You've heard of a Flea Circus… now get ready for the Germ Circus!

Thinking Ahead: Bacteria Anticipate Coming Changes In Their Environment

LOL!!! Something a bit more than Shapiro's "cellular intelligence," researchers at Princeton have demonstrated some interesting intelligence in e.coli per anticipating future conditions and turning genes on or off based on that acquired knowledge.

In addition to shedding light on deep questions in biology, the findings could have many practical implications. They could help scientists understand how bacteria mutate to develop resistance to antibiotics. They may also help in developing specialized bacteria to perform useful tasks such as cleaning up environmental contamination.

Huh. An understanding of evolution as endogenous adaptive mutagenesis looks to "have many practical implications?" Who'd a thunk?

The researchers say that their findings open up many exciting avenues of research. They are planning to use similar methods to study how bacteria exchange genes with one another (horizontal gene transfer), how tissues and organs develop (morphogenesis), how viral infections spread, and other core problems in biology.

By golly, here we have actual biological scientists at an Ivy League institution and publishing in Science reporting that life anticipates the future at the most rudimentary level and adapts itself accordingly. Who was it who predicted years ago that science would eventually come to accept an EAM-ish version of intelligent design in biological evolution because it offers better solutions to 'problems' the RM-NS paradigm simply cannot explain?

Very cool.

In his book, Vital Dust, Nobel Laureate Chritian de Duve writes, "A bioengineer attempting to construct a cell designed to proliferate as fast as possible could not come up with anything better than a bacterial cell." Indeed. In fact, as I point out in The Design Matrix, reproduction is the means by which a front-loading designer can perpetuate designs far into the future. Yet the simple perpetuation of design through reproduction would not be enough. The cell, as a vehicle that both expresses and carries the design, would be designed with sufficient resiliency to persist across deep time. It is this inherent resiliency that prevents the blind watchmaker from relying entirely on mutation and reproduction such that the original designs would all be erased over deep time due to countless selection pressures. Resiliency, in essense, represents a phenotypic space where the blind watchmaker is not needed. This combination (balance?) of enhanced proliferation and resiliency would allow the designed life forms to spread a network of deep roots into and througout the entire Earth, further ensuring many existing populations are significantly tied to their original ancestral states "“ the designed state (ie., front-loading).

Recent discoveries about the resiliency of bacterial life continue to impress scientists. One recently discovered species, Chryseobacterium greenlandensis, is quite remarkable:

Read the rest of this entry »

Mike has highlighted the importance of proteins. Proteins are involved in all sorts of cellular functions including their own synthesis. Each step in the pathway to protein synthesis involves proteins. That includes the regulation of genes (whether or not a gene coding protein will be expressed), the transcription process and translation. It takes proteins to generate proteins. The proteins involved in the synthesis of other proteins are synthesized by the same cellular mechanisms they become part of.

There are two ways of analyzing the role of proteins. Proteins illustrate the interdependence of cellular functions and the dependence of cells on the proper coordination of its separate parts. That in turn is evidence of downward causation- a paradigm favorable to ID.

But we could continue to approach the matter of life's origin solely from a reductionist perspective. After all reductionism has led to success in other fields and provides an inductive argument for its continued utilization in origin of life research. Spinning wheels can keep an occupant in the same place but rabbits have another means of advancing.

The biochemists studied yeast cells and found that mitochondria, which generates 90 percent of the cell's energy, can be the deciding factor "“ the "brain power" "“ behind how fast cells divide.

"The finding changes the traditional view of the mitochondrion from an "˜energy depot' at the service of its larger cellular host to a "˜command center' that directs cell division," Polymenis said.

Polymenis said the research showed that when a yeast cell's mitochondria decided to "turn on the switch," the cell's nucleus "“ which carries most of the genetic material "“ received the message and cell division began.

Here

Cells keep a close watch over the transcriptome "“ the totality of all parts of the genome that are expressed in any given cell at any given time. Researchers at the Salk Institute for Biological Studies and the University of Missouri-Kansas City teamed up to peel back another layer of transcriptional regulation and gain new insight into how genomes work.

Converting the "genetic blueprint" into molecular building blocks requires two basic processes: transcription, which copies the information from DNA into RNA transcripts and takes place in the cell's nucleus, and translation, where the RNA serves as a template to manufacture proteins outside the nucleus.

But before transcripts can guide protein synthesis or take on regulatory functions, they have to undergo a strict mRNA surveillance system that degrades defective, obsolete, and surplus transcripts. In their study, published in the Dec. 28 issue of Cell, the scientists zoomed in on a specific subclass of transcripts that are under the control of the exosome, a molecular machine in charge of controlled RNA degradation.

