Physicist Stephen Hawking made a splash this week when he announced that he had solved a vexing conundrum that had puzzled generations of leading physicists -- including the 73-year-old scientific superstar himself -- for the better part of a half-century.
Brief book overview of Matthew Cobb's "Life’s Greatest Secret" from The Economist.
For those interested in some of the history behind genetics, evolution, biology and information theory, the following book, which I just saw the attached review in The Economist, is likely to be of interest:
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.
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.Syndicated copies to:
“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: HomeSyndicated copies to:
August 10-13, 2015 – UC San Diego, La Jolla, California
Application deadline: June 7, 2015
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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
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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 Edge.org's interview with Richard Dawkins.
“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 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.Syndicated copies to:
Category theory looks set to become the dominant foundational basis for all mathematics. It could, in fact, already have achieved that status through stealth.
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Beauty, even in Maths, can exist in the eye of the beholder. That might sound a little surprising, when, after all, what could be more objective than mathematics when thinking about truth, and what, therefore, could be more natural than for beauty and goodness, the twin accomplices to truth, to be co-joined ?
In the 70 odd years since Samuel Eilenberg and Saunders Mac Lane published their now infamous paper “A General Theory of Natural Equivalences“, the pursuit of maths by professionals (I use here the reference point definition of Michael Harris – see his recent publication “Mathematics without Apologies“) has become ever more specialised. I, for one, don’t doubt cross disciplinary excellence is alive and sometimes robustly so, but the industrially specialised silos that now create, produce and then sustain academic tenure are formidable within the community of mathematicians.
Beauty, in the purest sense, does not need to be captured in a definition but recognised through intuition. Whether we take our inspiration from Hardy or Dirac, or whether we experience a gorgeous thrill when encountering an austere proof that may have been confronted thousands of times before, the confluence of simplicity and beauty in maths may well be one of the few remaining places where the commonality of the “eye” across a spectrum of different beholders remains at its strongest.
Neither Eilenberg nor Mac Lane could have thought that Category theory, which was their attempt to link topology and algebra, would become so pervasive or so foundational in its influence when they completed and submitted their paper in those dark days of WW 2. But then neither could Cantor, have dreamt about his work on Set theory being adopted as the central pillar of “modern” mathematics so soon after his death. Under attack from establishment figures such as Kronecker during his lifetime, Cantor would not have believed that set theory would become the central edifice around which so much would be constructed.
Of course that is exactly what has happened. Set theory and the ascending magnitude of infinities that were unleashed through the crack in the door that was represented by Cantor’s diagonal conquered all before them.
Until now, that is.
In an article in Science News, Julie Rehmeyer describes Category Theory as “perhaps the most abstract area of all mathematics” and “where math is the abstraction of the real world, category theory is an abstraction of mathematics”.
Slowly, without fanfare, and with an alliance built with the emergent post transistor age discipline of computer science, Category theory looks set to become the dominant foundational basis for all mathematics. It could, in fact, already have achieved that status through stealth. After all, if sets are merely an example of a category, they become suborned without question or query. One might even use the description ‘subsumed’.
There is, in parallel, a wide ranging discussion in mathematics about the so called Univalent Foundation that is most widely associated with Voevodsky which is not the same. The text book produced for the year long univalence programme iniated at the IAS that was completed in 2013 Homotopy type theory – Univalent Foundations Programme states:
“The univalence ax-iom implies, in particular, that isomorphic structures can be identified, a principle that mathematicians have been happily using on workdays, despite its incompatibility with the “official”doctrines of conventional foundations..”
before going on to present the revelatory exposition that Univalent Foundations are the real unifying binding agent around mathematics.
I prefer to think of Voevodsky’s agenda as being narrower in many crucial respects than Category Theory, although both owe a huge amount to the over-arching reach of computational advances made through the mechanical aid proffered through the development of computers, particularly if one shares Voevodsky’s view that proofs will eventually have to be subject to mechanical confirmation.
