Synthetic biology

Synthetic biology is riff on nano/bio tech – according to Rudy Rucker, “it’s about building slippery wetware entities that might live in the real world.” Rucker has a rich post about the field, and its promises (“we ought to be able to design some kind of microorganism that eats
inexpensive crud and generates energy in some usable form or another”) and problems (“what’s to stop a particularly virulent synthetic organism from eating everything on earth?”) Ending with a cool science friction premise:

Suppose it were possible to encode a person’s memory
and personality into a single, very large, DNA-like molecule. Now
suppose that someone turns himself into a viral disease that other
people can catch. If I were you—sneeze—oh, wait, I guess I am.

Gesundheit.

Politics and Climate Change

I like to think climate change is settled – we have scientific consensus, we know it’s happening, we generally understand the human actions that have accelerated climate change since the dawn of the industrial era. Many of us are feeling energy about reducing our carbon footprint and our overall planetary impact and concern that it’s too late for mitigation, time for adaptation. I personally have been involved with projects like Austin350, Worldchanging, and Powersmack, and I’ve blogged about global warming at Change.org. I’ve been thinking and writing about global warming since Bruce Sterling made me aware of it in the late 1990s. I worked with him on the Viridian Design Movement and wrote an article on climate change for the issue of Whole Earth Magazine he edited. In researching the article, “Being Green in 2001,” I learned that scientists were concerned that their commitment to scientific method – to hypotheses rather than certainties – was misinterpreted as uncertainty about the anthropogenic drivers of climate change. Since then broad scientific consensus has developed, especially via the UN’s Intergovernmental Panel on Climate Change, IPCC.

I was surprised, then, to have a conversation recently with an intelligent, articulate local businessman who told me that this scientific consensus doesn’t exist, and while he could acknowledge that the climate is changing, it’s a natural cycle associated with solar activity. He’s sent me various charts and links. He’s just forwarded an email that mentions Ian Plimer and his book Heaven and Earth, Bjorn Lomborg, and Kimberley Strassel’s Wall Street Journal op ed piece, “The Climate Change Climate Change,” which says that “the number of skeptics is swelling everywhere.” Among other things, she mentions a list that Senator Jim Inhofe has assembled of scientists who supposedly deny that human action is associated with global warming, and says that the earth’s temperature “has flatlined since 2001.” (Has it?) If you read the comments on the op-ed piece, you see that the question of human action and climate change has been politicized – challenged by the right as a left-wing scam. This is really unfortunate – the science is lost in a fog of political wrangling.

I’m not so sure about the good-bad thing…

Sex, beer, wine, pot… and maggots! Top 10 bad things that are gooood for you. (Via Lane Becker!)

They’re creepy, slimy and altogether ooky, but maggots can save your life. These squirmy larvae are science’s newest wonder-cure and were approved in 2003 as the Food & Drug Administration’s only live medical device. Placed on serious wounds, maggots mimic their “wild” lifestyle and munch on bacteria and dead tissue, stimulating healing and helping to prevent infection.

A law of evolving patterns in living systems

Constructal law can predict patterns in living sysems. [Link]

“Our finding that animal locomotion adheres to constructal law tells us that – even though you couldn’t predict exactly what animals would look like if you started evolution over on earth, or it happened on another planet – with a given gravity and density of their tissues, the same basic patterns of their design would evolve again,” [Penn state biologist James] Marden added.

The law, which [Adrian] Bejan started describing in 1996, is the principle that flow systems evolve in time to balance and minimize imperfections, reducing friction or other forms of resistance, so that they flow more and more easily in time. He is fond of using illustrations to make his point. For example, he has used images ranging from the branching symmetries of the lungs, river basins and trees touching top-to-top.

Darwin and Buddhism

Darwin Fish
Psychologist Paul Ekman believes that Charles Darwin may have been inspired by Tibetan Buddhism. Says Ekman,

The Buddhist view, like Darwin, said that the seed of compassion is in mothering, global compassion: focus on others as mother. When I see you suffer it makes me suffer, and that motivates me to reduce your suffering so I can reduce my suffering. The Dalai Lama says compassionate acts help me more than the person I help. That’s identical in Buddhism and in Darwin’s explicit writings

Darwin knew something of Tibetan Buddhism, but there’s no established link between his views and Buddhist thinking. However “his view on the nature of commpassion is identical in almost the exact words to the view of Tibetan Buddhism.”

