Archive for the 'Uncategorized' Category



20
May
10

Big deal: Venter creates first synthetic cell

Here’s what I’d consider a Big F***ing Deal (in the words of  Joe Biden): the J Craig Venter Institute is reporting it has created the first synthetic cell that can survive and reproduce itself. The DNA for this bacterial cell (Mycoplasma mycoides JCVI-syn1.0) was synthesized from DNA fragments. The bacterium is a new species not produced in nature: hence, the name “JCVI-syn1.0.” The code for the cell is very akin to software. Presumably there will be versions 1.1, 2.0, and so on. This is a lot like baking a cake from scratch, from the raw ingredients.

The team of 25 researchers took Mycoplasma capricolum bacteria and completely rewrote its genetic code of more than 1 million base pairs of DNA. The data was sequenced as chemical DNA fragments and sewn together using yeast and E. coli bacteria.

To make no mistake that the genome was synthetic the scientists encoded quotations in the DNA including a line from “A Portrait of the Artist as a Young Man” by James Joyce: “To live, to err, to fall, to triumph, to recreate life out of life.”

So the era of fully human-designed and engineered organisms is at hand. Venter, et al.,  have been working for several years to create new life forms from the minimal elements required for life. It’s happening.

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11
May
10

Esther says it well

Release 1.0's Esther Dyson. This photograph wa...

Image via Wikipedia

Addendum: After posting about the change signaled by the OTC genetics testing kit that’s going on sale at Walgreen’s, I bumped into this article posted a couple of weeks ago by Esther Dyson on HuffPo. She makes a strong statement about how big the market for self-tracking products and services for health is getting. There’s a big movement afoot by users and by service providers for folks to dig deeper into their health characteristics. Her remarks are right in line with what I see happening.

03
May
10

Helping Mother Nature…with a glue gun

My wife and I discovered a bunch of twigs on our outside deck. We were puzzled for a while until I noticed that a dove couple was trying to build a nest on top of the light fixture up against the house and over the deck. They must be inexperienced because as hard as the male worked fetching twigs they just fell off on the deck. I told my wife to let nature take its course and if they couldn’t finish the job they’d learn something.

But, nooo! With her bottom lip sticking out my wife went to the garage and came back with the glue gun, a bag of raffia, and a clear plastic saucer used to catch water under a plant. A few minutes later there I was gluing the saucer to the top of the light fixture, stuffing raffia in the bottom and then stacking some of the doves’ twigs on top so they would think they’d done it. As I write this I can hear the whir of wings. Is this helping nature or interfering with the process of the ecosystem?

21
Apr
10

good news from the abyssal plain

I saw something the other day about life on Earth that gave me a lift. Science Now reported that the Census of Marine Life, after a decade of surveying marine organisms all over the world, has documented that 90% of the ocean’s biomass consists of microbes, larvae, and plankton. The total mass of these little critters is equivalent to 240 billion elephants! Elephant-equivalents. The researchers pulled the creatures from the sea itself, from the mud, from the deep-sea vents, and from the bottom of the abyssal plain. (The phrase “abyssal plain” gives me the chills!)

Using new generation sequences researchers identified 18 million DNA sequences. Mich Sogan, a Woods Hole scientist, says “there could be as many as a billion bacteria and archaea, another group of single-cell organisms like bacteria.” A couple of interesting findings are: 1) the microbial diversity increased the deeper they looked in the water column, 2) but sometimes a microbe’s environment  is simply one other organism.

A bonus interest for me is to learn that the richest marine organism environment is the plateau off the Pacific Northwest Coast where 25,000 to 35,000 different microorganisms live in each litre of sea water. I’m writing this post from Beaverton, Oregon, where my wife and I are planning to move next month. So I can just drive to the coast and wade in the rich microbial soup.

All this lifts me because I relish the thought that here on Earth, whether or not we humans commit to being responsible stewards to the one life-perfect planet we know of, the richness of life code on the planet is ineradicable. Human affairs often discourage me, but life is indomitable. The Earth has occupied a sweet-spot for life for billions of years and will continue to for many more.

15
Apr
10

playing doctor with the iphone

Below is a video from Nature Medicine. It’s intended to introduce the journal’s readers — I imagine MDs and PhDs — to iPhone apps from the iTunes Medical category. Not a bad idea. When I posted a couple of weeks ago my take on whether or not the public needs doctor navigators when getting health info from the internet (Not!) I said at the end the docs ought to check-out the iPhone apps if they want an eye-opening experience. Here’s the Nature Medicine’s video.
Vodpod videos no longer available.
more about “Mobile Medicine”, posted with vodpod
I suppose some people will feel there is something forbidden about a non-physician looking at the Medical apps and will avoid them, but there’s nothing that prohibits them from downloading and using them. You don’t need a license or degree to download, say, the Drugs and Medications app, or the Instant ECG: An Electrocardiogram Rhythms Guide, or the Stethoscope Expert app. Anybody can download any of them. I’ve got the University of Maryland Medical Center Medical Reference on my iPhone right now. I’ve had others.
My point is just this: some doctors are freaked-out that their patients are getting access to health information over the net. It troubles them and I suspect the medical profession wishes the internet would just go away. The truth is, not only is the internet not going away, direct access to information and information tools formerly available to doctors exclusively is more readily available to the public with each passing day. Millions of people are already walking around with health and medical information tools in their pockets or purses. This availability is on the verge of explosive expansion because many entrepreneurs see a golden opportunity in the public’s well-documented desire for health and medical information. My recommendation to the medical community is to get with it and start participating in projects to help make this development as constructive as possible for all concerned.
12
Apr
10

books that changed my life

My wife and I are moving out of state next month, so we’re unloading stuff we don’t want to transport. I’ve had to look at my book collection and cull the ones I can live without. In the process I realized there’s a small set of books that have framed my way of looking at the world and kindled passions that will continue the rest of my life. They’re the books that have old yellow stickies sprouting from between the pages, yellow highlights and scribbles in the margins. I donated about 60 books to the local library, but these I’ll keep to the end.

