Biology and Geology: A Necessary Symbiosis

by
Dawn Y . Sumner

2002, On Line column in Palaios


The first law of thermodynamics dictates that biology can not exist without geology. Life needs energy to grow and reproduce; that energy comes from chemical gradients produced by geochemical cycles. The details of these cycles throughout Earth history have imprinted themselves into the metabolism of bacteria and the metals used in enzymes. The success of the Eubacterial and Archaeal domains is due to numerous specializations taking advantage of specific chemical gradients. With multi-cellular organisms, we are used to thinking of geology shaping populations by isolating them or by providing catastrophic events that change the rules for survival. However, the internal regulatory controls of all life, including unicellular organisms, are a biological response to their need to survive in a physical and chemical environment. Earth has shaped almost every detail of life.

Geology is less dependent on biology. Mars and Venus function as planets in the absence of life. However, life has extensively modified geology on Earth's surface, making geology and biology inseparable. Life has shaped Earth, and Earth has shaped life. Although it is possible to study some aspects of each field without a knowledge of the other, almost all studies of Earth's surface and extant organisms can benefit immensely from a knowledge of both fields. Unfortunately, biology and geology have evolved into separate academic pursuits, with both physical walls and language barriers dividing them. These walls have been and are being scaled by many of my scientific heroes, my colleagues, and our students, with striking results. Here, I would like to highlight some of the biological-geological synergies that have sparked my excitement in the hopes of inspiring one more scientist to overcome the language barrier to take full advantage of the symbiosis between geology and biology.

Modern geology and biology developed as sister disciplines. Early geologists and biologists were "naturalists." Advances in each discipline depended on a thorough knowledge of the other, and the benefits of using theories and observations from both biology and geology were indisputable. The theory of evolution by natural selection is firmly based in both geological and biological observations. The two founders of the theory of evolution by natural selection, Charles Darwin and Alfred Wallace, were strongly influenced by "The Principles of Geology" published by Lyell in 1830. This book provided a conceptual framework for interpreting Earth as shaped by slow-acting processes over long periods of time. This same concept was applied to changes in life; gradual processes operating over millions of years could select for specific biological traits (Darwin, 1859). These systematic changes in fauna through time were preserved in sedimentary rocks and were well documented in the first geological map, published by William Smith in 1815 (see Winchester, 2001). Changes in organisms from underlying older rocks to overlying younger rocks documented the evolution of animals through time in a systematic and testable way. These and many other geological observations required a theory in which life changed gradually over long periods of time.

Of course, the rock record provides only a fraction of the information necessary to understand evolution. Darwin (1859) took great pains to demonstrate that evolution was biologically possible. He extensively documented the evolution of domestic animals and birds to argue that life could evolve, in this case due to human selection. The ability of organisms to change through time and the conceptual framework of inheritance were critical to demonstrating the biological side of evolution (Darwin, 1859). The core strength in "Origin of Species" is the thorough discussion of both biological and geological arguments that support the theory of evolution by natural selection.

Today, most people (paleontologists excepted) consider evolution an exclusively biological process and the study of evolution a biological pursuit. Studies of genetics have revolutionized evolutionary theory and the way we think about phylogenetic relationships. Seemingly wild proposals, such as the symbiotic theory for the eukaryotic acquisition of organelles, have been validated by genetics. Microbial phylogeny has been revolutionized through genetic studies, in part because morphological variations are small and biochemical evolution is the most important selective process. Genetic characterization of "simple," single-celled organisms led to recognition of a new domain of organisms, the Archaea (Woess et al., 1990).

