David Deamer: Line Arbitrary Twixt Life Non-Life

When I reached origins of life investigator David Deamer by phone at his lab at the University of California, Santa Cruz, he told me the NASA Astrobiology program he’s part of encourages public outreach, since it is publicly funded, and that he’d …


David Deamer: Line Arbitrary Twixt Life & Non-Life

By Suzan Mazur

When I reached origins of life investigator David Deamer by phone at his lab at the University of California, Santa Cruz, he told me the NASA Astrobiology program he’s part of encourages public outreach, since it is publicly funded, and that he’d be happy to do an interview. But in the next breath Deamer revealed that the NASA Astrobiology program had no funds: “There’s no money available to send out any new grants at all.”

There is also currently no overall manager for the Astrobiology program, with the recent departure of John Rummel, and appointing one may be on hold until a new White House administration takes over.

It was David Deamer’s spelunking adventures growing up in Ohio that first sparked his curiosity about origins of life. By 1957, he was recognized in a Westinghouse Science Talent Search for his investigation of the self-organization of protozoa. Deamer says “Ilya Prigogine’s pioneering of complexity was an inspiration — for us all.”

A half century and many awards later, David Deamer is Professor of Biomolecular Engineering and Research Professor of Chemistry and Biochemistry at the University of California, Santa Cruz where he directs a lab on self-assembly processes and the origin of cellular life. The lab has been supported for over 20 years by the NASA Exobiology program and for over 10 years by the National Institute of Health.

He is also part of the Carnegie Astrobiology team affiliated with the Carnegie Institution in Washington, which has been investigating “Astrobiological Pathways: From Interstellar medium, through Planetary Systems, to the Emergence and Detection of Life”. And he is informally associated with NASA Ames Research Center.

Deamer was a professor of zoology at University of California, Davis for more than 25 years before coming to UCSC. He has chaired various academic departments at UCSC and UC, Davis (Zoology, Biophysics, Biomolecular Engineering) as well as conferences – including a NATO Advanced Research Workshop in Hungary: “Polymers in Confined Spaces”.

In 1988, with musician Susan Alexjander, Deamer put DNA to music to make “microtones”.

He has six patents and is the author of 126 peer-reviewed papers as well as 10 books, including Being Human: Principles of Human Physiology, The World of the Cell, Origins of Life: The Central Concepts – with another forthcoming (2010) from the University of California Press: Stars, Planets, Life.

Last year Deamer lectured at the “What is Life” Symposium in Kyoto, Japan and the year before that on “Self-assembly processes in the prebiotic environment” at the Royal Society in London. He will be a featured speaker again on self-assembly at the upcoming AAAS meeting in Chicago.

Deamer’s Ph.D. is in physiological chemistry from Ohio State University School of Medicine and his B.S. in chemistry from Duke. His current research involves how DNA can make its way through nanoscopic pores in membranes.

Honors include: Fellow, International Society for the Study of the Origin of Life (2002), Distinguished Lecture series, Graduate Center, CCNY (2004), Distinguished Lecturer, Royal Society of New Zealand (1989), Guggenheim Fellow (1986) and the Westinghouse Science Talent Search (1957), among others.

He lists a dozen public service roles on his CV. He currently serves on the editorial boards of the Journal of Bioenergetics and Biomembranes, Astrobiology and Origins of Life and Evolution of the Biosphere. He previously served on the NASA Space Science Advisory Committee, NASA Astrobiology Roadmap Panel, and chaired the NASA Panel on Exobiology (1991-1995).

My phone conversation with David Deamer follows.

Suzan Mazur: The scientific establishment and the mainstream media are slow to accept that there are mechanisms involved in evolution beyond Darwinian natural selection. Part of the problem is that they are unclear what these other mechanisms are. Can you tell me, for example, what the process of self-assembly is and self-organization and how they differ from one another?

David Deamer: It would be good to have more precise definitions because I’ve tended to use the terms more or less as synonyms. Let’s start with self-assembly, which I define as a molecular process that produces ordered structures from disordered components, yet is energetically downhill, in the sense that an external energy input is not required to get it to happen.

In contrast, most life processes are energetically uphill. A source of external energy is required for polymerization of amino acids into proteins, which is the main growth process of life. Self-assembly is more like what happens to soap molecules in solution. Do you want me to go into technical detail?

