Sunday, December 30, 2012

Strange Behavior: New Study Exposes Living Cells To Synthetic Protein

I actually found this pretty fascinating. These researchers fabricated a synthetic protein, introduce it into the cell of a living bacteria and sat back and watched what the reaction would be. Would it reject it ? Would it be damaged ? Would it simply spit it out through one of it's exit doors ? Or would it accept it just as any old protein and utilize it some how ?  Remember my last previous post below on genetic information below ?
 "The Disinformation on Information: What Science Doesn't Know and Won't Admit" 
So what happened here ?
This was actually kool, but it could be a bit boring, so bare with me. I won't quote everything, just a few pertinent points or paragraphs which are outstanding. Remember that DNA is the smallest informational compression storage mechanism known to Science. The massive volumes of information as mentioned before would fit into a small library if we could actually translate everything it accomplishes into human language and publish into encyclopedia sized books. Inside a single cell, it is clear that there are all manner of Programs, Files, Apps and other guidance system mechanisms to be activated or specific systems may even be shut down at a moment's notice if needed as a defense mechanism. This appears to be what happened here. What fascinates me is that the behavior observed and written about by these researchers is something similar to what trees do when there is an outside intrusion. But let's first see what happened in this Synthetic Protein introduction experiment. Below is a quote from ASU researcher John Chaput with questions similar to what I  asked myself when I first read the paper and referenced above at the top of this post. 

"If you take a protein that was created in a test tube and put it inside a cell, does it still function ?" Chaput asks. "Does the cell recognize it ? Does the cell just chew it up and spit it out ? This unexplored area represents a new domain for synthetic biology and may ultimately lead to the development of novel therapeutic agents."
(source)
https://asunews.asu.edu/20121227_livingcells_syntheticprotein 

I find this very interesting because I have to imagine most people simply envision what they believe the word Protein itself means, simply meat or flesh of an organism. But if you slow down your thought processes for a moment,  think and reason carefully, not all proteins are equal. Seriously, taking just the human being, we have all manner of proteins which make up different organs, membranes, skins, muscles, etc etc etc. There are specific coded instructions for specific proteins for specific building and maintenance purposes. There are instructions for the way these proteins fold and shape themselves into the structures needed for a specific function. So do all proteins manufactured by a specific organism's cells have a trace of identifying codes which define itself from all the others ? Perhaps this synthetic protein which was done in the lab was nothing more than an assortment of building blocks amino acids by which to make a protein according to the scientist's limited knowledge of just what a protein should be. To the cell, it no doubt appeared to be a blank slate and definitely read as a foreign intrusion. So what was the response ? Here is what took place inside the cell when infiltrated with the synthetic protein named "DX".
"After exposure to DX, the normally spherical E. coli bacteria develop into elongated filaments. Within the filamentous bacteria, dense intracellular lipid structures act to partition the cell at regular intervals along it's length (see figure 1). These unusual structures, which the authors call endoliposomes, are an unprecedented phenomenon in such cells."

Credit: The Biodesign Institute at Arizona State University
Notice the normal bacterial cell compared to the elongated one ? Watch as under closer magnification as the rectangular compartmental structure is revealed and the foreign protein is contained so as not to influence any other cell functions.
"Somewhere along the line of this filamentation, other processes begin to happen that we haven't fully understood at the genetic level, but we can see the results phenotypically," Chaput says. "These dense lipid structures are forming at very regular regions along the filamented cell and it looks like it could be a defense mechanism, allowing the cell to compartmentalize itself." This peculiar adaptation has never been observed in bacterial cells and appears unique for a single-celled organism." 
These compartmentalization structures, as perhaps a possible  defense mechanism are what fascinate me. I am quite familiar with these structures and processes for a defense mechanism in larger forms of life like trees or even people. Briefly take the human body as an example. In these later days of pollution created by primitive outdated technologies or knowingly irresponsible scientific innovations utilized by modern man, we now all manner of tumors and cancers which are quite common. The body cannot always deal with the tumorous growths to stop them , so it will quite often build a dense protein layer wall around these mutated cells in an effort to contain them and save the rest of the body in the process, while it's immune system may try and figure out what other responses may be necessary to kill and rid the body of these abnormal growths.