Participatory Medicine

In a retreat today and tomorrow with founders of a participatory medicine movement at Cook’s Branch near Houston. In participatory medicine, the patient comes first, and is part of a team that also includes patient groups and communities, healthcare providers, and clinical researchers (paraphrasing the Wikipedia article, which has much more on the subject):

Participatory medicine is a phenomenon similar to citizen/network journalism where everyone, including the professionals and their target audiences, works in partnership to produce accurate, in-depth & current information items. It is not about patients or amateurs vs. professionals. Participatory medicine is, like all contemporary knowledge-building activities, a collaborative venture. Medical knowledge is a network.

Thoughts about perception and communication

Carnegie Mellon scientists are studying how the brain makes sense of natural scenes using a computational model of visual processing. “The model employs an algorithm that analyzes the myriad patterns that compose natural scenes and statistically characterizes those patterns to determine which patterns are most likely associated with each other.”

The bark of a tree, for instance, is composed of a multitude of different local image patterns, but the computational model can determine that all these local images represent bark and are all part of the same tree, as well as determining that those same patches are not part of a bush in the foreground or the hill behind it.

Whether the theory is exactly correct or not, in thinking about it, I realize that we take understanding and perception quite a bit for granted. Our comprehension of the world is supported by complex internal processes that, like all characteristics of living systems, can vary from one “bundle” (human being) to another. We evolve diverse assumptions about the world based on our diverse interpretations. When we communicate, we generally think we share assumptions about reality, but our assumptions are only similar, and less similar where we have differences that will color perception (culture, language, internal process). Communication is far more difficult than we imagine. How do you communicate more of your substructure, so that the things you write or say are understood because your specific neural context is understood? I studied Irish author James Joyce quite a bit when I was in college, and I recall that, with Finnegans Wake, he created a book that could only be understood if you read what he’d read and could get into his head. He understood that a reader’s experience of a book will differ from the experience the author might have intended, depending on the reader’s background, perception, interpretation, culture… so each reader’s experience of a book is different, and if you’re trying to convey your unique sense of the world as you sensed it, you have to demand that the reader crack your code by following a path similar to the path you followed in reading, thinking, writing.

Obama on Technology and Innovation

The Obama presidency hopefully starts today, not January 20 – and it’s time for all of us to start real work on a future that’s not just survivable, but thrivable. My particular interests are social technology and sustainability, and on the tech side, I’m particularly interested in the ambitious plan set forth in Obama’s white paper, “Connecting and Empowering All Americans through Technology and Innovation” (linked as pdf). The doc incorporates some of the best thinking about where we should focus…

Ensure the Full and Free Exchange of Information through an Open Internet and Diverse Media Outlets – including a clueful paragraph on protecting the openness of the Internet and another on encouraging diversity in media ownership.

Create a Transparent and Connected Democracy. Tals about online tools for open government, and “bringing government into the 21st Century,” using tech “to reform government and improve the exchange of information between the federal government and citizens while ensuring the security of our networks.” To that end, he wants to appoint a Chief Technology Officer. (D’oh – you mean we didn’t already have one?)

Deploy a Modern Communications Infrastructure – great news for the “Freedom to Connect” crowd, including yours truly. “Barack Obama believes that America should lead the world in broadband penetration and Internet access,” so he’s going to push for a redefinition of what constitutes broadband in the U.S., i.e. fatter pipes. He also wants to open spectrum for more and better wireless deployment.

Employ Technology and Innovation to Solve Our Nation’s Most Pressing Problems, such as lowering health care costs by doing more to integrate records and facilitate digital claims processing. Healthcare systems are a patchwork mess, so this will be a huge challenge – it’s definitely time to take it on.

Invest in Climate-Friendly Energy Development and Deployment. Those of us who are interested in clean energy development know that it’s all about technology – we replace resource extraction with knowledge development and engineering to support greater efficiencies as well as the development of new forms of energy. Obama has several items for supporting the development of the clean energy sector, and for upgrading education so that our schools will produce more science and engineering graduates, and “[tap] the diversity of America to meet the increasing demand for a skilled workforce…so that we can retain and
grow jobs requiring 21st century skills rather than forcing employers to find skilled workers abroad.” He’ll also modernize public safety networks.

