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 ?


Friday, December 28, 2012

The Disinformation on Information: What Science Doesn't Know & Won't Admit



Our world is controlled by wealth obsessed global corporations which shackle otherwise potentially good Scientific Researchers into pursuing a very ecologically destructive form of  science. But let's be realistic here, bad science is in the business of creating wealth for their Corporate Masters. I often jokingly refer to a twist of an old saying which is traditionally called, the "Golden Rule" [you know, "Do unto others" ?] , but in today's society it instead goes like this - "Remember the Golden Rule. The one with the Gold makes the Rules". Would you not agree that this is exactly the twisted practice of how the 21st Century world we all live in really works ? In the so-called democratically run countries, the Ideologues insist that it's the power of the people that accomplishes great change through civil disobedience, protest and/or various forms of Activism. I remember growing up when Activism was just starting to become popular & was all the rage during the 1960s. While it did bring great Social awareness and outrage on many popular environmental issues which drew much attention to such well known expressions and terminologies like Ecology, Earth Day, etc. Yet today, people are even more out of touch and disconnected from these issues than ever before in the past. The breakdown of our planet's natural world  mechanisms today reflects the massive ignorance of the average human being to ecological issues and this isn't restricted to the popular view of uneducated or illiterates, this also includes our globe's self-promoting intellects who run the planet. Right now at this moment in time, there is the very real possibility of total or complete breakdown of life's self-sustaining  mechanisms found out in Nature. But thus far, all the Activism in the world hasn't prevented the present mess from revealing this ugly truth about our so-called enlightened 21st Century. Unfortunately, it can be pinpointed to Corrupted Science which is what presently rules and dominates our planet. This same scientific orthodoxy totally ignores what the real neutral science has discovered. Notice to all Science Defenders, I said corrupted science, not Science  (- see - The Folly of Scientism by Austin L Hughes Evolutionary Biologist) There are many religiously driven science types with an ideological perspective that any new "technology based on Science" is automatically good for us no matter what. Historically speaking however, this hasn't always been the case. For example when I was growing up in the late 1950s thru the 1960s, a drug called Thalidomide was hailed as a miracle cure for pregnant woman with morning sickness. Later of course this was discovered to have caused all the numerous birth defects I personally was witness to during my school years. In my personal experience growing up, it was common to see a family I knew to have a sibling with some sort of birth defect. Of course, if you were against his, you were labeled anti-science. There seems to be a cowardly strategy used in any science debate that if you go against the what is considered the conventional ideological norm in science you must therefore be an anti-science Luddite. It's an effective tool as a debate strategy, especially when the offending person has absolutely zero to back up their position or claims and if they believe they've got consensus on their side backing them up. Now this takes me to the subject of GMOs.

Let's take a moment and reflect on some of the biggest major blunders by the Corporate Science Gang which has already had major consequences for our planet, some of which may never be reversed under the present system of things. This is of course the controversy of the Biotech Innovation called Genetically Modified Organisms (GMOs). Now before we go there, let's first consider as an example the debates surrounding the informational content of the Genetic Code. Some say DNA is not real information. They say it is nothing more than meaningless patterns formed by blind undirected forces, while others say the informational content originated from some sort of intelligence. First off, I want to clarify that I am neither an Evolutionist nor a CreationistI view both of these positions as nothing more than ideological power movements for the advancement of each one's personal biased politico-social agendas. Personally, I could never write a scientific paper and explain how these mysterious blind undirected forces of physics & chemicals or just how exactly any intelligence accomplished anything when it comes to the origin of the informational content of DNA. I simply recognize that this is impossible at this time. The best I can do is stick to personal observation and the reality of how nature really works (that is why I look at nature from a Biomimicry or Biomimetics viewpoint) as opposed to the religio/politico theories & hypothesis advanced forth and shoved down other's throats by both of these groups (no offense of course, just say'n). There is a HUGE difference between debating and arguing with an Ideologue as opposed to having an intelligent discussion with another civil human being who cherishes facts and evidence. But once again, I am bringing this up to highlight the glaring flaws behind the controversy surrounding the GMO technology and what they (Science defenders of this technology) don't know or will refuse to admit they don't know. Ultimately, the very real informational content that does exist within DNA.