Eric Jantsch, The Self-Organizing Universe: Scientific and human implications of the emerging paradigm of evolution, 1979.

Actually, I found this book after reading James Gleick’s, Chaos. Chaos was an unusual best-seller in ~1987 I guess because we all experience “chaos” (in the colloquial sense) in our lives, and people evidently were looking for some insight. A lot of readers never finished the book because it explored the physics and mathematics of chaos, not necessarily the common term. Nevertheless, Chaos made the term “butterfly effect” part of our vernacular. It was a good introduction to chaos theory, but by the end of the book I was wondering: “With chaos being so pervasive in nature, how is it we see order and organization?” Jantsch’s book tackled that conundrum.

Basically, Jantsch presented a framework for how the world organizes via hierarchical systems from the fundamental dynamics of the micro (atomic forces, molecules and basic physical properties) through simple living entities, complex organisms, ecosystems, and social systems. It is a set of concepts that are a theory of organization from basic dynamics up through the most complex things we know, living systems and our own societies. Here’s how Jantsch defines systems:

The notion of system itself is not longer tied to a specific spatial or spatio-temporal structure nor to a changing configuration of particular components, nor to  sets of internal or external relations. Rather, a system now appears as a set of coherent, evolving interactive processes which temporarily manifest in globally stable structures that have nothing to do with the equilibrium and solidity of technological structures.

The mind-blowing idea that came through in this work is that there are processes that, when fed by external energy flows, can become so stable that we think of them as things. Especially in living systems, a lot of things are really just processes that persist as long as the right conditions exist and only that long. They’re called “process structures.” It looks like an oxymoron, but you can perceive some persistent processes as structures. When you get that, it tends to alter your notions of permanence and change. Some complex systems such as living organisms persist during what we call life, but when the sustaining conditions end the processes collapse and it’s all over.

Humberto Maturana and Francisco Varela, The Tree of Knowledge: The biological roots of human understanding, 1987.

The authors of this book set out to show that cognition is not simply our eyeballs and brain somehow internalizing what’s “out there” but is absolutely contingent on our biological structure and processes. Moreover, cognition is a result of our experience and interaction with other people through language. Their notions are pretty trippy. The book’s cover art is a Salvador Dali painting. But the key for me is that they build their argument for how “knowledge” works from the ground up, starting with processes of self-organization at the molecular level. From there they describe how living things come about through a process of  “learning” clear up through humans with our shared knowledge and shared cognition.

Maturana and Varela’s key idea here is autopoiesis, self-organizing systems similar to Jantsch’s ideas.

Our proposition is that living beings are characterized in that, literally, they are continually self-producing. We indicate this process when call the organization that defines them an autopoietic organization. […] The most striking feature of an autopoietic system is that it pulls itself up by its own bootstraps and becomes distinct from its environment through its own dynamics, in such a way that both things are inseparable.

Werner Loewenstein, The Touchstone of Life: Molecular information, cell communication, and the foundations of  life, 1999.

Backing up all the way, Loewenstein goes about explaining the organization that enables the complexity of living things by starting with entropy and information theory. You can’t get more basic than the laws of thermodynamics!

Neither Jantsch’s or Maturana and Varela’s books deal in detail with how information in chemistry figure into their notions of self-organization, but it’s there. Loewenstein makes the idea of information the theme of his book and caries it through from the idea of macromolecules clear up through cells, intracellular information exchanges, inter-cellular communication, and special information structures like neurons. But what I took away from this treatise is that the molecular structures at the cellular level are information devices as surely as the laptop I’m using to write this post. We’re so used to thinking of information in terms of human language and symbols that it seems strange to think that the conformations of proteins, DNA chains, “messenger” RNA and the intricate interactions among them are just as informational. But the robust and growing science of bioinformatics is based on just such ideas.

Dennis Bray, Wetware: A computer in every cell, 2009.

Actually, I’m just finishing this one. It’s a very interesting look at the internal informational working of cells that give these basic units of living things a capability of awareness and appropriate responsiveness that deserves more attention and respect. Cells aren’t just bricks in the wall; they’re participants in some astute biology. Wetware brings together in the cell Loewenstein’s molecular informational processes and Maturana and Varela’s philosophical views of life processes as forms of cognition and learning.

What runs through all these books is the idea that the universe’s fundamental properties and rules allow the emergence of processes of great complexity; complexity sufficient to reach the level of life and at least one organism — us — with the capacity for self-awareness and splendidly subtle thought. That’s a truly amazing range of possibilities based on some very foundational laws. How this is possible is a chain of events that we can only partially explain at this point. The rest of the story requires details we’re only getting a glimpse of right now. It’s certainly a set of riddles that will keep me fascinated the rest of my days.

12
Apr
10

A lot of computer security wastes a huge amount of time and isn’t worth it

Have you ever wondered, as I have, when trying to get around the “password not recognized” messages from some innocuous web site, how much time people spend simply trying to get something done with their computer but are messed up because they’re locked out by some snafu? Answer: a lot! An article says that all the messing around with passwords that is forced on us costs us a lot of wasted time while not really protecting things of value. As an old friend of mine from Mississippi used to say, “The juice ain’t worth the squeezin”.” http://www.boston.com/bostonglobe/ideas/articles/2010/04/11/please_do_not_change_your_password/?page=1




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