Suzan Mazur: If you could describe these terms so a general audience can understand the science without being too technical, that would be great. The concepts now are ignored and dismissed as magic, “woo-woo,” because of the spontaneous way they happen

David Deamer: Okay, let’s talk a little more about self-assembly. It is extraordinary what certain kinds of molecules can do in an aqueous environment. The example that I use is soap molecules in water. A soap molecule is just an oily hydrocarbon chain with a hydrophilic, or “water-loving” group at one end. When they are in a dilute solution soap molecules float around at random and pay no attention to each other.

But if the concentration is increased the soap molecules begin to aggregate into little clumps called micelles which are composed of a few hundred soap molecules each.

What drives this is a law of physics that controls the way that water molecules interact with the hydrocarbon chains of the soap molecules. [emphasis added]

Everyone has heard that “oil and water don’t mix.” At a certain concentration of soap there is no more room for the hydrocarbon chains to fit into the water structure, so they begin to stick together in micelles with all the oily chains pointing into the micelle, away from the water.

Now let’s add more soap. When we get up to a concentration we call the CVC, or critical vesicle concentration, the micelles begin to aggregate into membranes and the membranes form beautiful little vesicles.

These are microscopic versions of the soap bubbles that everybody has seen at the macroscopic level. But if you look at soapy water under the microscope, what you see are microscopic vesicles that form compartments with an interior volume that is separated by a membrane from the external environment.

The point is that the membranes of cells are also produced by self-assembly. Nothing in the genes tells a membrane how to be a membrane. Instead the genetic information in the genes tells the cell how to make the fatty acids (the scientific word for soap) and how to assemble the fatty acids into more complex lipids. The lipids then assemble spontaneously into membranes, the boundary structures of all living cells.

Suzan Mazur: Would you describe self-organization? Self-organization is an open
system?

David Deamer: Yes. If self-assembly is a spontaneous, energetically downhill process, I would define self-organization as a step up from self-assembly in which more complex structures, including living organisms, use energy to organize themselves into functional aggregates.

Suzan Mazur: You say it’s a step up. So you see it as some sort of . . .

David Deamer: Increase in complexity.

Suzan Mazur: Are you saying there’s a connection between self-assembly and self-organization?

David Deamer: It’s analogous to the connection we might make between inorganic chemistry and organic chemistry. Organic chemicals can be much more complex than simple inorganic chemicals. Self-organized systems are more complex than self-assembled systems and can even include populations of organisms that organize themselves in the ecosystem.

Suzan Mazur: Cell biologist Stuart Newman told me in a recent interview that self-organization requires a “flux of matter or energy to keep the structure in place”.

David Deamer: I would agree with that. In contrast, self-assembly is spontaneous, and depends only on the interactions between molecules and with the environment.

Suzan Mazur: Change of subject. Why does NASA promote natural selection as the only mechanism of evolution in its literature – for example, in Astrobiology Primer, whose editor is a priest, and on television in the program Origins of Life?

David Deamer: NASA is speaking to the general public. They’re just trying to keep it simple and explain evolution to people who may not know much about it.

Suzan Mazur: But there are other mechanisms contributing to evolution. The public is not being told about this. Not informing the public is not really serving the public.

David Deamer: The Astrobiology Primer and the Origins of Life program are intended for a lay audience. Biologists agree that life started simple and became more complex through a natural process, and at the most general level we call that process evolution.

If I were teaching an advanced class in evolutionary biology to a college level audience, they would have enough preparation to deal with the other aspects that go into the evolutionary process beyond Darwin’s initial explanation. It takes a lot of background to understand the details that contribute to the evolutionary process.

For instance, the Altenberg 16 you have written about are professional biologists who are trying to go beyond the simplistic explanations that involve nothing more than natural selection. They are bringing to the table ideas that require considerable knowledge to understand their argument.

I certainly wouldn’t want to state that natural selection is the only process driving evolution, but if I am going to explain what that means my audience needs to have enough information to understand the questions that are being raised.

Suzan Mazur: But as Stuart Newman, one of the Altenberg 16 scientists has pointed out, there would be more of an acceptance of evolution if the science was where it should be. He also says “old science” is being pushed in the mainstream media.