I started this blog, "Earth's Internet" because I view the natural world as a fully functional brilliantly sophisticated piece of machinery with countless important components which deserve our admiration and respect. For the most part human beings as a general rule worldwide never really get this. My main focus here on this blog of course is plants, but I also recognize the important interconnected roles that all other forms of life play in this complexity of biological existence. Focusing mainly now on plants, I view each individual species of plant as being run by it's own computer operating system which comes with pre-installed programming with a sort of fully functional version of 7.0 Horticultural Software on steroids with the ability to manage most life functions with an extremely large selection of specialized Apps with countless programs and files which may be accessed upon at a moment's notice to problem solve and doing so at faster than super-computer speeds. 
So let's start off by looking at a very familiar illustration below. 



image: boominscience.weekly.com

Okay, so this is basically a 3-D animation or illustration of a single cell, probably similar to those you've all seen in various scientific textbooks from your School days. Many have made the comparison of a single living cell to that of a well fortified protected city with it's central command & communications Centre, transportation systems, waste disposal departments, messenger components, Manufacturing Plants, etc etc etc. But I want you to now go beyond this and consider it as an entire molecular version of an ecosystem. So what is an ecosystem ? All ecosystems have foundational species which serve to promote any specific type of system that may exist anywhere on the globe. Within all ecosystems there are checks and balances and as we all now know, instead of that  mistaken dogma of survival of the fittest, we now know that there is generally a harmonious mutualistic cooperation going on in every ecosystem. But here is where the Biotechs go wrong. They only have tunnel vision. They have no peripheral vision to look at the consequences of disrupting a cooperative sophisticated complex harmonious system by introducing a sort of species component [foreign gene] which comes along and disrupts the harmony which once existed in the system they are attempting to modify under the guise of a better designed product. In this case we are talking about the informational content of DNA which is specified to one organism and placing this within another radically different organism which could be compared to a micro-ecosystem. The question is, how will the introduction of a foreign gene component react with it's newer neighbours and vice versa ??? 

Let's start off our stroll down the "Earth's Internet" Information Highway by reviewing something we call all relate to. In this blog I write a great deal about various ecosystems that I am familiar and have worked with, how things function and harmonize within all these varying ecosystems and how we can replicate practices which work with as opposed to against such ecosystems. This is what mankind and Science from our historical  past has failed to recognize. Nothing is simple in Nature, in fact it is extremely complex and sophisticated. One of the promotional  points that I always find irritating with those defending the biotech industry and GMO technology is when say "we're just talking about Genes or DNA. DNA is DNA or Genes are just Genes." Well, no they are not. Take the illustration of that cell above. That could be any cell which is specified blueprints within any certain specific organism. It's informational content is specified to the building and maintaining of that specific organism irrespective of how any religiously motivated ideologue from either side of debate thinks it got that way. I think everyone gets that. Instructions for building a Giraffe are far different in the extreme than those found in the cell of a Elephant for actually building an Elephant. So why do GMO Scientists and Researchers justify their technology in such simplistic terms ? Because it's mostly a business model which is being defended, with the argument of a better science being used as a cloak for it's flaws. In almost all cases, it's never been necessary to build a better plant when nature has a plethora of tools in it's Tool-Kit arsenal for handling any self-defense situations. Also, plants need insects as well as insects need plants, but it's finding that balance which should make more Eco-sense. The real reason behind what Biotechs strive for are Patents and monopolizing our globe's food production industry. It has zero to do with them only wanting to help feed mankind out of the goodness of their dear sweet hearts which is often used as a smoke screen. 

But their technology also exposes the flawed background of their understanding as to just what the informational content of DNA really and truly is. Because of their willful ignorance comfort zone on just how the genome really works, we & Nature in general are all paying the price for such complacent ignorance. Their simplistic view and Public Relations "Just Add Water" explanation is that there is this thing called a genome, where this thing called DNA exists, some Genes are there within DNA and they can do certain things, we then simply take that gene from organism "A" and put it into some other DNA or Genome of organism "B" and it does what we want it to. It's just as simple as that. Except it's not as simple as that. Instructions which worked specifically along side the first BT Cry gene [ecosystem species which we'll call "A"] are no longer around to keep the original checks and balances within the new genome ecosystem [organism "B"] which has a completely different set of genes [or like foreign species of a completely different ecosystem]. One thing we do know now with the BT Cry gene is that it produces a far more potency of toxin within it's new ecosystem [Corn or Soybean] than it did in it's original ecosystem because there was something called non-coding DNA which provided the checks and balances. Those checks and balances were what many religiously & ideologically driven scientists often called Junk DNA sometime back. Many still do, but with the ENCODE project, Scientists are finding out these have more function and purpose than originally thought. So these non-coding genes have been providing much more function all this time in the form of guidance, instructions, blueprints, regulation etc in what that protein coding gene did and didn't do. It was simply a coding for protein gene for which it contained instructions for manufacturing. This is just like any other organism which is taken from it's native ecosystem and presented either purposely or accidentally within a completely foreign context. The entire system can be thrown out of balance. But they didn't anticipate this when they first started ? So what has happened thus far ?