In recent years, geneticists also have tried to quantify rates of evolution, and they have looked to geology for help. Certain genes appear to mutate at approximately constant rates or possibly at rates that can be calibrated (e.g. Bromham et al., 2000). If so, evolutionary time can be extrapolated from genetic difference. However, even if rates were constant, they have to be calibrated against processes spanning at least millions of years; this requires geological data. Doolittle et al. (1996) published an early attempt to predict the divergence time of the largest branches in the tree of life based on constant mutation rates. It was calibrated by pinning vertebrate divergence times to genetic differences among living descendants of the fossil forms. This revolutionary article provided a perfect straw-man for demonstrating the need for geological data; Doolittle et al. (1996) proposed that cyanobacteria, the original source of oxygen-producing photosynthesis, evolved after the oxidation of Earth's atmosphere. Geology clearly proves his timing wrong. Recent improvements in techniques have produced more reasonable results (e.g. Wang et al., 1999), but results are still variable. Estimates of the early diversification of animals range from 1170 to 670 million years ago, depending on the sequenced genes, analytical methods used to account for variable mutation rates, and the calibration to geological data (see discussion in Brooke 1999). As biologists and geologists collaborate to reconcile the discrepancies in current interpretations, additional insights into the meaning of genetic differences and interpretations of the rock record will be forthcoming.

One intriguing question that Doolittle et al.'s (1996) paper raised in many people's minds is, "Why should the rate of vertebrate morphological evolution be similar to microbial biochemical evolution?" Bacteria and vertebrates obviously differ in reproduction, environmental flexibility, and behavior. Thus, the response of the organisms to various selection processes are likely to be different; the processes of genetic mutation and lateral gene exchange probably had substantially different effects on single-celled organisms and on complex vertebrates. In bacteria, genes can be activated to produce organic molecules that allow them to thrive in diverse environments; they contain the genetic machinery for survival and use it when necessary. In contrast, activation of genes during the growth of an animal is particularly important for influencing morphology, which can be imprinted in the rock record.

A beautiful example of variations in the timing of gene expression was highlighted in a recent National Geographic article on dogs (Lange and Clark, 2002). Dog skulls are very sensitive to small changes in the relative timing of developmental gene activation. For example, dogs with long, slender noses, such as the borzoi, start nose growth as a fetus, whereas the bulldog's nose does not start to develop until after it is born (Lange and Clark, 2002). The result is a striking difference in skull structure for the two breeds. This developmental flexibility is one of the features that gives dogs such a diversity of expressions, even though genetically, they are almost identical to wolves. Paleontologists (in the distant future) working on the evolution of dogs could come to dramatically different conclusions depending on the quality of the geological record. With an abundant fossil record, a skilled paleontologist could recognize the morphological flexibility of dogs' skulls based on the presence of numerous gradational forms; however, with a sparse population, interpreting a pug and an afghan hound as two species would be an easily justifiable interpretation. Although humans have strongly influenced the divergence in dog skull morphology, there are also natural examples of morphological flexibility. During a severe drought in the 1970's in the Galapagos Islands, finches with strong beaks were highly selected for because they could eat the only food available - hard seeds (Gibbs and Grant, 1987). When conditions returned to normal, smaller birds were again favored and the population evolved in response within a few years (Gibbs and Grant, 1987). Organisms also respond to external stimuli such as the presence of predators. Barnacle shells change shape when grazing snails are present (Lively, 1986). The origin of morphological changes in the absence of genetic mutation is one of the most intriguing research problems facing studies of metazoan evolution. The complexities of gene activation allow the survival of complex organisms that are highly dependent on their environment.

Single-celled bacteria and archaea also show gene activation in response to external stimuli. Many can switch metabolic processes based on the chemistry of their local environment. However, because they are single celled organisms, they do not have the complex genetic controls for cell differentiation. This leads to some of the most interesting questions in evolution: "How did the genetic controls necessary for cell differentiation develop?"; "Were the controls present in early eukaryotic cells?"; "How much have genetic controls evolved since the divergence of plant and animal cells?". Parts of these questions can be addressed through genetic studies of extant organisms. Others, will require data from the geological record.

Organic biomarkers may help. Life consists of highly specialized chemical reactions catalyzed by specialized molecules. These molecules can be unique to specific organisms. Biomarkers identified in the rock record can be used to infer the presence of the organisms. One of the most exciting results to date is the isolation of steranes from 2.7 Ga shales that imply the evolution of eukaryotic cells by late Archean time (Brocks et al., 1999). Did these eukaryotes have the genetic capabilities for cell differentiation? If so, why did it take 2 billion years for multicellular fossils to appear in the rock record? If not, when did they evolve the genetic controls for cell specialization?