David Deamer: I get the point. Unfortunately, creationists have politicized the science so much that the very fact of evolution is being questioned.

Perhaps this is why scientists tend to fall back on the bedrock of Darwin’s basic concepts when they speak in a public forum. No one denies the factual basis of evolution, but we are still learning how evolution takes place, particularly in animal and plant populations in ecosystems.

I have debated creationists and intelligent design people in public forums, and my impression is that they are not looking for scientific truth. Instead they are working to advance their political aim, which is to get Christian fundamentalism taught in public schools as an alternative to evolution.

Suzan Mazur: Cytogeneticist Antonio Lima-de-Faria from the University of Lund refers to the “cycle-of-submission” within academia where scientists are unnecessarily conservative, stick together, protect their foundation grants instead of recognizing the validity of alternative mechanisms and advancing the science. This kind of fundamentalism feeds a creationist perspective.

David Deamer: No matter what we do, the creationists are going to focus on things we don’t know and forget about all the things we do know. I’m not sure there is any fundamental disagreement among scientists about the basic facts of evolution.

Suzan Mazur: There is clearly a horde mentality alive on the science blogosphere.

Should more scientific inquiry into the origins of life be encouraged by opening up the peer-review process? Often the papers of independent researchers are rejected because they’re outsiders and may take an unorthodox approach.

David Deamer: I would like to see the evidence you cite that independent researchers are rejected because they’re outsiders.

Suzan Mazur: They may take an unorthodox approach. In other words, they may not use all the science jargon that the scientific establishment is used to seeing in papers. So reviewers may reject a paper because it’s not written with a tight science jargon. Rejection, you don’t speak our language.

David Deamer: For every example you might give of a rejected unorthodox investigator, I could cite a counter-example. I’ll mention just one, Gunther Wachtershauser, a Swiss patent attorney. Wachtershauser came up with an idea all of his own. He was an absolute outsider.

His idea was published first in 1988 in Microbiology Reviews. Because of the strength and the novelty of his idea and the elaboration that he was able to give to that initial publication, it really caught people’s attention.

He followed this up with a Scientific American article and a series of other papers. I’ve been in meetings with Gunther. He’s not one of the gang by any means, and yet we are paying attention and are testing his ideas. Some of them stand up to critical tests, others don’t.

I would cite Wachtershauser as a clear example of an outsider breaking into the scientific process on the force of his ideas.

Then there are other independent researchers whose ideas just don’t stand up to critical evaluation. They complain that they can’t get their paper published, but the fact is that their ideas just don’t make sense.

Peer review is the only process we have for sorting out the good ideas and getting them out there for others to think about.

Suzan Mazur: What is the standard for acceptance of a paper?

David Deamer: The standard is based on judgment calls by knowledgeable referees and editors.

Suzan Mazur: Acceptance doesn’t require use of the same tight scientific jargon. It’s essentially about a concept and clear thinking.

David Deamer: It’s like being a good chess player. That’s not a bad metaphor. A good chess player wins whether or not he or she is a member of a club.

If they come in and begin to win games based on unorthodox strategies, they are going to gain automatic respect. It’s the same in science, which tends to attract people who think they have good and interesting ideas. I really doubt that there is a significant number of independent researchers who have really good ideas but are being rejected just because they are outsiders.

Suzan Mazur: Do you see any conflict of interest with many of the Astrobiology journal board members being NASA employees or NASA-affiliated?

David Deamer: It’s a bit of a problem, but we deal with it. It comes down to numbers. There are 10,000 researchers who call themselves neurobiologists, and perhaps 30,000 – 40,000 chemists. But there are probably fewer than a hundred researchers who call themselves astrobiologists. Because their research is usually funded by NASA, it can be hard to find knowledgeable people to serve on editorial boards who don’t have a perceived conflict with their NASA grants.

Suzan Mazur: But you’re looking to include outsiders on the board?

David Deamer: Most of the board members are not NASA employees. There are eight senior editors, two of whom are civil servants at NASA Ames. There are 75 members of the editorial board, but only five NASA employees. Over a third of the board members are from other countries, so I think we are well represented internationally.

We certainly want to get more people into the Astrobiology program, and it is growing. There are now 500 people who attend the annual Astrobiology meeting, both younger researchers and people like me who’ve been associated with astrobiology since it began in 1996.