Improve America’s Competitiveness. “Barack Obama supports doubling federal funding for basic research, changing the posture of our federal government from being one of the most anti-science administrations in American history to one that embraces science and technology.” Obama proposes making the R&D tax credit permanent, reforming immigration, doing more to promote American business abroad, ensuring competitive markets, protecting American intellectual property abroad and at home, and (big one) reforming the patent system. “By improving predictability and clarity in our patent system, we will help foster an environment that encourages innovation. Giving the Patent and Trademark Office (PTO) the resources to improve patent quality and opening up the patent process to citizen review will reduce the uncertainty and wasteful litigation that is currently a significant drag on innovation.”

This is a lot to accomplish, but vision, attitude, and powerful intention will go a long way in getting us where we need to be after eight years of backward thinking and indifference. Personally, I’m putting my nose to the grindstone and plowing ahead with the the two areas of focus I’ve had for years – on the social web and on sustainability, both well-addressed by Obama’s plan – and I’m feeling invigorated knowing that the new administration will be supporting, not obstructing, progress in both areas.

Attention, multitasking, and persistent panic

I used to tell people that “I’m a multitasking fool,” and in recent years, I’ve seen greater emphasis on “fool” – yes, I was good at balancing many tasks, I could keep a lot of balls in the air without dropping them. As I matured, I realized that depth has more value than breadth, and in recent years I’ve been trying to learn to focus and do a few things well.

Alina Tugend in The New York Times notes a multitasking trend since the 1990s, saying that “while multitasking may seem to be saving time, psychologists, neuroscientists and others are finding that it can put us under a great deal of stress and actually make us less efficient.” As a good case study who’s thought about it a lot, I felt real resonance with the quote from Edward Hallowell, author of CrazyBusy: Overstretched, Overbooked, and About to Snap!: “Multitasking is shifting focus from one task to another in rapid succession. It gives the illusion that we’re simultaneously tasking, but we’re really not. It’s like playing tennis with three balls.”

….despite what many of us think, you cannot simultaneously e-mail and talk on the phone. I think we’re all familiar with what Dr. Hallowell calls “e-mail voice,” when someone you’re talking to on the phone suddenly sounds, well, disengaged.

“You cannot divide your attention like that,” he said. “It’s a big illusion. You can shift back and forth.”

The article goes on to discuss overload, fragmentation, and the neural overhead of task-switching.

Dr. Hallowell has termed this effort to multitask “attention deficit trait.” Unlike attention deficit disorder, which he has studied for years and has a neurological basis, attention deficit trait “springs entirely from the environment,” he wrote in a 2005 Harvard Business Review article, “Overloaded Circuits: Why Smart People Underperform.”

“As our minds fill with noise — feckless synaptic events signifying nothing — the brain gradually loses its capacity to attend fully and gradually to anything,” he wrote. Desperately trying to keep up with a multitude of jobs, we “feel a constant low level of panic and guilt.”

Sound familiar?

The loophole in the second law of thermodynamics

A Scientific American article asks, regarding the second law of thermodynamics: “if the world is steadily becoming more disordered, how do you explain the self-organization that often occurs in nature?” [Link]

At root, the trouble is that classical thermodynamics assumes systems are in equilibrium, a placid condition seldom truly achieved in the real world.

A new approach closes this loophole and finds that the second law holds far from equilibrium. But the evolution from order to disorder can be unsteady, allowing for pockets of self-organization.

The article goes on to say that “the second law is universal but also found that it is not nearly as gloomy as its reputation suggests,” because “it applies only when the system under study is in a quiescent state called equilibrium,” i.e. “thermodynamics…deals only with situations of stillness.” However nature, generally, isn’t standing still, but is in a persistent state of flux (ask any buddhist). The conclusion of the article:

…the development of order from chaos, far from contradicting the second law, fits nicely into a broader framework of thermodynamics. We are just at the threshold of using this new understanding for practical applications. Perpetual-motion machines remain impossible, and we will still ultimately lose the battle against degeneration. But the second law does not mandate a steady degeneration. It quite happily coexists with the spontaneous development of order and complexity.