Let's see if you can help me understand just what is going wrong with the Biotech Business model. Take a Dollar [or a Euro, Pound, Dinar, Yen, etc] bill out of your wallet now. With arms stretched straight out and holding the currency bill far away from you, what else can you see. Your peripheral vision allows you to see many things. I can see the scenery outside of my window. I can see all the other furnishings within the house. I can see actually hundreds of other things and perhaps so can you. But now bring that bill up to your face. What do you see now ? Nothing but that one dollar bank note. You are blinded and oblivious to anything else all around you. This is where the biotech researchers have been all this time. They have no peripheral view of the molecular-ecosystem and the potential for consequences of introducing an invasive species [Gene of another Micro-Molecular-Ecosystem] that doesn't belong in the radically unrelated new genome ecosystem. So the Biotech industry's original technology was based on a horribly flawed dramatically incomplete understanding of the genome when they started over 20+ years ago. Our present understanding now has dramatically changed. Now one thing you need to understand is that none of these Biotechs will ever be willing to admit this publicly. Frankly, the all have a vested business-stock options interest in seeing their business model succeed. No surprise there.
Invasive Tamarisk (credit: Earlham College) 
Now lets bring this up to a real world level we can all understand where we can actually see and picture things in real life. Let's see if this helps you understand the dire seriousness of the subject  better. We all know how easy it is to disrupt any ecosystem anywhere on Earth. For example, I come from the southwestern part of the United States. Over a century ago, the agricultural scientific consensus there said that it would be a great idea to bring in a tree called a Tamarisk which was native to the Sahara and other parts of the Deserts in the middle east to be used as a windbreak in the southwestern US desert areas to prevent crops from being dried out by desert wind desiccation. So Tamarix plus Windbreak equals problem solved. Right ??? Wrong !!! There were unforeseen consequences which plague this very area of the American Southwest & Mexico to this very day. These trees have had a dramatic riparian ecosystem disruption effect everywhere their seed blows, germinates and they take over. They crowd out almost all other native plant species and have replaced important food and shelter sources for many other species dependent on the Native plant life of that specific area. Oddly enough, one of the very species they have replaced around some desert habitats, Mesquite (Prosopis), are actually invasive to other parts of the earth because as the result of another scientifically inspired bright idea to bring them overseas and was also based on flawed Agricultural decision making on the part of bad science in those regions decades ago. Incredibly, nobody thought to use local native resources like a combination of desert plants covering a constructed dune barrier in replication of what actually occurs naturally in nature. Why ? Because nobody pondered and mediated on consequences and taking short cuts for quick fixes to make a buck tends to cloud good judgement.

Let's take one more failed scientific idea that has had massive dire consequences in Australia back in the 1930s. Australia has one of the largest global sugar cane industries in the world. But the cane beetle caused huge problem for the sugar cane Industry in Australia. Then the Cane Toad was introduced from Central America to eat those evil Cane Beetles down under in Australia. This was believed to be such a simple logical scientific solution. All you have to do is introduce a predator "A" [Cane Toad] to eat the prey "B" [Cane Beetle] and problem solved "C". Why it was as easy as "ABC", except it wasn't. As everyone at this time surely knows, this toad has taken over Australia, and has become a continent-wide problem. The native Australian Predators like Crocodiles, Snakes and large Monitor Lizards cannot even consume these Toads because these creatures exude a toxic poison from their skin and the predator dies. Those researchers back then were totally ignorant about the way that Australian ecosystem worked. They had tunnel vision influenced by the potential for profit. They rejected allowing enough time to consider possible consequences which means they actually chose to ignore their peripheral vision for the sake of instant gratification we call short term profits. The same is true of our world's modern day Biotech's genetic engineering and its unintended consequences on the genome. What may seem to be benign may in fact have dramatic unintended consequences, but nobody wants to discuss this. Watch this trailer below and look at the unintended consequences of the Cane Toad introduction into Australia. Here is how things have turned out for the Aussies who did not question the Science of the day.