One billion years later, at about 1.5 Ga, possible protists show a robust distribution in abundance and diversity with depositional environment (Javaux et al., 2001). These simple fossils provide the opportunity to study early eukaryotic ecology, and to Javaux et al. (2001) results suggest that they already had a "long" history of natural selection and evolution. During the next billion years, algal diversity increased, but little is known about animal evolution. The oldest (probable) animals are embryos that have been identified in 570 Ma phosphorites from China (Xiao and Knoll, 2000). Few animal embryos have been identified from the rock record, in part because they tend not to be preserved and in part because they are difficult to identify. However, Xiao and Knoll's work on several-celled fossils from approximately 570 Ma phosphorites provided sophisticated arguments for an animal origin for half-millimeter phosphatic spheres (Xiao and Knoll, 2000). By using cell wall rheology, the geometry of early cell division, and the structure of cell clumps, they have documented the presence of both algal and animal embryos. Although the embryos are not distinctive enough to be identified with specific adult forms, some show similar characteristics to the embryonic stages of extant sponges, cnidarians, and bilaterians (Xiao and Knoll, 2000). Additional research is likely to provide more specimens and better insights into the evolution of early animals.

Despite the advances in both biology and geology since 1859, we are still left with the question that Darwin felt was the biggest problem with the theory of evolution by natural selection: How and why did complex multicellular organisms suddenly appear near the base of Cambrian strata? We now know that there was a very long history of evolution during Precambrian time, but we are still very far from knowing how the transition from single-celled life to multi-celled life evolved and what processes promoted it. One missing element in understanding this transition is our lack of appreciation for how life has affected Earth. Multi-celled life requires O2 as an energy source, and O2 is produced (almost) exclusively through photosynthesis. Biological influences on Earth's atmosphere and surface made large life possible.

Life controls Earth's climate and surface chemistry. Weathering is substantially enhanced by land plants. Life is obviously a major component of the carbon cycle. Biological processes regulate Earth's surface temperature through greenhouse gas cycling. For example, during Archean time, rapid biogenic methane production may have been essential for providing enough greenhouse warming to prevent Earth's oceans from freezing (Kasting et al., 2001). Life's largest influence, however, was changing the oxidation state of Earth's surface. The production of enough O2 to oxidize Earth's oceans and atmosphere resulted in the most profound environmental change in Earth's history. The presence of O2 changed global cycles of iron and other redox metals, dramatically increasing weathering rates and changing weathering products. At mid-ocean ridges, hydrothermal convection of oxidized rather than reduced sea water into sea floor basalts changed the reactions occurring in the shallow oceanic crust. In addition, the reoxidation of hydrothermal water on returning to the oceans leads to complex deposits of oxides, sulfides, and sulfates (which are densely colonized by bacteria). These mineral assemblages are different than those predicted from sea floor alteration with anoxic sea water. Deposition of organic carbon, carbonate, and silica from pelagic organisms increases the biological influence on oceanic crust composition. When this crust is subducted, it carries a biological fingerprint into the mantle. For example, diamonds from the upper mantle contain carbon isotopic signatures indicative of subducted organic carbon (Kirkley et al., 1991). We have yet to determine how substantially life has affected the bulk chemistry and dynamics of Earth's deep interior; some have proposed that the influences are substantial (Nisbet and Sleep, 2001). It is clear, however, that biological influences on weathering and erosion affect some tectonic processes such as rates of mountain uplift and basin subsidence by altering denudation rates. To the extent that these rates influence deeper processes, one can argue that on Earth, all geology is influenced by life.

We are on the verge of substantial advances in understanding how pervasively life has affected Earth. And we are on the verge of understanding how Earth has affected life. By integrating the best of biology and geology, we can continue to make progress in answering the questions where are we and how did we get here? Along the way, we will increase our understanding and appreciation of the deep connections between life and Earth.