Tree Care - Prunning & Planting
But for me it's mainly the behavior of trees in their ability at compartmentalization with which I am familiar. I actually learned this from understanding proper and improper branch pruning techniques. Take this illustration over here on the right of a tree's branch collar. These branch whorls are at regular intervals and quite often represent a years growth from which it began at a particular spring bud break. Now take a look at those familiar wrinkled bark patterns where the branch collar meets the trunk. These are specialized cells for the purpose of growing over and containing an open wound in the tree, such as a branch being broken or cut off. Some people get the not so bright idea of making what they consider neat cuts which are flush to the trunk. The wrinkles in the branch collar are the tree’s first line of defense against the invasion of micro-organisms. The final cut should be made just outside these wrinkles. Fail to do that and you shorten the life of the tree through fungal spore intrusion which leads possibly to rot of the trunk's interior. Trees do not heal like you and I. They rather contain an injured area through compartmentalization and enclosure of the wound. When it comes to tree trimming and pruning, it's almost like the tree is telling you where it wants to be cut if that becomes necessary. So pay attention to the clues. 


compartmentalized callous
around a bird's nest cavity
The outside growth covering is obvious to an observer, but the inside also has other specialized cells which act to enclose the the branch which often can be seen as a knot in lumber. This harder calloused specialized wood prevents the fungal spores from entering the main trunk which would definitely rot out the interior heartwood and shorten the lifespan of the tree. In some cases, rot may occur in the branch interior, but containment inside doesn't allow for complete rot out. Instead, quite often a woodpecker will find it an easier assignment for creating a nesting cavity from the softer rotted material, later to be utilized by other birds. I see quite a lot of this over here in Sweden. Let's take another very common plant compartmentalization ability like that of the giant Saguaro of the Sonoran Deserts of Arizona.

Credit: Steve Zamek
We've all seen those cute little Elf or Pigmy Owls who make a nest in a Saguaro Cactus. Of course the Owl has no equipment for drilling or pecking a hole in this giant of a cactus. This is accomplished by the Gila Woodpecker who makes this desert it's home. Elf or Pigmy Owls simply search for abandoned burrows or nesting cavities in these Saguaros. But the cactus tissue while soft and easy for a well equipped woodpecker  to make easy work of it's soft pulp flesh, has another defense mechanism for any water loss or rot containment. It creates inside the cavity a hardened calloused growth of cells which are tougher than leather. In fact there is an actual name for such compartments which are quite often found in a long dead Saguaro called a Cactus Boot. Take a look at the one below and an illustration someone who did very well in her description of just what happens inside the Cactus.


Credit: Terri Casper

Terri's Painted Daisies: Cactus Monday - 'Cactus 'Boot'
Terri actually does a very nice illustration of the cactus boot and the location inside of the arm or trunk of the Saguaro Cactus.
I suppose one might be lost on my point here, but don't be. This blog "Earth's Internet" is concerned with looking at nature as a brilliantly constructed biological system which should be recognized and respected. In so doing, understanding and learning should be done from a Biomimicry or Biomemetics perspective. You should ask yourself, what practical applications can be applied in the urban landscape or habitat restoration ? What does all of this similar defense mechanism tell me about the very real informational instructions contained not only in organisms we can see and observe, but also right down to the single celled lifeform that we cannot see without the aid of a microscope ? It should tell you that rather than meaningless patterns that got lucky, there is clear specific written programming no matter how either side wants to spin play origins. DNA is never the less real information. This is clearly something not totally respected and accounted for by the GMO industry despite their quite often Public Relations Misinformation sham campaigns which insist that they KNOW what they are doing for our own good whether we like it or not. Spooky isn't it! Let's take one more final point from that article's discovery.
"The study also examined the ability of E. coli to recover following 'DX' exposure. The cells were found to enter a quiescent state known as viable but non-culturable (VBNC), meaning that they survived ATP sequestration and returned to their non-filamentous state after 48 hours, but lost their reproductive capacity. Further, this condition was difficult to reverse and seems to involve a fundamental reprogramming of the cell."
This is really kool. Now they say it lost it's ability after recovery for reproduction capacity. But did it really lose anything ? There was an experiment done in which DNA strands were damaged to observe it's repair mechanisms at work. Amazing indeed. Yet when they went too far and created too much extensive damage, the cell killed itself, rather than attempt an imperfect repair which may be mistakenly past on to future generations. So scientists know that  cells have kill switches, just as they know certain specific different cells within the body have cell death switches for specific lengths of time for different cells which are than replaced. In the past science hasn't paid too much attention to this, but are doing more so now. Could it be that the information contained within the DNA of that E.coli bacteria cell deliberately shut down voluntarily it's own reproductive ability so as not to pass on any defective traits that even these researchers are unable to detect ? Now why would it do that ? Does an E.coli care or reason out about it's descendants on down it's own genetic lineage ? I don't think so. I don't think an E.coli is capable of caring or reasoning as we do. Scientists also know that they are able to pull out a program file for the building of a propulsion mechanism like that of an outboard motor boat to be able to hunt in wolf packs towards new sources of food to consume and assimilate. Now why would they do that ? They have also found that they communicate with each other through a chemical type of messaging which triggers specific actions and responses from other bacteria. Now why would they do that ? Isn't this thing called "Junk DNA" wonderful ?


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