Posts Tagged ‘Organism


is synthetic life approaching?

By Richard Wheeler (Zephyris) 2007. Lambda rep...
Image via Wikipedia

There has always been a metaphysical aura about life. In addition to the material in a cell or other living thing, most people seem to think that when we say “life” we’re talking about a spark or energy that transcends the material constituents of that living thing.

But suppose that organisms that show all the properties of life can be created by off-the-shelf raw materials of our world and made to function as living through human-designed processes? At no point would some spark or energy be added to jump-start life processes although complex chemical reactions are central to synthesizing the constituent parts. (Is the term Frankenmolecules already taken?)

Researchers are working on just such approaches in an effort to understand the details of how living things get organized, and just recently another step was  taken. Princeton chemist Howard Hecht and his team built proteins from scratch, put them in bacteria, and the bacteria used them to grow and carry on just like the proteins they naturally generate. They demonstrated that there’s nothing mystical or magical about molecules generated in vivo. Actually, there were two artificial steps: they designed artificial DNA that then generated the synthetic proteins.

“What we have here are molecular machines that function quite well within a living organism even though they were designed from scratch and expressed from artificial genes,” said Michael Hecht, a professor of chemistry at Princeton, who led the research. “This tells us that the molecular parts kit for life need not be limited to parts — genes and proteins — that already exist in nature.”

“What I believe is most intriguing about our work is that the information encoded in these artificial genes is completely novel — it does not come from, nor is it significantly related to, information encoded by natural genes, and yet the end result is a living, functional microbe,” said Michael Fisher, a co-author of the paper who earned his Ph.D. at Princeton in 2010 and is now a postdoctoral fellow at the University of California-Berkeley. “It is perhaps analogous to taking a sentence, coming up with brand new words, testing if any of our new words can take the place of any of the original words in the sentence, and finding that in some cases, the sentence retains virtually the same meaning while incorporating brand new words.”

Although millions of proteins from evolved DNA already exist, the ones Nature has produced is only a small fraction of the proteins that could be produced by heretofore unseen DNA and protein combinations. The potential design space is vast. Some people think living things were produced by intelligent design from the beginning, but I think these experiments are getting us closer to the truth. Evolution of the world’s material into living things over a hell of a long time gave us what has gone before, but we’re getting closer and closer to true design of life forms from a huge set of possibilities that will become part of our world in the not-too-distant future.


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.


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.

Umm, Delicious Bookmarks


RSS The Vortex

  • An error has occurred; the feed is probably down. Try again later.