"We found evidence for widespread exosome-mediated RNA quality control in plants and a "˜deeply hidden' layer of the transcriptome that is tightly regulated by exosome activity," says Joseph R. Ecker, Ph.D., professor in the Plant Biology Laboratory and director of the Salk Institute Genomic Analysis Laboratory"¦"¦"¦"¦"¦ "It is likely that these RNAs that are usually "˜deeply hidden' become important for genome function or stability under some circumstances", adds co-first author Julia Chekanova, an assistant at the University of Missouri-Kansas City. "We need to do more work to figure out what these circumstances are."

HERE

Imagine you are a soldier on a very dangerous patrol in Iraq. During this patrol, you are likely to experience fear, as you feel that your life is in danger. While your conscious brain attends to the environment, looking for suspicious activity, the unconscious part of your brain is busy altering your body's physiology in anticipation of an impending threat. Your heart will start to beat faster and much of your blood that would otherwise be traveling to your kidneys and digestive organs is rerouted to your muscles and nervous system. The liver dumps extra sugar into your blood and the airways in your lungs open wider, allowing them to deliver more oxygen to the blood that pulses more quickly. Your sweat glands are more active and the pupils of your eyes dilate. This is what is called the "fight or flight" response, made possible by the hormone epinephrine, better known as adrenalin. The net result of this response is that your muscles are stronger and faster and your brain is more alert. In other words, your body is optimized to fight the enemy, or if need be, to flee.

More

According to Mats Ljungman, a researcher at the University of Michigan Medical School, as many as 20,000 lesions occur daily in a cell's DNA. To repair all this continual damage, how does the cell first detect it? Ljungman's research identified the logical candidate "“ RNA polymerase (the machine that reads the DNA and makes an RNA copy). Apparently, whenever the RNA polymerase encounters a lesion, it signals to p53, a master protein that activates all sorts of DNA repair processes.

According to the press release:

"These two proteins are saying, "˜Transcription has stopped,'" says Ljungman. These early triggers act like the citizen who smells smoke and sounds a fire alarm, alerting the fire department. Then p53, like a team of fire fighters, arrives and evaluates what to do. To reduce the chance of harmful mutations that may result from DNA damage, p53 may kill cells or stop them temporarily from dividing, so that there is time for DNA repair.

Recently, the ENCODE consortium determined that the majority of DNA in the human genome is transcribed:

This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.

Of course, one could also argue that all this transcription simply speaks to the sloppy and wasteful nature of the cell. Yet here's a thought. It would seem to me that Ljungman's research now raises a third possibility: all that transcription is just another layer of error surveillance.

From here:

Kinase mediated phosphorylation is generally recognised as the major regulator of virtually all metabolic activities in eukaryotic cells including proliferation, gene expression, motility, vesicular transport and programmed cell death. Dysregulation of protein phosphorylation plays a major role in many diseases such as cancer and neurodegenerative disorders. In addition, the elucidation of many kinase cascades has proved pivotal for understanding and manipulating cellular behaviour in a variety of divergent eukaryotes.

Within these organisms a wide rage of kinases has been defined. The human genome contains over 500 protein kinase genes, whereas the genome of a small plant like Arabidopsis thaliana, the mouse-ear cress, contains nearly 1,000. Despite this diversity, a team led by Maikel Peppelenbosch, PhD, a professor of Cell Biology at the University Medical Center in Groningen, the Netherlands, has established that all eukaryotic kinases share a common set of substrates, nine amino acid segments shared by all proteins that are known to be phosphorylated.
["¦]
These results indicate that, although probably thousands of different kinases have developed during the 2.4 billion years of eukaryotic evolution, they show no significant functional difference. Furthermore, the results suggest the presence of a set of kinase substrates in an ancestral eukaryote that has remained unchanged in eukaryotic life, so the earliest eukaryotes may have been less "˜primitive' than generally thought.

Here is some more evidence that the nucleus is a rather organized environment rather than a soup. In this case, damaged DNA appears to be shuttled to specific zones within the nucleus for repair:

Researchers have previously proposed the existence of "repairosomes" in mammalian cells, similar to specific regions where DNA is repaired in yeast, although these have never been observed in mammals. The fact that RIF concentrate in specific regions of the human cell nucleus "” and apparently tend to move toward shared sites "” is highly suggestive of such repair centers, where activities like the necessary clamping and orientation of the broken strands take place.

On another topic, immunity in social amoeba suggests ancient beginnings. Once again, another seed of multicellularity seems to have existed long before the existence of animals and plants:

Sentinel cells circulate within the slug, engulfing invading bacteria and sequestering poisons or toxins, eventually eliminating these from the slug. These cells often operate through a particular mechanism in the cells controlled by a Toll/Interleukin-1 Receptor domain protein (TirA), Kuspa and his team found. This signaling pathway or a very similar one is present in plants and animals, he said.