Friday, December 14, 2012

The Algorithmic Origins of Life

Revolutionary Paper Tackles Definition of Life. 
In the newly published paper “The Algorithmic Origins of Life,” (1) Paul Davies and Sara Walker try to tackle the definition of life, and its evolution, from an informational system perspective rather than from the chemistry and the physical properties of the molecules that might have existed at the time on the planet. This is a unique and quite revolutionary way of re-conceptualizing what defines life and what would be needed to sustain, reproduce and evolve it.

Logical First Steps?
They begin by reviewing the analog versus the digital systems of information. The cell contains both an analog system (the continuous biochemical interactions between molecules in the cytoplasm) and a digital system (DNA) which is separate. Presently the favored idea of the original molecule of life is RNA. But as the paper argues, RNA is an extremely unstable molecule, susceptible to degradation by hydrolysis and difficult to synthesize in the first place under the conditions originally present on earth.

Sunday, December 2, 2012

The Human Genome is Chaotic

Premature Predictions proven incorrect. 
The story of the human genome is no longer about gene structure. To say that our enthusiasm was premature and our predictions bombastic after the human genome was mapped is an understatement. The evolutionary unit is not the gene—though genes do compete—but the complete cell or organism. Cell functions depend on the millions of regulatory interactions between the protein-coding genes, which comprise less than 2% of the genome, and the non-protein-coding genes which form the regulatory mechanism of gene expression. The recent ENCODE studies have given a glimpse of the immense complexity of the network of interrelated biofeedback loops of gene repressors and de-repressors which comprise an active, non-linear system. It is clear that we have only scratched the surface and that the genome will be shown to be even more complex.

Fractal Geometric Properties. 
One of the most significant discoveries in genomics is that the genome (1,2) as well as the cytoplasm (3) have chaotic fractal properties.  

Thursday, November 22, 2012


ENCODE Rethinks Evolution.
The recent results of the ENCODE program, which has revealed a level of complexity in the function of the genome never before imagined, has further raised doubts about the simple evolutionary model of random mutations and natural selection. Though our understanding of the level of complexity of gene control has grown exponentially, it is clear that, as we proceed further, the system will show itself to be even more complex, raising further calls for a more mature model for evolution.

It is only a Theory.
Even before the recent ENCODE studies, respected mainstream scientists have raised doubts about the simple evolutionary model. The Discovery Institute maintains a list (most recently updated in December 2011) of over 500 scientists that have signed the statement “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

“Junk” DNA No Longer Junk

More DNA Revealed.
The massive ENCODE project unveiled Sept. 5, 2012 with the simultaneous publication of multiple studies—the effort of hundreds of scientists at 32 institutions from around the world—has unveiled a genome that is much more complex than previously imagined.

Intelligent Attractions.
The area of DNA not coding for proteins previously thought to be “junk,” roughly 98% of the human genome, has now been found to possess over 4 million gene switches which control how and when the 20,000 or so genes that code for proteins are expressed. Until now they have found that 80% of the human genome has at least one function, not the mere 2% previously thought, and they believe they have only scratched the surface. These areas between protein-coding genes are filled with enhancers (DNA that regulates gene expression), promoters (points of initiation of DNA to RNA transcription), and genes that create RNA which then bind to other areas of DNA, even distant ones, to control gene expression.

Evolution & Chaos

Chaos theory has grown so much over recent years in both theoretical importance and practical applications that it is sometimes thought of as one of the three most transformative theories of our time, together with relativity and quantum physics. In terms of its applications, it is hard to find an area of science in which it is not used in some form. It can describe natural phenomena in such diverse areas as population growth, cloud structure, structure of ferns and other plants, coastlines, mountain ranges, military operations, epidemics, stock market swings, graphic technology, washing machines, weather predictions, and so on.

One of the characteristics of a chaotic system is fractal geometry and fractal scaling in which the shape of the detail (branching of tree branches, shape of a coastline) is similar at various levels of magnification.

In human physiology, the structures of lung bronchioles, arterial, venous and lymphatic systems, neuronal structure, surfaces of proteins, etc., all display fractal properties.

Wednesday, November 21, 2012

Where Do You Stand?

Evolution or Intelligent Design?  In the latest Gallup Poll in June 2012, 46 percent of Americans believe in creationism (that God created human beings in their present form within the past 10,000 years), 32 percent believe in theistic evolution (evolution with God guiding the process), and only 15 percent believe in evolution as a scientific process without divine intervention. These results have remained relatively
steady for the past 30 years. Among 18 industrialized countries, America was next to last, above Turkey, in the percent of the population which accepts evolution.

Where do you stand?

Tuesday, November 20, 2012

Skeptics and Scientists

Scientists from all over the world have debunked intelligent design and Behe’s concept of irreducible complexity, citing numerous lines of evidence depicting the evolution of complex systems like the eye from simpler ones throughout various species over billions of years. They also cite the fact that the theory doesn’t provide for any way to experimentally test it nor does it make any predictions—two necessary components...

Monday, November 19, 2012

Evidence of Doubt

One of the main proponents of intelligent design is Michael Behe, a professor of biochemistry at Lehigh University and a senior fellow at the Discovery Institute’s Center for Science and Culture. His concept of irreducible complexity argues that a complex system like the eye would have required dozens of random mutations to have occurred simultaneously in order for any one of them to have given the organism an ...

Sunday, November 18, 2012

Origins of Modern Intelligent Design Theory

The modern intelligent design movement began in 1989 with the publication by Charles Thaxton of Of Pandas and People, the first book to make use of the phrase “intelligent design,” though the term had been used in other contexts. The main argument of intelligent design is a negative one, that organisms are so complex that they could not have evolved through random mutations and that only an intelligent being ...

Saturday, November 17, 2012

What Science Backs Up, We Disregard

Evolutionary theory in its basic form states that random mutations in the genes of an organism produce some genes that are advantageous, which lead to that organism being more adaptive to the changing environment. Over billions of years, these genetic changes produce organisms with the diversity and complexity we see today. ...

Wednesday, July 11, 2012

The Book of Life

Beyond Base-Pairs: Mapping the Functional Genome
“We’ve known the precise alphabet of the human genome for more than a decade, but not necessarily how those letters make meaningful words, paragraphs or life,” said Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego. “We know, for example, that only one to two percent of the functional genome codes for proteins, but that there are highly ...