Robert Hazen is a research scientist at the Carnegie Institution of Washington’s Geophysical Laboratory and Clarence Robinson Professor of Earth Science at George Mason University. Robert Hazen is also author of “Intelligent Design and the College Science Classroom: Should We “Teach the Controversy?”” Hazen, R. M. Intelligent design and the college classroom: Should we “teach the controversy”? Astrobiology 6, 106. (2006)
On the other hand, every student can benefit from an examination of the epistemological arguments that underlie this case. The fundamental distinction between science and religion as ways of knowing was central to the Dover case, and can serve to develop the critical thinking skills of all students. Of special relevance is the exploration of “gaps” in our scientific understanding. ID proponents point to these gaps (leaps of “irreducible complexity”) in their invocation of a designer. Scientists, on the other hand, see such gaps as opportunities for further research and exploration, especially in instances of “emergent complexity,” such as the origin of life.
05-14-2008: Note: During my final editing I switched from to an earlier version of the article and lost many edits. I have attempted to restore the article to its original state.
- “ID and the College Classroom: Should we ‘teach the controversy’?”. Presented several times during 2006-2007 as the Dover, Pennsylvania intelligent design trial evoked much debate. [PPT]
- Achieving Scientific Literacy: A Catechism for Science Education Reform”. This is my basic lecture on how to design science courses for undergraduates who are not science majors. [PPT]
There are many excellent resources available online and I recently ran across a conference organized by John C. Avise and Francisco J. Ayala called In the Light of Evolution I: Adaptation and Complex Design
In the presentation that caught my initial interest, Hazen explains the various steps necessary for the origin of life and defines complexity and shows how complexity can increase. I have combined notes on his lecture with additional papers and presentations by Hazen, in order to outline that which many creationists insist, does not exist: a scientific explanation of the origins of life.
I predict that ID creationists will be quick to argue that these are just so stories, and yet, these are stories which present testable hypotheses. And thus I invited ID creationists to present the best explanation as to how ID explains these data?
Seems fair enough.
Supporting slides can be found here. In the presentation he explains the various steps necessary for the origin of life and defines complexity and shows how complexity can increase. The talk has two objectives
- Describe life’s origins in terms of a sequence of emergent processes
- Propose a predictive, quantitative model of complex systems
Three reasonable assumptions are made about the origin of life
- First life forms were carbon based
- Life’s origin was a chemical process relying on water, air and rock (raw materials)
- The origin of life required a sequence of emergent chemical steps of increasing complexity
From the simplicity of a geochemical world to the complexity of a biochemical world
Emergent phenomena arise from the interactions among numerous agents. Their collective behavior is much greater than that of the individual particles. Examples include sand dunes, galaxies (spirals), ant colonies.
Sand dunes and spiral galaxies: Natural emergent phenomena
And for example the slime mold, Dictyostelium which basic response to local chemical gradients results in complexity. Similarly, many individual neurons collectively form consciousness. Emergence happens at all scales: molecules, cells, organisms.
Origin of life in 4 steps
Experimentally the origin of life is a tough problem so break it down
- Emergence of biomolecules
- Emergence of organized molecular systems
- Emergence of self-replicating molecular systems
- Emergence of natural selection
Emergence of biomolecules
The first step is pretty easy: use simple molecules to build larger molecules. Start with water (H2O), CO2, volcanic gases… The Miller Urey experiment showed how simple processes can create molecules found in life such as amino-acids, sugars, lipids, nucleic acid bases. There are many ways to make simple organic molecules. Examples in nature include the “dense molecular clouds”. These clouds are studied in NASA chambers with temperatures as low as 10K while UV radiation is added. The resulting chemicals eventually rain down on early earth. Other examples include black smokers, and the deep mantle. So how do we study the processes that take place in black smokers?
Relevant PT articles
- Primordial Soup’s On: Scientists Repeat Evolution’s Most Famous Experiment
Bada discovered that the reactions were producing chemicals called nitrites, which destroy amino acids as quickly as they form. They were also turning the water acidic—which prevents amino acids from forming. Yet primitive Earth would have contained iron and carbonate minerals that neutralized nitrites and acids. So Bada added chemicals to the experiment to duplicate these functions. When he reran it, he still got the same watery liquid as Miller did in 1983, but this time it was chock-full of amino acids. Bada presented his results this week at the American Chemical Society annual meeting in Chicago.