In contrast, the journey, post Russell, for type theory based clarificatory approaches to formal logic continues in various ways, but Category theory brings a unifying effort to the whole of mathematics that had to wait almost two decades after Eilenberg and Mac Lane’s paper when a then virtually unknown mathematician, William Lawvere published his now much vaunted “An Elementary Theory of the Category of Sets” in 1964. This paper, and the revolutionary work of Grothendieck (see below) brought about a depth and breadth of work which created the environment from which Category Theory emerged through the subsequent decades until the early 2000’s.
Lawvere’s work has, at times, been seen as an attempt to simply re-work set theory in Category theoretic terms. This limitation is no longer prevalent, indeed the most recent biographical reviews of Grothendieck, following his death, assume that the unificatory expedient that is the essential feature of Category theory (and I should say here not just ETCS) is taken for granted, axiomatic, even. Grothendieck eventually went much further than defining Category theory in set theoretic terms, with both Algebraic Topology and Mathematical Physics being fields that now could not be approached without a foundational setting that is Category theory. The early language and notation of Category Theory where categories ‘C’ are described essentially as sets whose members satisfy the conditions of composition, morphism and identity eventually gave way post Lawvere and then Lambek to a systematic adoption of the approach we now see where any and all deductive systems can be turned into categories. Most standard histories give due credit to Eilenberg and Mac Lane as well as Lawvere (and sometimes Cartan), but it is Grothendieck’s ‘Sur quelques points d’algebre homologique’ in 1957 that is now seen as the real ground breaker.
My own pathway to Category theory has been via my interest in Lie Groups, and more broadly, in Quantum Computing, and it was only by accident (the best things really are those that come about by accident !) that I decided I had better learn the language of Category theory when I found Lawvere’s paper misleadingly familiar but annoyingly distant when, in common with most people, I assumed that my working knowledge of notation in logic and in set theory would map smoothly across to Category theory. That, of course, is not the case, and it was only after I gained some grounding in this new language that I realised just how and why Category theory has an impact far beyond computer science. It is this journey that also brings me face to face with a growing appreciation of the natural intersection between Category theory and a Wittgensteinian approach to the Philosophy of Mathematics. Wittgenstein’s disdain for Cantor is well documented (this short note is not an attempt to justify, using Category theory, a Wittgensteinian criticism of set theory). More specifically however, it was Abramsky and Coecke’s “Categorical Quantum Mechanics” that helped me to discern more carefully the links between Category Theory and Quantum Computing. They describe Category Theory as the ‘language of modern structural mathematics’ and use it as the tool for building a mathematical representation of quantum processes, and their paper is a thought provoking nudge in the ribs for anyone who is trying to make sense of the current noise that surrounds Quantum mechanics.
Awodey and Spivak are the two most impressive contemporary mathematicians currently working on Category Theory in my view, and whilst it is asking for trouble to choose one or two selected works as exemplars of their approach, I would have to say that Spivak’s book on Category Theory for the Sciences is the standout work of recent times (incidentally the section in this book on ‘aspects’ bears close scrutiny with Wittgenstein’s well known work on ‘family resemblances’).
Awodey’s 2003 paper is as good a recent balance between a mathematical and philosophical exposition of the importance of category theory as exists whilst his textbook is often referred to as the standard entry point for working mathematicians.
Going back to beauty, which is how I started this short note. Barry Mazur wrote an article in memory of Saunders Mac Lane titled ‘When is one thing equal to another‘ which is a gem of rare beauty, and the actual catalyst for this short note. If you read only one document in the links from this article, then I hope it is Mazur’s paper.