Suzan Mazur: How many academics are now in the Astrobiology program?

David Deamer: It’s a few hundred if we include graduate students and post doctoral associates along with the principal investigators. Each member organization within the Astrobiology Institute has a Principal Investigator who assembles a small team of a few other faculty members that will get support from the program. And each faculty member might have one or two graduate students and a postdoc supported by the grant.

Suzan Mazur: And your affiliation with NASA at this point is…

David Deamer: I am associated with the Carnegie Astrobiology program that is funded through the Carnegie Institution of Washington. I’m also informally associated with the program at NASA Ames.

Suzan Mazur: You’re not a NASA employee.

David Deamer: No. The only funds I receive through NASA is in the form of grants that typically support one postdoc and a grad student.

Suzan Mazur: So academics are not being lured into the Astrobiology program because of the money.

David Deamer: Definitely not! The research funds available are much less than grants from the National Institute of Health, They being lured into it because of the interest and excitement generated by this new field.

Suzan Mazur: The NASA Astrobiology funds are not expanding?

David Deamer: No. In fact, last year the budget was so restricted that new proposals could not be funded and were put on hold.

Suzan Mazur: Do we know very much about astrobiology 10 years or so on in the investigation?

David Deamer: Yes, absolutely. Astrobiology has put life on the Earth into a larger context of our solar system and our galaxy. The origin of life on Earth is likely to be a universal process, and that’s why we are so excited by the discovery that Mars once had shallow seas. Perhaps in the next decade we will have clear evidence that life began there as well, by the same process of self-assembly that we discussed earlier.

It also has given us a vast amount of information about the history of life on the Earth. We now know that oceans were present well over four billion years ago, and there is evidence for life in the isotopic record that goes back about 3.8 billion years ago.

Suzan Mazur: Do you take a position as to whether life began outside Earth or on Earth?

David Deamer: I use plausibility arguments to answer questions like that. Plausibility is an individual judgment call based on knowledge. In my judgment it is implausible that life came to the Earth in the form of extraterrestrial spores or microrganisms. We can’t rule it out but I consider it to be a very low probability.

On the other hand, I consider it to be very plausible that the organic compounds required for life to begin on the Earth were delivered to the Earth by comets and meteorites during late accretion, and that synthetic reactions were producing complex organic molecules in the early Earth environment. I think life most likely began on the Earth by a self-assembly process in which moderately complex chemicals self-assembled into vast numbers of microscopic encapsulated systems. By a yet unknown process, a very few of these happened to be able to capture energy and nutrients from the environment and began to grow by polymerization reactions. There is much more to the story, but this is my guess about how life began.

Suzan Mazur: Can you tell me who is making the decisions following the departure of John Rummel?

David Deamer: I know John has left and there is an acting director now, but not much more than that.

Suzan Mazur: What do you think the origin of the gene is?

David Deamer: I think genetic information more or less came out of nowhere by chance assemblages of short polymers. We don’t know that these polymers were exactly like RNA and DNA of contemporary life, but in the laboratory we use those polymers as experimental model systems.

Most people are open to the possibility that there are simpler molecules that we haven’t discovered yet that could contain what we now call genetic information. There may also have been specific sequences of monomers within a polymer that happened to allow it to fold into a catalytically active molecule. One idea is that RNA could have acted both as a catalyst and as a genetic molecule, so that at one stage in evolution life existed in an RNA World.

Suzan Mazur: So you see the line between life and non-life as being arbitrary?

David Deamer: Yes. There was probably an extensive mixing of genetic information at that time, as Carl Woese and others have suggested. This means that there was no tree of life at that time, instead just countless numbers of microscopic experiments occurring everywhere as the first catalysts and genes learned to work together in cellular compartments.

Suzan Mazur: Then does life have a beginning or is it just part of a process inherent to the universe?

David Deamer: It’s part of a process.

Suzan Mazur: Evolution starts when the universe is born?

David Deamer: It depends on what you want to call evolution. The universe is over 13 billion years old, but life originated on the Earth around 4 billion years ago. Biological evolution began with the transmission of genetic information between generations, and selective processes acting on variations within microbial populations.

Suzan Mazur: But can it be separated from the rest? Do you see biological life as relying on certain previous footprints?

