Jef's web files - Biological

Startling Scientists, Plant Fixes Its Flawed Gene

Wed, 23 Mar 2005 09:26:30 -0500

In a startling discovery, geneticists at Purdue University say they have found plants that possess a corrected version of a defective gene inherited from both their parents, as if some handy backup copy with the right version had been made in the grandparents' generation or earlier.

The finding implies that some organisms may contain a cryptic backup copy of their genome that bypasses the usual mechanisms of heredity. If confirmed, it would represent an unprecedented exception to the laws of inheritance discovered by Gregor Mendel in the 19th century. Equally surprising, the cryptic genome appears not to be made of DNA, the standard hereditary material.

The discovery also raises interesting biological questions - including whether it gets in the way of evolution, which depends on mutations changing an organism rather than being put right by a backup system.

"It looks like a marvelous discovery," said Dr. Elliott Meyerowitz, a plant geneticist at the California Institute of Technology. Dr. David Haig, an evolutionary biologist at Harvard, described the finding as "a really strange and unexpected result," which would be important if the observation holds up and applies widely in nature.

NASA Astrobiologist Identifies 'Extreme' New Life Form

Thu, 24 Feb 2005 12:07:00 -0500

The end of a scientific journey - started five years ago in a frozen tunnel deep below the Alaska tundra - came in January for NASA astrobiologist Dr. Richard Hoover.

It proved a long, arduous journey for Hoover and his colleagues to complete the process of identifying a unique new life form. For the life form itself, a new bacterium dubbed Carnobacterium pleistocenium, the journey to discovery took much longer - some 32,000 years.

The bacterium - the first fully described, validated species ever found alive in ancient ice - is NASA's latest discovery of an "extremophile."

Testing Darwin

Mon, 14 Feb 2005 11:16:33 -0500

If you want to find alien life-forms, hold off on booking that trip to the moons of Saturn. You may only need to catch a plane to East Lansing, Michigan.

The aliens of East Lansing are not made of carbon and water. They have no DNA. Billions of them are quietly colonizing a cluster of 200computers in the basement of the Plant and Soil Sciences building at Michigan State University. To peer into their world, however, you have to walk a few blocks west on Wilson Road to the engineering department and visit the Digital Evolution Laboratory. Here you'll find a crew of computer scientists, biologists, and even a philosopher or two gazing at computer monitors, watching the evolution of bizarre new life-forms.

These are digital organisms-strings of commands-akin to computer viruses. Each organism can produce tens of thousands of copies of itself within a matter of minutes. Unlike computer viruses, however, they are made up of digital bits that can mutate in much the same way DNA mutates. A software program called Avida allows researchers to track the birth, life, and death of generation after generation of the digital organisms by scanning columns of numbers that pour down a computer screen like waterfalls.

After more than a decade of development, Avida's digital organisms are now getting close to fulfilling the definition of biological life. “More and more of the features that biologists have said were necessary for life we can check off,” says Robert Pennock, a philosopher at Michigan State and a member of the Avida team. “Does this, does that, does this. Metabolism? Maybe not quite yet, but getting pretty close.”

One thing the digital organisms do particularly well is evolve.“ Avida is not a simulation of evolution; it is an instance of it,” Pennock says. “All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If that's central to the definition of life, then these things count.”

The Darwinian Interlude

Sat, 05 Feb 2005 10:03:42 -0500

Carl Woese published a provocative and illuminating article, “A New Biology for a New Century,” in the June 2004 issue of Microbiology and Molecular Biology Reviews. His main theme is the obsolescence of reductionist biology as it has been practiced for the last hundred years, and the need for a new biology based on communities and ecosystems rather than on genes and molecules. He also raises another profoundly important question: when did Darwinian evolution begin? By Darwinian evolution he means evolution as Darwin himself understood it, based on the intense competition for survival among noninterbreeding species. He presents evidence that Darwinian evolution did not go back to the beginning of life. In early times, the process that he calls “horizontal gene transfer,” the sharing of genes between unrelated species, was prevalent. It becomes more prevalent the further back you go in time. Carl Woese is the world’s greatest expert in the field of microbial taxonomy. Whatever he writes, even in a speculative vein, is to be taken seriously.