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.Syndicated copies to:
Michael A. Nielsen, the author of one of our favorite books on Quantum Computation and Quantum Information, is writing a new book entitled Neural Networks and Deep Learning. He’s been releasing portions of it for free on the internet in draft form every two or three months since 2013. He’s also maintaining an open code repository for the book on GitHub.Syndicated copies to:
The Postdoctoral Experience Revisited builds on the 2000 report Enhancing the Postdoctoral Experience for Scientists and Engineers. That ground-breaking report assessed the postdoctoral experience and provided principles, action points, and recommendations to enhance that experience. Since the publication of the 2000 report, the postdoctoral landscape has changed considerably. The percentage of PhDs who pursue postdoctoral training is growing steadily and spreading from the biomedical and physical sciences to engineering and the social sciences. The average length of time spent in postdoctoral positions seems to be increasing. The Postdoctoral Experience Revisited reexamines postdoctoral programs in the United States, focusing on how postdocs are being guided and managed, how institutional practices have changed, and what happens to postdocs after they complete their programs. This book explores important changes that have occurred in postdoctoral practices and the research ecosystem and assesses how well current practices meet the needs of these fledgling scientists and engineers and of the research enterprise. The Postdoctoral Experience Revisited takes a fresh look at current postdoctoral fellows - how many there are, where they are working, in what fields, and for how many years. This book makes recommendations to improve aspects of programs - postdoctoral period of service, title and role, career development, compensation and benefits, and mentoring. Current data on demographics, career aspirations, and career outcomes for postdocs are limited. This report makes the case for better data collection by research institution and data sharing. A larger goal of this study is not only to propose ways to make the postdoctoral system better for the postdoctoral researchers themselves but also to better understand the role that postdoctoral training plays in the research enterprise. It is also to ask whether there are alternative ways to satisfy some of the research and career development needs of postdoctoral researchers that are now being met with several years of advanced training. Postdoctoral researchers are the future of the research enterprise. The discussion and recommendations of The Postdoctoral Experience Revisited will stimulate action toward clarifying the role of postdoctoral researchers and improving their status and experience.
The National Academy of Sciences has published a (free) book: The Postdoctoral Experience (Revisited) discussing where we’re at and some ideas for a way forward.
Most might agree that our educational system is far less than ideal, but few pay attention to significant problems at the highest levels of academia which are holding back a great deal of our national “innovation machinery”. The National Academy of Sciences has published a (free) book: The Postdoctoral Experience (Revisited) discussing where we’re at and some ideas for a way forward. There are some interesting ideas here, but we’ve still got a long way to go.
Finally, after 140 years, Robert Strain and Philip Gressman at the University of Pennsylvania have found a mathematical proof of Boltzmann’s equation, which predicts the motion of gas molecules.
In the last two years, at least 10 law schools have made their grading systems more lenient to give their students a better chance in a soft job market.
Is GPA tampering and grade inflation going too far with changes like this?
Imagine having your back cut open, part of your spine removed, a stabilizing device that resembles a mini oil rig mounted on your back, the outer membrane of your spinal cord sliced open and experimental stem cells injected into it -- all for the advancement of science because it's not expected to benefit you.
Another article announcing the first stem cells being transplanted into a human patient in the United States. I worked with the researchers and surgeon in this experiment and built the microinjectors that were used in the lead up experiments as well as for this first patient.
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Atlanta, Georgia — Imagine having your back cut open, part of your spine removed, a stabilizing device that resembles a mini oil rig mounted on your back, the outer membrane of your spinal cord sliced open and experimental stem cells injected into it — all for the advancement of science because it’s not expected to benefit you.
John Cornick, 51, did just that earlier this month as part of a groundbreaking clinical trial.
Almost a year ago, Cornick was told he had ALS — better known as Lou Gehrig’s disease. The diagnosis left him “fairly devastated,” he says.
He knew the prospects were grim because there is no cure.
But John wasn’t giving up so quickly, nor was his wife, Gina.
“I knew he was a fighter from the beginning and he really wanted to do something,” Gina Cornick says. She found information about a clinical trial on online and immediately signed him up, even though she had no idea where it was being held.
ALS destroys the nerve cells in the brain and spine which control muscle movement. When the brain can no longer tell muscles to move, they eventually die, depriving the patient of the ability to move arms and legs and eventually breathe.
The goal of this phase 1 trial is to determine whether fetal stem cells can safely be injected into the spinal cord. Ultimately, researchers hope to show that these cells may slow or halt the progression of the fatal disease.
But for now, the only goal is establishing safety.
The Cornicks live in North Carolina, just a few hours from Atlanta, Georgia’s Emory University, the site of the trial. It is the first FDA-approved clinical trial to inject fetal stem cells directly into the spinal cord of an adult.
Dr. Jonathan Glass, director of Emory’s ALS center, is overseeing the trial. Cornick and two previous patients in the trial are heroes, says Glass, because at this point, the trial will likely produce only information, not results.