Hazen Powerpoint Lectures:
- What factors promote the emergence of biocomplexity”. This lecture was delivered at the first Kavli Futures Workshop (“From Nano to Bio”) in Ilulliset, Greenland (June 2007). [PPT]
- “From Geo to Bio: The emergence of biochemical complexity”. This lecture was delivered as the NSF Biosciences Distinguished Lectureship presentation in June, 2007. [PPT]
- “Genesis: The scientific quest for life’s origins”. This lecture, based on my book of the same name, is aimed at a general audience and has been presented at many universities and public lecture series. [PPT]
- H. James Cleaves, John H. Chalmers, Antonio Lazcano, Stanley L. Miller and Jeffrey L. BadaA Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres, Origins of Life and Evolution of Biospheres, Volume 38, Number 2, pp. 105-115 April, 2008
Abstract The action of an electric discharge on reduced gas mixtures such as H2O, CH4 and NH3 (or N2) results in the production of several biologically important organic compounds including amino acids. However, it is now generally held that the early Earth’s atmosphere was likely not reducing, but was dominated by N2 and CO2. The synthesis of organic compounds by the action of electric discharges on neutral gas mixtures has been shown to be much less efficient. We show here that contrary to previous reports, significant amounts of amino acids are produced from neutral gas mixtures. The low yields previously reported appear to be the outcome of oxidation of the organic compounds during hydrolytic workup by nitrite and nitrate produced in the reactions. The yield of amino acids is greatly increased when oxidation inhibitors, such as ferrous iron, are added prior to hydrolysis. Organic synthesis from neutral atmospheres may have depended on the oceanic availability of oxidation inhibitors as well as on the nature of the primitive atmosphere itself. The results reported here suggest that endogenous synthesis from neutral atmospheres may be more important than previously thought.
- Brandes, J.A., R.M. Hazen, H.S. Yoder, Jr., and G.D. Cody (2000) “Early pre- and post-biotic synthesis of alanine: an alternative to the Strecker synthesis.” In Perspectives in Amino Acid and Protein Geochemistry. (G.A. Goodfriend, M.J. Collins, M.L. Fogel, S.A. Macko, and J.F. Wehmiller, eds.). Oxford University Press, NY. pp. 41-59
- Cody, G.D., R.M. Hazen, J.A. Brandes, H.J. Morowitz, H.S. Yoder, Jr. (2001) “Geochemical roots of autotrophic carbon fixation: Hydrothermal experiments in the system citric acid, H2O-(Â±FeS)-(Â±NiS).” Geochim. Cosmochim. Acta, 65, 3557-3576.
- Hazen, R.M. (2001) “Life’s rocky start.” Scientific American, 284, #4, 76-85.
Take gold tube reactors, seal ingredients. Add high pressure and temperature and analyze. Especially Carbon Carbon bonds: Small molecules become larger molecules through the addition of CH2 groups (Fisher- Tropsch (FT) synthesis). So let’s take CO2, H2 and H20, iron metal catalyst, 300C, 500 atm, 24 hrs.
Relevant Publications Hazen Publications
- Robert M Hazen et al High pressure and the origin of life 2002 J. Phys.: Condens. Matter 14 11489-11494
- Cody et al Chemistry and Origins of Living Systems Astrobiology. September 1, 2001, 1(3): 293-316.
The results showed an ‘explosion’ of molecules, not just chain molecules but also other products.
A similar process called Hydroformylation (add CO groups) is used to form carboxilic acid (important formetabolism). Now study FT and hydroformylation as function of minerals added. With cobalt and Nickel CO groups arise, FT synthesis happens almost everywhere. An “explosion” of molecules are generated in these vents.
Self assembling amphiphiles
When amphiphiles are exposed to water, they are ‘forced’ to form vesicles. So the question is: How to form such amphiphiles, since they self assemble into bilayer vesicles.
Hazen Powerpoint Lectures:
- “Hydrothermal production of amphiphilic molecules from pyruvate.” Presented at the American Chemical Society Spring Meeting (San Diego, April, 2001). [PPT]
Hazen, R.M. and D. Deamer (2006) “Hydrothermal reactions of pyruvic acid: synthesis, selection, and self-assembly of amphiphilic molecules.” Origins of Life and Evolution of the Biosphere 37, 143-152.
Abstract Selection and self-assembly of organic compounds in aqueous phases must have
been a primary process leading to emergent molecular complexity and ultimately to the origin of
life. Facile reactions of pyruvic acid under hydrothermal conditions produce a complex mixture
of larger organic molecules, some of which are amphiphiles that readily self-assemble into cell-
sized vesicular structures. Chemical characterization of major components of this mixture
reveals similarities to the suite of organic compounds present in the Murchison carbonaceous
chondrite, some of whose molecules also self-assemble into membranous vesicles. Physical
properties of the products are thus relevant to understanding the prebiotic emergence of
molecular complexity. These results suggest that a robust family of prebiotic reaction pathways
produces similar products over a range of geochemical and astrochemical environments.
Hydrothermal Production of Amphiphilic molecules form pyruvate
Another experiment, this time with pyruvic acid at conditions mimicking hydrothermal environments.