David Deamer: Yes to both questions.

Suzan Mazur: Lima-de-Faria speaks of four levels of evolution – atomic, chemical, mineral and biological. He says there are coincidental patterns arising in organisms because they have the same atoms with the symmetries of the minerals transferred intact to the cell and organism level.

David Deamer: I agree to a certain extent, but there is still little evidence that minerals played an essential role in the process. Certainly astrobiology has given us a satisfying narrative of how life came to the exist on the Earth, all the way from stellar nuclear synthesis to planet formation and habitability and then self-assembly of organics in aqueous environments. When energy sources impinge on these self-assembled structures they capture some of that energy and then interesting processes begin to emerge. So there’s a narrative describing a continuum from which life gradually emerges.

Suzan Mazur: Do we have enough data to construct a periodic table in biology like that in chemistry?

David Deamer: I think we can construct a hierarchy of increasing complexity. It’s possible to think of the periodic table as a hierarchy of complexity in which hydrogen is the least complex atom. As the elements become progressively heavier with the addition of protons, neutrons and electrons, each level has a different set of chemical properties and therefore a different set of potential complexities as they interact with each other. In this sense I think we could describe a hierarchy of complexity levels in life, but I don’t think we would find much periodicity.

I’m writing a book about the origin of life for the University of California Press that is scheduled for publication in 2010. This is the approach that I’m taking in the book, that we can understand the origin of life in terms of the emergent properties of interacting systems of molecules.

Suzan Mazur: You’ve commented a little bit about the Altenberg group already – do you think that the extended synthesis is something the biology community will embrace at this point?

David Deamer: Epigenetic phenomena is one example of what can happen that is well beyond the usual idea that genes are all we need to understand evolution.

Suzan Mazur: Epigenetics has actually been tucked under the umbrella term plasticity in the extended synthesis.

Do you think the extended synthesis was a good call, that the biology community will embrace this graft onto the modern synthesis?

David Deamer: This is how good science happens, when either an individual or a group of scientists think they might know something beyond the current consensus. They try to construct a new synthesis of ideas that has better explanatory power, and if they have a convincing argument their peers will follow. Science should be open to these kinds of challenges.

This is what Steven J. Gould did with punctuated equilibrium, which caused so much controversy at first. Ed Wilson did this with sociobiology, and a consensus is slowly building that we can understand behavior in evolutionary terms.

Suzan Mazur: Along those lines, Stuart Newman predicts “a big turnaround in evolutionary theory”. He cites non-linear and saltational mechanisms of embryonic development contributing to evolution. Newman has told me: “It was Darwin who said that if any organ is shown to have formed not by small increments but by jumps, his theory would therefore be wrong.”

What are your thoughts about this?

David Deamer: I’d need to know more about this to have a knowledgeable comment. I don’t know what Darwin really meant by his statement, or how it could be tested now that we understand so much more about embryological development.

*************


Suzan Mazur is the author of Altenberg 16: An Exposé of the Evolution Industry. Her interest in evolution began with a flight from Nairobi into Olduvai Gorge to interview the late paleoanthropologist Mary Leakey. Because of ideological struggles, the Kenyan-Tanzanian border was closed, and Leakey was the only reason authorities in Dar es Salaam agreed to give landing clearance. The meeting followed discovery by Leakey and her team of the 3.6 million-year-old hominid footprints at Laetoli. Suzan Mazur’s reports have since appeared in the Financial Times, The Economist, Forbes, Newsday, Philadelphia Inquirer, Archaeology, Connoisseur, Omni and others, as well as on PBS, CBC and MBC. She has been a guest on McLaughlin, Charlie Rose and various Fox Television News programs. Email: sznmzr @ aol.com

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3 comments:

  1.  

    [...] the building blocks of RNA, e.g., fatty acids (simple lipids) found in meteorites as per Dave Deamer's papers and (2) they come in thousands of different kinds, allowing the assembly to be [...]

     
  2.  

    [...] Deamer, who I’ve previously interviewed  has six patents and is the author of 126 or so papers as well as 11 books, among them Being [...]

     
  3.  

    [...] Deamer, who I’ve previously interviewed  has six patents and is the author of 126 or so papers as well as 11 books, among them Being [...]

     

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