“In reality what do these patients have? Time, families and their life and we’re putting all of these at risk,” says Glass.
Dr. Lucie Bruijn, science director of the ALS Association, says the progress being made in this clinical trial is exciting. “We’ve been able to move it forward … from animal testing now into actual patients.” The treatment had not been tried in humans before.
Glass hopes this trial will lead to a new form of treatment for people with ALS. “We’re testing multiple things: We’re testing the safety of the surgery; we’re testing the cells; we’re testing immunosuppressants[because scientists do not know whether the body will reject the cells].” They are also testing how well Cornick handles this major surgical procedure, says Glass.
“After we’re finished with the first 12 or 18 patients we will know whether this is surgery that patients can tolerate.”
As he was prepped for surgery, Cornick was hopeful but realistic. “Well, of course you’d like to get up and walk … but I know that’s not going to happen.”
The stem cells used in the surgery are shipped overnight from Maryland, where Neuralstem, the company funding the trial, is based. The stem cells’ source is donated tissue from the spinal cord of an 8-week old aborted fetus, which was donated to the company. The company has developed a method that enables growth of millions of stem cells from this single source of human nerve stem cells.
Before the surgery can begin, a technician at Emory has to verify that a majority of stem cells made it to Atlanta alive. At least 70 percent have to be viable. In this case three samples under the microscope showed 85 percent of the cells arrived alive.
Lead researcher Dr. Eva Feldman, a neurologist at the University of Michigan, designed the trial just four years ago. After a lot of animal testing, her team determined that using fetal nerve stems rather than human embryonic or adult stem cells (such as bone marrow stem cells) was most effective, she says.
Stem cells have the ability to turn into different cells in the body. However, human embryonic stem cells, which come from 4- or 5-day-old embryos, also been found to sometimes turn into cancer cells. Fetal stem cells, such as those used in this trial, are a few weeks older and have already taken on a specific identity — in this case nerve cells.
Feldman says the fetal stem cells used in this trial did not become any of the unwanted cell types. “That’s very, very important,” she says.
Animal testing also proved very useful when it came to figuring out how to actually inject the stem cells. Emory University’s neurosurgeon Dr. Nicholas Boulis invented the device that holds the needle that injects the stem cells. The goal is to inject the cells without injuring the spine and causing even more paralysis. He practiced on 100 pigs before attempting the procedure on a human.
Boulis says it’s critical that the injection be done in a very slow and controlled way.
“If you inject quickly, you’re going to create pressure at the head of the needle and that can cause damage,” Boulis says. That pressure can also inflate an area in the spinal cord which could cause the stem cells to seep back out of the cord when the needle is pulled out, he says. “So by pumping [cells] in slowly you have more security that you are not going to have reflux and you’re not going to have damage.”
Dr. Jeffrey Rothstein, who heads the ALS research center at Johns Hopkins University and is not connected to this trial, said work on this method is a big achievement. “This is purely about how to surgically deliver cellular therapy to spinal cord,” he says. “It’s never been done before.”
After the spinal cord was exposed, the injections began. Cornick got five — each one contains about 100,000 stem cells.
The four-and-a-half hour surgery went smoothly, Boulis, says. “There were no surprises.”
A day after surgery, Cornick was lying flat in a hospital bed, chatting and laughing with some friends from North Carolina.
One week after surgery, he says he felt amazingly well and was still hopeful the cells would do some good for him.
Two weeks later Cornick’s stitches were removed and he was able to drive home. But he will be making frequent visits back to Atlanta as Glass and his team continue to monitor him.
Neuralstem’s Chief Scientific Officer Karl Johe says after the trial’s safety board reviews all existing data, including Cornick’s results, a fourth patient can be treated with the stem cells.
“Patients Four, Five and Six will receive twice as many [stem cell] injections,” Johe says. They will get five more injections on the other side of the spinal cord compared with Cornicks’s surgery.
Cornick expects the researchers will follow his progress for a long time. He says he understands the need for people to be willing to participate in experimental research like this.
“For me it just seemed like the right thing to do. I almost felt I had an obligation to do this,” he says. “To help other people and myself.”