Brief book overview of Matthew Cobb's "Life’s Greatest Secret" from The Economist.
Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code. By Matthew Cobb. Basic Books; 434 pages; $29.99. Profile Books; £25.
Brief book overview of Matthew Cobb's "Life’s Greatest Secret" from The Economist.
Life’s Greatest Secret: The Story of the Race to Crack the Genetic Code. By Matthew Cobb. Basic Books; 434 pages; $29.99. Profile Books; £25.
The underlying mathematics of what he’s discussing are fantastic (though he doesn’t go into them in his book), but the overarching implications of his ideas with relation to the future of humankind as a function of our economic system and society could have some significant impact.
“César visits the RSA to present a new view of the relationship between individual and collective knowledge, linking information theory, economics and biology to explain the deep evolution of social and economic systems.
In a radical rethink of what an economy is, one of WIRED magazine’s 50 People Who Could Change the World, César Hidalgo argues that it is the measure of a nation’s cultural complexity – the nexus of people, ideas and invention – rather than its GDP or per-capita income, that explains the success or failure of its economic performance. To understand the growth of economies, Hidalgo argues, we first need to understand the growth of order itself.”
It also not coincidentally is the root of the vast majority of the problems the world is currently facing. There are so many great quotes here, I can’t pick a favorite, so I’ll highlight the same one Kimb Quark did that brought my attention to it:
How a mathematical breakthrough from the 1960s now powers everything from spacecraft to cell phones.
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):
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.”
Source: MPP: Home
Source: INFOGRAPHIC: A world of languages – and how many speak them
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.”
Top chefs and Harvard researchers explore how everyday cooking and haute cuisine can illuminate basic principles in physics and engineering, and vice versa.
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”
- Social events and fun activities
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
I’ll let their site speak for itself below, but they already have an interesting line up of speakers including:
Additional details about the conference including the participants, program, venue, and registration can also be found at their website.
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:
https://www.youtube.com/playlist?list=PLRyq_4VPZ9g-3869ozbY_eEp6jZhWL0UE
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.
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.
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.
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.