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Wednesday, July 27, 2011


A report in ScienceDaily shows how fine-tuned biological logic can be--even down to the way a single electron is used in a strange but smart way to achieve the desired result with maximum efficiency.

The enzyme photolyase, which is naturally produced in the cells of plants and some animals (but not in mammals, including humans) repairs DNA by damaged by sunlight by tearing open the misshapen, damaged area in two places and reforming it into its original, undamaged shape.

But the enzyme does not break up the injury in both pieces at once. It is a two-step process that sends a single electron through the DNA molecule in a circuitous route from one breakup site to another.

Ultraviolet (UV) light damages DNA by exciting the atoms in the DNA molecule, causing accidental bonds to form between the atoms. The bond is called a photo-lesion, and can lead to a kind of molecular injury called a dimer. Dimers prevent DNA from replicating properly, and cause genetic mutations that lead to diseases such as cancer.

The dimer in question is called a cyclobutane pyrimidine dimer, and it is shaped like a ring that juts out from the side of the DNA.

For those organisms lucky enough to have photolyase in their cells, the enzyme absorbs energy from visible light--specifically, blue light--to shoot an electron into the cyclobutane ring to break it up. The result is a perfectly repaired strand of DNA.

Thursday, July 21, 2011


Researchers at the California Institute of Technology have made an artificial neural network of DNA, creating a circuit of interacting molecules that can recall memories based on incomplete patterns, just as a brain can.

'The brain is incredible,' says Lulu Qian, a Caltech senior postdoctoral scholar in bioengineering and lead author on the paper that described the work, published in the July 21 issue of the journal Nature, and reported on ScienceDaily. 'It allows us to recognize patterns of events, form memories, make decisions, and take actions. So we asked, instead of having a physically connected network of neural cells, can a soup of interacting molecules exhibit brainlike behavior?'

The answer was yes.

Beyond technological challenges, engineering these systems could also provide indirect insight into the evolution of intelligence. 'Before the brain evolved, single-celled organisms were also capable of processing information, making decisions, and acting in response to their environment,' says Quian. The source of such complex behaviors must have been a network of molecules floating around in the cell. 'Perhaps the highly evolved brain and the limited form of intelligence seen in single cells share a similar computational model that's just programmed in different substrates.'

'Our paper can be interpreted as a simple demonstration of neural-computing principles at the molecular and intracellular levels,' says co-author Jehoshua Bruck. 'One possible interpretation is that perhaps these principles are universal in biological information processing.'

Which is what this blog has been saying for years.

Tuesday, July 12, 2011


This story in ScienceDaily shows how finely tuned biological logic is. This split-second timing of a vital process in cellular life could never be achieved by hit-and-miss means, only by very precise logic.

Researchers from the RUB-Department of Biophysics of Prof. Dr. Klaus Gerwert have succeeded in providing evidence that a protein is capable of creating a water molecule chain for a few milliseconds for the directed proton transfer. The combination of vibrational spectroscopy and biomolecular simulations showed the proton-pump mechanism of a cell-membrane protein in atomic detail. The researchers demonstrated that protein-bound water molecules play a decisive role in the function.

Protein-bound water is decisive: specific proteins can transport protons from one side (uptake side) of the cell membrane to the other side (release side)--a central process in biological energy conversion.

Full story here.


Genetic instructions for developing limbs and digits were present in primitive fish millions of years before their descendants first crawled on to land, researchers have discovered. Genetic switches control the timing and location of gene activity. When a particular switch taken from fish DNA is placed into mouse embryos, the segment can activate genes in the developing limb region of embryos, University of Chicago researchers report in Proceedings of the National Academy of Sciences. The successful swap suggests that the recipe for limb development is conserved in species separated by 400 million years of evolution.

As that story in ScienceDaily shows, the long-term intelligent processing of biodevelopment had begun 400 million years before Darwin-worshippers could even dream up the slightest excuse for what they like to call 'evolutionary pressure.' The switches for limbs and digits, which fish do not need, do not want, and cannot benefit from, were starting to be formed. Biodevelopment's intelligent processing was beginning to work out a higher form of animal.