Sea Genes Multiply
A potential paradigm-shifting discovery has been made in the doldrums of the Sargasso Sea: there are many more genes in plankton than expected. Craig Venter’s Celera team sampled the genetic content of microbes off the Bermuda coast, and in 1500 liters of surface seawater, found 1.5 million new genes. Falkowski and de Vargas, writing about this in the April 2 issue of Science,1 appear quite surprised:
Our evolutionary heritage is imprinted in the genes of microbes that live in the oceans, yet that genomic information is barely understood, let alone written in biological textbooks. … Such an enormous number of new genes from so few samples obtained in one of the world’s most nutrient-impoverished bodies of water poses significant challenges to the emerging field of marine molecular microbial ecology and evolutionary biology.
The “shotgun sequencing” approach of Celera, superior to the older PCR (polymerase chain reaction) method for detecting new genes, has unveiled a previously hidden superabundance of biodiversity among ocean microorganisms. Genomes range from 20 Mb (megabases, or base pairs of DNA) to over 2000 Mb. Some dinoflagellates, of which there are some 2000 varieties, have genomes comparable in size to humans.
Falkowski and de Vargas repeat the usual evolutionary scenario, that “The diversity of microbes in the world’s oceans is the outcome of over 3.8 billion years of evolution.” They discuss the “metabolic experimentation and innovation” that led to photosynthesis. To them, this biodiversity reflects what happened after photosynthesis took over: “This accommodation has been manifested over the past ~2 billion years as biological adaptations that strive to protect nature’s investment in the old, anaerobic biological machinery. On a macroscopic scale, these adaptations include the evolution of secondary metabolic pathways, behaviors, morphologies, diversification, and species redundancy that ensures the survival of geochemically critical biological processes.” Nevertheless, they acknowledge ignorance: “Arguably, nowhere on Earth is this microbial diversity–poorly understood as it is–more apparent than in the contemporary oceans.” And they admit that this latest genetic survey of the oceans raises many questions about ecology, and about evolution itself:
The huge panoply of new functional genes unveiled by this first shotgun sequencing of the oceans begs fundamental questions in marine microbial ecology. For example, what ecological and evolutionary processes maintain such high microbial diversity in the oceans? How many new functional components are there? Have we been missing major players, or is the apparent diversity the expression of an extreme redundancy? What is the tempo of evolution in marine microbes? Is their diversity the outcome of Darwinian selection through vertical inheritance, or is it due to nearly neutral modes of evolution in which the hundreds of millions of viral and bacteriophage particles in any milliliter of seawater act as major agents of horizontal gene transfer and genome scrambling?
This list of questions merely suggests that the approach described by Venter et al. is neither a beginning nor an end to understanding marine microbial ecology. Rather, it is a clear signpost on a longer journey that will occupy a broad spectrum of the scientific community for decades.
Obviously, they remind us, “Most marine microbes are not preserved in the fossil record; hence, their evolutionary pathways can best be inferred from genetically heritable molecules.” And this will “require substantial investments in new technologies.” But “These efforts are critical to understanding how life evolved.”
The work of Venter’s team is published in the same issue of Science.2 The abstract states, “These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.”
1Paul G. Falkowski and Colomban de Vargas, “Shotgun Sequencing in the Sea: A Blast from the Past?” Science, Vol 304, Issue 5667, 58-60, 2 April 2004, [DOI: 10.1126/science.1097146].
2J. Craig Venter et al., “Environmental Genome Shotgun Sequencing of the Sargasso Sea,” Science, Vol 304, Issue 5667, 66-74, 2 April 2004, [DOI: 10.1126/science.1093857].
These surprising data are too preliminary for anyone to understand them satisfactorily. They rely on techniques involving some guesswork and statistics, such as comparing similar sequences and identifying unique species out of billions of base pairs. Still, the results so far appear to contradict evolutionary assumptions. In a strictly Darwinian world, the fittest survive and the weak go extinct. Yet in the oceans, where the generation rates are the fastest and the opportunities for competition over resources are plenteous, there is a superabundance of biodiversity. Why would organisms “strive to protect nature’s investment in the old, anaerobic biological machinery,” if photosynthesis is superior? Can the impersonal strive? What is machinery, if not made by intelligent design? And if horizontal gene transfer has been the rule, or neutral evolution widespread, “scrambling”’ the genomes of these organisms, how could any phylogenetic tree be constructed? How could a scientist have any confidence that a phylogenetic tree even reflects natural history at all? Falkowski and de Vargas would not be asking the questions if they knew how “evolutionary processes” (how’s that for an oxymoron) could “maintain such high microbial biodiversity,” or why such “extreme redundancy” should exist in a “nutrient-impoverished” environment, where Malthus and Darwin would have expected only the fittest to survive. They see no clear “Darwinian selection through vertical inheritance” jumping out of the published data. An outside observer might claim Darwin’s predictions have been falsified.
This is not to assert that creationists have a ready answer to explain why there would be so many rhodopsin-like photoreceptors, or why a dinoflagellate would have a genome comparable in size to a human. We have already seen that the genome is only part of a more complex picture of gene regulation and development (e.g., see 05/23/2003 entry). A creationist could argue the truism that each organism, by its very persistence, possesses what it needs to survive, and that this fits a creation paradigm as well as (if not better than) an evolutionary one. Overall, however, the emerging picture of oceanic biodiversity does not appear to represent what an evolutionist would expect. The basal life forms, prokarya and bacteria, already possess complex machinery and a diversity of functions beyond what seems needed for mere survival. Superabundance of genetic information points to a commensurate cause: a superabundance of intelligent design.