BIO: Having worked in Joe Kirschvink's lab at Caltech as an undergraduate, Dawn Sumner should have left with a rich understanding of the importance of biology to geology. However, she started graduate school with John Grotzinger at MIT under the impression that chemistry and thermodynamics were the critical things for understanding early Earth. Luckily, Dawn quickly zeroed in on a suite of Archean carbonates dominated by cements -- and microbial mats. Her dad, a physicist, persistently asked her the irritating question, "Why did this crystal form here instead of there?" Dawn spent many long hours articulating why this question was unanswerable. The act of trying to deny that it was important provided insights into the role of biology in controlling local geochemistry. The mats influenced, if not determined, the sites of calcite nucleation, and the sites of nucleation depended on mat geometry (Sumner, 1997). Dawn finished her Ph.D. in 1995 convinced that biology, particularly microbiology was one of the most interesting topics for a geologist to study. Since then, she has been led down an exciting path into the worlds of microbiology, metabolism, and biogeochemistry at the micron scale by her own and her students' questions. Dawn is still firmly rooted in geology and is grateful to her colleagues in the Geology Department at UCDavis who provide the natural selection that promotes the evolution of good ideas.


References

BROCKS, J. J., LOGAN, G. A., BUICK, R. & SUMMONS, R. E., 1999, Archean molecular fossils and the early rise of eukaryotes: Science, v. 285, p. 1033-1036.

BROMHAM, L., PENNY, D., RAMBAUT, A., AND HENDY, M. D., 2000, The power of relative rates tests depends on the data: Journal of Molecular Evolution, v. 50, p. 296301.

BROOKE, M. DE L., 1999, How old are animals?: Trends in Ecology and Evolution, v. 14, p. 211-212.

DARWIN, C., 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. First Edition, transcribed by Project Gutenberg EText, available at ftp://ibiblio.org/pub/docs/books/gutenberg/etext98/otoos10.txt

DOOLITTLE, R. F., FENG, D.-F., TSANG, S., CHO, G. & LITTLE, E., 1996, Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock: Nature, v. 271, p. 470-476.

GIBBS, H. L., AND GRANT, P. H., 1987, Oscillating selection on Darwin's finches: Nature, v. 327, p. 511-513.

JAVAUX, E. J., KNOLL, A. H., AND WALTER, M. R., 2001, Morphological and ecological complexity in early eukaryotic ecosystems: Nature, v. 412, p. 66-69.

KASTING, J. F., PAVLOV, A. A. & SIEFERT, J. L. (2001) A coupled ecosystem-climate model for predicting the methane concentration in the Archean atmosphere. Origins of Life and Evolution of the Biosphere, 31, 271-285.

KIRKLEY, M. B., GURNEY, J. J., OTTER, M. L., HILL, S. J. & DANIELS, L. R. M. (1991) The application of C isotope measurements to the identification of the sources of C in diamonds; a review. Applied Geochemistry, 6(5), 477-494.

LANGE, K. E. AND CLARK, R. (photographer), 2002. Wolf to woof, National Geographic, v. 201, p. 2-11.

LIVELY, C. M., 1986, Predator-induced shell dimorphism in the acorn barnacle Chthamalus anisopoma: Evolution, v. 40, p. 232-242.

NISBET, E. G. AND SLEEP, N. H. 2001, The habitat and nature of early life: Nature, v. 409, p. 1083-1091.

SUMNER, D. Y.,1997, Late Archean calcite-microbe interactions: Two morphologically distinct microbial communities that affected calcite nucleation differently: Palaios, v. 12, p. 300-316.

WANG D. Y.-C., KUMAR S., AND HEDGES, S. D., 1999, Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi: Proceedings of the Royal Society of London, B., v. 266, p. 163-171.

WINCHESTER, S., 2001, The Map That Changed the World: William Smith and the Birth of Modern Geology. Harper Collins, 352 pp.

WOESE, C. R., KANDLER, O. & WHEELIS, M. L., 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA v. 87, 4576-4579.

XIAO, S., AND KNOLL, A. H., 2000, Phosphatized animal embryos from the Neoproterozoic Doushantou Formation at Weng'an, Guizhou, South China: Journal of Paleontology, v. 74, p. 767-788.



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Dawn Y. Sumner
Department of Geology
University of California
Davis, CA 95616
sumner@geology.ucdavis.edu

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