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Topic Name: Rice University's researcher finds biological complexity arises from self-organizing structure of genes

Category: Environmental engineering

Research persons: Michael Deem

Location: Rice University, United States

Details

What is the fundamental creative force behind life on Earth" It's a question that has vexed mankind for millennia, and thanks to theory and almost a year's worth of number-crunching on a supercomputer, Rice University physicist and bioengineer Michael Deem thinks he has the answer: A changing environment may organize the structure of genetic information itself.

Deem's research is available online and slated to appear next month in Physical Review Letters.

"Our results suggest that the beautiful, intricate and interrelated structures observed in nature may be the generic result of evolution in a changing environment," Deem said. "The existence of such structure need not necessarily rest on intelligent design or the anthropic principle."

The information that allows all living things to survive and reproduce is encoded in genes. Deem's theory probed the structure of this genetic information, looking for patterns that were created over time.

The study by Deem and postdoctoral fellow Jun Sun found the structure of genetic information becomes increasingly modular when two conditions are taken as givens: horizontal gene transfer (HGT) and a changing environment. Like modular furniture that can be rearranged in different functional patterns, modular genes are standardized components that lend themselves to flexible rearrangement, and this genetic modularity arises spontaneously because of the selective pressure of a changing environment and the existence of horizontal gene transfer.

Genes are typically transferred vertically. People, plants and animals pass genes vertically, from generation to generation, through sexual reproduction. Bacteria transfer genes vertically via conjugation. HGT allows genes, pieces of genes and collections of genes to move between species, even in cases where vertical transfer is physically impossible.

Though scientists have known about HGT for years, it was thought to be rare and infrequent until sophisticated tools opened the genetic history of many species in the 1990s. Today, HGT is widely accepted as the primary reason for antibiotic drug resistance, and Deem said HGT played a significant role in human development as well. "Our acquired immune system is a product of horizontal gene transfer and is organized in a modular fashion," he said.

Deem's study found that an organism's fitness -- the likelihood that it and its descendants will survive in a rapidly changing environment -- increases as the modularity of its genetic code increases. Another finding was that the faster the environment changes, the more modular genetic information becomes.

Because modularity begets complexity, the more modular genetic information becomes, the more complex the web of life becomes. For example, human beings are far more complex than singled-celled yeast, yet they have only about four times as many genes. The complex nature of multicellular plants and animals derives not only from the genes themselves, but also from the complex regulatory networks that control the production and interaction of the products of genes -- proteins -- to fulfill multiple roles. This regulatory network is another example of modular organization.

"Modularity and hierarchy are prevalent in biology, from the way atoms are arranged in molecules, molecules into amino acids and amino acids into secondary structures, domains and proteins," Deem said. "This hierarchy continues with multiprotein complexes, protein regulation pathways, cells, organs, individuals, species and ecosystems. Our research suggests that modularity and hierarchy are prevalent because genetic information self-organizes into increasingly more modular forms. A changing environment and the biochemistry of horizontal gene transfer appear to be part of the source for this fundamental creativity of life."

The research was supported by the Defense Advanced Research Project Agency.

Note for Anthropic principle

In physics and cosmology, the anthropic principle states that humans should take into account the constraints that human existence as observers imposes on the sort of universe that could be observed. Originally proposed as a rule of reasoning, the term has since been extended to cover supposed "superlaws" that in various ways require the universe to support intelligent life, usually assumed to be carbon-based, and occasionally to be specifically human beings. Anthropic reasoning involves assessing these constraints by analyzing the properties of universes with different fundamental parameters or laws of physics from the current one, and has frequently concluded that essential structures, from atomic nuclei to the whole universe, depend, for stability, on delicate balances between different fundamental forces; balances which occur only in a small minority of possible universes — so that ours seems to be fine-tuned for life. Anthropic reasoning also attempts to explain and quantify this fine tuning. Within the scientific community the usual approach is to invoke selection effects from a real ensemble of alternate universes, which cause an anthropic bias in what can be observed; competing strategies, occasionally also called anthropic, include intelligent design.

Note for Horizontal gene transfer

Horizontal gene transfer (HGT), also Lateral gene transfer (LGT), is any process in which an organism transfers genetic material to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved. Most thinking in genetics has focused on the more prevalent vertical transfer, but there is a recent awareness that horizontal gene transfer is a significant phenomenon. Michael Syvanen was among the earliest biologists to explore the potential significance of lateral gene transfer. Syvanen published a series of papers on horizontal gene transfer starting in 1984, predicting that lateral gene transfer exists, has biological significance, and is a process that shaped evolutionary history from the very beginning of life on earth. Artificial horizontal gene transfer is a form of genetic engineering.

Note for Sexual reproduction

Sexual reproduction is a union that results in increasing genetic diversity of the offspring. It is characterized by two processes: meiosis, involving the halving of the number of chromosomes; and fertilization, involving the fusion of two gametes and the restoration of the original number of chromosomes. During meiosis, the chromosomes of each pair usually cross over to achieve genetic recombination.

About Defense Advanced Research Projects Agency

The Defense Advanced Research Projects Agency (DARPA) is an agency of the United States Department of Defense responsible for the development of new technology for use by the military. DARPA has been responsible for funding the development of many technologies which have had a major impact on the world, including computer networking, as well as NLS, which was both the first hypertext system, and an important precursor to the contemporary ubiquitous graphical user interface.

Its original name was simply Advanced Research Projects Agency (ARPA), but it was renamed DARPA (for Defense) on March 23, 1972, then back to ARPA on February 22, 1993, and then back to DARPA again on March 11, 1996.

DARPA was established in 1958 in response to the Soviet launching of Sputnik in 1957, with the mission of keeping the USA military technology ahead of its enemies. DARPA is independent from other more conventional military R&D and reports directly to senior Department of Defense management. DARPA has around 240 personnel (about 140 technical) directly managing a $3.2 billion budget. These figures are "on average" since DARPA focuses on short-term (two to four-year) projects run by small, purpose-built teams.

About Researcher:

MICHAEL W. DEEM 
Rice University 
6100 Main Street - MS 142 
Houston, TX 77005-1892 
(713) 348-5852 
(713) 348-5811 (confidential fax) 
mwdeem@rice.edu

Education 
B.S., California Institute of Technology (1991) 
Ph.D., University of California at Berkeley (1994) 
Postdoctoral Fellow, Harvard University (1995-1996)