfish’ genes, and some startling recent developments in brain research.

Comments: Accepted for publication in History of Psychiatry. 31 pages including 3 footnotes. Based on a lecture given at Santa Clara University, February 28th 2014, at a Bannan Institute Symposium on ‘Science and Seeking: Rethinking the God Question in the Lab, Cosmos, and Classroom.’

The original arXiv article also referenced two lectures which are appended below:

[Original Draft of this was written on December 14, 2015.]

References

[1]
D. Forsdyke R., “‘A vehicle of symbols and nothing more’. George Romanes, theory of mind, information, and Samuel Butler,” History of Psychiatry, vol. 26, no. 3, Aug. 2015 [Online]. Available: http://journals.sagepub.com/doi/abs/10.1177/0957154X14562755
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Quantum Biological Information Theory by Ivan B. Djordjevic | Springer

Quantum Biological Information Theory by Ivan B. Djordjevic (Springer, 2015)

Springer recently announced the publication of the book Quantum Biological Information Theory by Ivan B. Djordjevic, in which I’m sure many readers here will have interest. I hope to have a review of it shortly after I’ve gotten a copy. Until then…

From the publisher’s website:

This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects.

  • Integrates quantum information and quantum biology concepts;
  • Assumes only knowledge of basic concepts of vector algebra at undergraduate level;
  • Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology;
  • Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models on tumor and cancer development, quantum modeling of bird navigation compass, quantum aspects of photosynthesis, quantum biological error correction.

Source: Quantum Biological Information Theory | Ivan B. Djordjevic | Springer

9783319228150I’ll note that it looks like it also assumes some reasonable facility with quantum mechanics in addition to the material listed above.

Springer also has a downloadable copy of the preface and a relatively extensive table of contents for those looking for a preview. Dr. Djordjevic has been added to the ever growing list of researchers doing work at the intersection of information theory and biology.

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The Information Theory of Life | Quanta Magazine

The Information Theory of Life by Kevin Hartnett (Quanta Magazine)
The Information Theory of Life: The polymath Christoph Adami is investigating life’s origins by reimagining living things as self-perpetuating information strings.

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

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

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Molecular Programming Project

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

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

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
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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.

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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 #entropyWS, 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 #ITBio

 

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Probability Models for DNA Sequence Evolution

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
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