The existence of functional, non-protein-coding DNA is all too frequently portrayed as a great surprise uncovered by genome sequencing projects, both in large media outlets and in scientific publications that should have better quality control in place. Eric Lander, writing a Human Genome Project 10th anniversary retrospective in Nature, explains the real surprise about non-coding DNA that was revealed by big omics projects.
Georg, over at Lattice Points noted a piece about open science in Physics World:The adoption and growth of scientific journals has created a body of shared knowledge for our civilization, a collective long-term memory that is the basis for much of human progress. This system has changed surprisingly little in the last 300 years. Today, the Internet offers us the first major opportunity to improve this collective long-term memory, and to create a collective short-term working memory — a conversational commons for the rapid collaborative development of ideas.
There's a line that politicians opposed to embryonic stem cell research have been peddling lately: recent breakthroughs in stem cell technology have now made ethically questionable embryonic stem cell research obsolete and unnecessary. This isn't a new line - for years, opponents of embryonic stem cell research have always claimed that the latest research (whatever it happens to be) has obviated the need for embryonic stem cells.
Engineering A Biological Pulse GeneratorI've got my issues with synthetic biology. Either synthetic biologists do something trivial dressed up in elaborate engineering language, or they achieve something impressive and complex the old fashioned way (the way molecular biologists have been doing it for decades) - genetic engineering through trial and error, with very little principles-based engineering involved.What I want to see is a result that falls somewhere in between these two extremes: genetic engineering that's non-trivial, but not so complex that it's impossible to use simulation and the rudimentary quantitative design principles that are useful in biology.
With hot, new technologies, biologists are taking higher-resolution snapshots of what's going on inside the cell, but the results are stirring up controversy. One of the most interesting recent discoveries is that transcription is everywhere: DNA is transcribed into RNA all over the genome, even DNA that has long been thought to have a non-functional role. What is all of this transcription for? Does the 'dark matter' of the genome have some cryptic, undiscovered function?
Have we really stopped evolving? In Cosmos magazine, Steve Jones argues that human evolution is coming to an end:The question I have is: will human evolution really continue? I think the evidence shows that human evolution has largely come to a halt.He lists three components necessary for human evolution:First of all there's variation, which comes from mutation. Second, natural selection, which comes from inherited differences between individuals and their ability to reproduce.
Graduate education in the humanities may have its problems, but don't try to tar science with the same brush. In a NY Times Op-Ed, by Dr. Mark Taylor, the chairman of Columbia's religion department, we're told that graduate education in general is in need of a major overhaul.Graduate programs train students for jobs that most of them won't get:
Many computational biologists are interested in taking gene expression data, and using that data to computationally infer the underlying regulatory network that controls the observed pattern of gene expression.Why? Because doing the experiments to determine the structure of these regulatory networks is hard; if we could use more easily obtained data to reliably tease out the network structure, we'd be able to quickly characterize networks in unexplored cell types or in poorly studied microbes.
Bora has posted an interesting draft policy on social media from an unidentified "Big Research Institution" (BRI).It's already stimulating some good discussion (follow the link for more links) - no surprise, since the policy guidelines contain juicy quotes like these:All BRI social media output is the intellectual property of BRI.Whether you are setting up new BRI social media pages within the BRI website or on an existing social media site such as Flickr or Facebook, they need to follow the BRI interactive project process.
What's the key to everlasting youth? For years now, evidence has steadily accumulated, from studies on mice, flies, worms, and even yeast, that cutting calories is the secret to a long lifespan - at least in a wide range of non-human organisms. But does this work in humans?
The problem of how to model a biological system has been staring me in the face every day in recent months, and I need a place to indulge in baseless speculation. So if you stick around here at Adaptive Complexity for the next few weeks, you are going to get treated to a dose of half-baked, semi-coherent (at best), partially thought-out musings on what it takes to model a biological system.
One more book to pile on my to-read list. Via Carl Zimmer (go follow the link for a bloggingheads video interview), a fascinating book on bioengineering, Learning to Fly, by Rob Carlson, is coming out this fall.He has some insightful thoughts:
Today, if you like playing with electricity, you can hop over to Amazon and buy the Extreme Snap Circuits set and put together transistors, switches, lamps, motors, resistors, and capacitors to build all sorts of fun projects, from an auto-off night light to the perpetually entertaining space war timer. More ambitious engineers can buy off-the-shelf parts to build appliances, computers, and control systems for Boeing's 787 Dreamliner.What if you could engineer biology this way? What would you build? Physicist and scientific prophet Freeman Dyson would love to build genetically engineered pets and ornamental plants. Standford biologist Drew Endy envisions a collection of standardized biological parts called BioBricks, off-the-shelf modules that biological engineers can assemble like snap circuits into amazing biological machines. An annual undergraduate competition, the International Genetically Engineered Machine competition draws teams of biogeeks who design glowing microbes that spell "Hello World" on an agar plate and gut bacteria that smell like mint or bananas.This all sounds exciting, but what's the reality? Do biological engineers, or synthetic biologists (as they are most commonly called) have anything close to the know-how of today's electrical or aerospace engineers? The answer, obviously, is no.