Amphiphiles form which form vesicles
Similarities between our experimental products and Murchison meteorite organics suggest a similar robust polymerization chemistry.
Chirality is important but what is chirality? Molecules have a ‘mirror’ image which cannot be formed through rotation of the molecule. These are truly different forms, just like a right and left hand. When amino acids are formed, they typically occur in equal quantities of left and right handed forms and yet life as we know it is almost exclusively left handed.
Relevant PT Articles
- Chirality of life: Another false positive?
- Chirality, the molecular version of right- and left-handedness, has intrigued chemists ever since Pasteur found mirror-image tartaric acid crystals. The synthesis of molecules in a single chiral form is usually achieved by using a chiral entity from the outset. But in some reactions the formation of a chiral product seems to be further amplified. Most current explanations implicate autocatalysis as the source of this asymmetry. An alternative mechanism is demonstrated this week. This new approach generates a strong bias towards one chiral form from a small initial imbalance, based on the equilibrium solid–liquid phase behaviour of amino acids. As this takes place in aqueous solution, the process might explain how a prebiotic world, with left- and right-handed molecules present in equal numbers, could turn into a living world where biomolecules favour one chiral form
- The Left Hand of Darwin
- One long-standing question in understanding the origin of life is the so-called “chirality problem”. While this is an unresolved question in our understanding of the origin of life, it is used by anti-evolutionists to beat evolutionary theory over the head. As we never tire of telling folk, the origin and subsequent evolution if life are two distinct issues.
- “Right and Left: Mineral surfaces and the origin of biochemical homochirality”. Explores possible roles of chiral mineral surfaces in the selection and concentration of chiral amino acids and sugars. I’ve given this lecture many times during 2006-2007. [PPT]
- “A combinatoric approach to the study of mineral-molecule interactions”. This lecture was delivered at the “Frontiers of Mineralogy” meeting in Cambridge England (June 2007) at a session I organized with Dimitri Sverjensky.
- Hazen, R.M. and D.S. Sholl (2003b) “Origins of biomolecular homochirality: selective molecular adsorption on crystalline surfaces.” Astrobiology 2, 598-599.
- Downs, R.T. and R.M. Hazen (2004) “Chiral indices of crystalline surfaces as a measure of enantioselective potential.” Journal of Molecular Catalysis 216, 273-285.
- Hazen, R.M. (2004) “Chiral crystal faces of common rock-forming minerals.” In G. Palyi, C. Zucchi and L Cagglioti, Eds. Progress in Biological Chirality. New York: Elsevier, Chapter 11, pp.137-151.
- Hazen, R.M. (2005) Genesis: The Scientific Quest for Life’s Origin. Washington, DC: Joseph Henry Press, 339 p.
- Hazen, R.M. (2005) “Genesis: Rocks, minerals and the geochemical origin of life.” Elements 1, #3 (June, 2005), 135-137.
- Hazen, R.M., T.R. Filley and G.A. Goodfriend (2001) “Selective adsorption of L- and D-amino acids on calcite: implications for biochemical homochirality.” Proceedings of the National Academy of Sciences (US), 98: 5487-5490.
- Asthagiri, A. and R.M. Hazen (2006) “An ab initio study of adsorption of alanine on the chiral calcite (2131) surface.” Molecular Simulation 33, 343-351
- Asthagiri, A, and R. M. Hazen (2008) An ab initio study of adsorption of aspartic acid on the chiral calcite (2131) surface. In preparation.
Chirality is important for life and medicine. Chiral impurities in Thalidomide which was used by pregnant women caused birth defects.
So how do we go from a racemic mixture to a homochiral mixture? There are a variety of proposals and Hazen prefers minerals to explain symmetry breaking. Minerals have facets and different facets bind to either left or right-handed molecules
- Examine the occurrence of chiral mineral surfaces in nature (Hazen 2004; Downs & Hazen 2004).
- Demonstrate chiral selectivity by mineral surfaces (Hazen et al. 2001; Castro-Puyana et al. 2007).
- Deduce mineral-molecule interactions (Asthagiri & Hazen 2006; 2007).
- Propose a general experimental research strategy (Hazen, Steele et al. 2005; Hazen 2006).
His work concludes that
- Chiral mineral surfaces are common.
- In oxides and silicates, larger chiral indices are often associated with the presence of both terminal cations and anions.
- Relatively large chiral indices are often associated with stepped and kinked surfaces.
- Calcite (214) crystal surfaces select D- and L-aspartic acid.
- They did not observe selective adsorption of glutamic acid or alanine on calcite.
- Maximum selective adsorption occurs on terraced crystal faces. This fact suggests that chiral selection may occur along linear features.
- The alignment of chiral amino acids on calcite may lead to homochiral polymerization.