Woese is postulating a golden age of pre-Darwinian life, during which horizontal gene transfer was universal and separate species did not exist. Life was then a community of cells of various kinds, sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell separated itself from the community and refused to share. Its offspring became the first species. With its superior efficiency, it continued to prosper and to evolve separately. Some millions of years later, another cell separated itself from the community and became another species. And so it went on, until all life was divided into species.

Spider webs untangle evolution

Sun, 14 Nov 2004 12:46:04 -0500

Similarity of construction shows 'convergent evolution' applies to behaviour.

The biologist Stephen Jay Gould famously proposed that if we could "rewind the tape" of evolution and play it again, chance would give rise to a world that was completely different from the one we live in now. But the concept that chance reigns supreme may ring less true when it comes to complex behaviours.

A study of the similarities between the webs of different spider species in Hawaii provides fresh evidence that behavioural tendencies can actually evolve rather predictably, even in widely separated places.

Todd Blackledge of the University of California, Riverside, and Rosemary Gillespie, of the University of California, Berkeley, studied species of Tetragnatha spiders on different Hawaiian islands. The spiders' webs vary significantly, with tissue-like 'sheet webs', disorganized cobwebs and spiral-shaped 'orb webs' as three of the most common types.

Each species had its own characteristic type of web. But the scientists found that in several cases, separate species of Tetragnatha spiders on different islands constructed extremely similar orb webs, right down to the number of spokes, and the lengths and densities of the sticky spiral that captures bugs.

Was this an example of similar environments producing the same complex behaviour, or did the spiders with corresponding webs share a common ancestor?

It's life, but not as God planned it

Sun, 04 Apr 2004 18:50:00 -0400

Scientists are often accused of trying to play God. Cloning experts, genetic engineers and atomic physicists have all fiddled with aspects of the world that many believe should remain the preserve of some higher power. But for one group of scientists in particular, playing is a serious business. They are seeking to create life itself, and in doing so could push God aside.

They are making astonishing progress. According to the Bible it took six days to create heaven, Earth and everything in them; the scientists already need only a fortnight to produce a totally synthetic organism. They are also figuring out how to expand life's genetic code, which has acted as a barrier to new forms of creation since time immemorial. "I don't think there's anything wrong with playing God," says Clyde Hutchison, one of the new breed of scientists learning to master creation. "As long as it's just playing."

Before tackling the creation of new life, the scientists have been forced to ask a more fundamental question: what, precisely, is it? What are the bare essentials life requires, the building blocks needed to make the most basic living organism? The answer has an almost profound significance, for it is these components that form the common denominator that links every living thing on Earth, from aardvarks to amoebae, zooplankton to zebras.

The common denominator for life is a package of genes that together do the bare minimum necessary to produce a living organism; enough to produce life, but no more. All other genes are add-ons, tweaks that nudge an organism into one species or other, that help grow fins or feet, trunks or tails.

At his lab at the University of North Carolina at Chapel Hill, Hutchison is trying to find the essentials for life by playing what seems a macabre game. He begins by taking a clutch of the most basic forms of life known to man, a bacterium called Mycoplasma genitalium. The bacterium has only 500 or so genes, compared with an estimated 42,000 genes found in humans.

Because M. genitalium has fewer genes than any other living organism, Hutchison says it is the closest nature has to the simplest possible life form. Most of the genes inside the bacterium are vital for its survival, helping the bacterium to grow its body, divide and convert nutrients around it into energy. But to find out the bare minimum required for life, Hutchison is systematically whittling down the bacterium by knocking out genes to find the point at which life becomes impossible. So far, he believes he's found up to 215 genes that are strictly superfluous for the microbe's survival, meaning that a cassette of fewer than 300 genes is required for life.

Association for Politics and the Life Sciences

Tue, 20 Jan 2004 15:51:35 -0500

There are living systems; there is no "living matter".

Sun, 01 Aug 2004 13:07:45 -0400

There are living systems; there is no "living matter".
- Jacques Lucien Monod

Life Itself

Sun, 30 May 2004 14:25:36 -0400

Life Itself: A Comprehensive Inquiry Into Nature, Origin, and Fabrication of Life

By Robert Rosen

Copyright 1991