A combinatoric problem
How do we evaluate interactions among the numerous possible mineral-molecule pairs? We need a combinatoric approach. Automation using microarrays.
Many mineral surfaces have the potential for chiral selection of plausible prebiotic molecules.
Chirality problem – Calcite (lime stone, coral reefs) has wonderful chiral surfaces allowing left and right handed molecules to be separated.
Self replication and natural selection
Self replicating groups of molecules Kauffman or networks of molecules becomes self perpetuating (Kauffman, Packard 1986) or Morowitz’s TCA cycle (citric acid). DNA world was likely preceeded by an RNA world: first self replicating molecule was a genetic polymer (and catalyst). RNA construction in prebiotic world is however implausible and requires a preceding stage (PAH world, Lipid world)
Emergence of natural selection
Self replicating system, add mutations, add competition, and selection follows. Transition from non-living to living systems.
Szostak lab. Start with random sequences of RNA, in vitro process, remove non-binding strands, collect bound RNA, PCR amplify with errors, transcribe DNA to new RNA, repeat. Strands evolve to become well adapted. RNA Aptamer work.
Need for quantitative models of complex systems Universal metric: Complexity is hard to define, depends on context. Complexity at many different scales and dimensionalities. Key to defining complexity is not structure but function. Szostak: Functional information: I as the fraction of configurations of a system [F(E)] that achives a specific degree of function (E)
I(E) = -log(2) [(F(E)]
Multiple functions means multiple values for I depending on functions Apply metric: How to test this? Lots of sequences and define the degree of function of those sequences. Use Avida (artificial life). Random Avido genomes from the set of 26 instructions. A small fraction will have one or more logic functions.
How to increase Complexity
- Increase the number of interacting agents.
- Increase the diversity of interacting agents.
- Increase selective pressures by environmental cycling
- Hazen, R.M., P.L. Griffin, J.M. Carothers and J.W.Szostak (2007) Functional information and the emergence of biocomplexity. Proceedings of the National Academy of Sciences USA 104, 8574-8581.
- Hazen, R. M. (2007) The emergence of chemical complexity: An Introduction. In L. Zaikowski and J. M. Friedrich [editors], Chemical Evolution I: Chemical Change across Space and Time. American Chemical Society Symposium, pp.2-14.
Quantify complexity using Avida. Use the following ‘phenotypes’: Addition, subtraction, NOT, NAND, ORN, OR, ANDN, NOR, XOR and EQU How many of one task exist ? How many of any task? How many different tasks?
Using 300 command Avida genomes and 10^7 trials, NAND function appears in 1 out of every 1000 genomes. We see gaps, gaps in the same spots. Sometimes random outliers. When we use different length genomes, we observe different gaps and outliers. Why do these gaps exist? Is there a Universal characteristics?
Distribution of the not/and (NAND) function in 300-line Avida genomes in a randomly generated sample of 107 genomes. The degree of function, E, is the number of times NAND is executed by the genome, whereas functional information, I (in bits), is -log2 of the fraction of all sequences that achieves at least that degree of function, F(E). Note the discontinuities, which are a recurrent feature in these experiments.
LEFT The frequency of the ADD function in 100-, 200-, 300-, and 500-line linear Avida genomes in randomly generated samples of 106 genomes. Degree of function, E, is the number of times the ADD function is executed by the genome, whereas functional information, I (in bits), is –log2 of the fraction of all sequences that achieves at least that degree of function, F(E). Note that maximum E increases with genome length.
RIGHT Schematic representation of four discrete functional classes, or “islands,” of solutions that display function. The vertical axis is degree of function, E, whereas the horizontal plane represents a two-dimensional projection in sequence space. The number of sequences with degree of function E corresponds to the area intersected by the horizontal plane at that height along the E axis. Increasing E above the heights of the flat-topped islands A and B will result in discontinuities in the function E versus I, as illustrated in Figs. 1 and 2. Island C is a cone-shaped distribution, and island D represents a discrete solution of the type that might not be discovered in random sampling experiments.
Observation: Sand dunes form at a critical density. Galaxies spiral arms at critical density. Swarm raiding ants require a critical number before they start their raids. Many reactions such as vesicle formation, condensation reactions all have critical number. The Concentration of agents is important.
Example for Avida
Start with highly functional genome 73 subtractions. Test every point mutation. Impact on functionality. 93% are neutral, tiny fraction lead to higher functionality, larger fraction detrimental.
Optimize experiments in origins of life. This means that molecular concentrations are essential. And ‘messy’ experiments may promote emergence (more interacting players) Design experiments that mimic environmental cycles since such cycling environmental conditions (wet/dry, free/thaw, etc) lead to complexity.
Explore more resources, courtesy of Robert Hazen