A very large part of the fault for the present ignorance by many for the disrespect of the informational content within all lifeform's DNA can be directly traced back to those dumb stupid debates between Evolutionists and creationists. Seriously, what a waste. These debates on Origins have been heated for some 150 years now since Darwin offered the world his own version of a worldview. Over this time period the various stories have been promoted of nothing more than physics and chemicals developing by chance the building blocks of life which are amino acids for building proteins. As we understand and observe proteins today, these proteins are only created by previously existing  instructions for doing so by already living complex sophisticated nano-machines. Countless experiments have been conducted to advance forth just how some unknown undirected blind process created a prebiotic soup of sorts from which the first original protein molecules formed a sort of primitive cell wall from a bubble. Interestingly, this is only someone's vision of an imaginary gut felt account of what could or might be, but that is all it is. The true question has always been. "Where did all the life giving information come from?" This of course infuriates the present ruling Scientific Orthodoxy which has never been able to satisfactorily explain or prove any of this without their own version of myth creation, which is what the world already gets with many of this world's religions today. Science claims to set itself apart from religion, yet it employs many of the same metaphysical story telling it accuses religions of employing. Take a look at the illustration below and the reason behind much of the heated origins dilemma. 

image: Jacob Sandry
Dumb arguments deliberately attempting to discredit genetic information as real & meaningful have been presented for as "Rocks in a landslide are information" or "cobblestones strewn on a beach are information" and my all time favourite, "Patterns in snowflakes are information", Except all of this is asinine and absurd.
The problem or dilemma here for many of the Origins fables is that the "Just Add Water" story of chemicals and physics without direction or intended goals is in direct conflict of this central dogma of molecular biology. And it truly doesn't give us any more satisfying account of what really happened way back when, then any of the conventional religious myths from this world's historical past. From all that we know and from what has been observed, proteins are only created for specific purpose from the DNA Instructions given to molecular nano-machines for the building of such specifically folded protein for an intended purpose within biological system. Also, proteins do not create new information, nor can they control what DNA's information content does or doesn't do. The rule here is the other way around. This is where the debate becomes the origin of the "Genetic Information Codes" and no experiment has yet to prove otherwise.

 I actually like the comparisons made of DNA to computer operating systems. As a human I get that. It's something simply illustrative of complex system that I would never otherwise understand. It's also something that about half of Earth's population is familiar with and relates to. Any good teacher will employ the use of illustrations drawn from familiar life situations to get a learning point across. In this case, even an animated illustration works well in teaching others. The whole argument with regard the definition of information is that all information we know the origin of comes from an intelligent mind. Mere chemicals and physics cannot account for the information we all use day after day. We all have an understanding of information (ideas, plans, writings etc) having first been originated from the mind. Through the skull and brain contained within, the mind and consciousness itself is nothing physical (and I'm not speaking of a mythology of an immortal soul which I don't believe in anyway). The only time information becomes material is if written down on paper, typed onto a computer monitor, etched in stone, or any other material no matter what the make up of that material. Going back to computer systems and the "Central Dogma" for biology comparison, the principles are almost identical. Like the "Central Dogma" your computer is controlled by Microsoft's Windows software which controls all functions and systems within. No amount of Computer hardware like the plastic shell casing, copper wiring, circuitry, electrical voltage or magnetic field will ever control or dictate anything to the software what it should and shouldn't do. Nor is any of your computer's hardware capable of inventing or creating any new information for the software. As we all know, the software programming was created by intelligent minds. Of course so was the hardware. The information was etched onto a plastic disc, but it can only truly be controlled and manipulated by human intelligence who created it. Even Microsoft has to continually send and upgrade newer and newer security patches, something the far more sophisticated DNA does continually and automatically. If anything, there is at least some scientific inference that perhaps the genetic information does come from an intelligent source, but any discussion of this leads to anger and hatred by those who control and run science the political entities they bed with. I personally see no reason for the anger, though I get the dislike of religion. I don't like their conduct and most of their beliefs either, but I'm also not going to replace it with equally kooky ideas and mythologies under the guise of intellectualism. Neither side can truly employ the scientific rules of Naturalistic and Physical explanations ONLY and explain to us how a creator did such and such, or how blind unguided mysterious forces without purpose, goals or intent built sophisticated complex nano-machines run by the most complex information compression storage system known to mankind. Therein lies the problem. How does anyone on either side explain origins of information or anything else for that matter under the strict scientific rules of Naturalistic Explanations ONLY in any  scientific paper without manufacturing a fable or myth to satisfy the personal bias of the group you represent ? Well guess what, you can't!
This is where it now gets really weird. The other side (Science) which presents itself as far more intellectually superior to it's opponents, actually destroys any such claim with the countless oddball explanations they give in the way of their own version of storytelling by actually incorporating their own version of Fables/Myths and there is this constant need of muddling just what the word "information" itself actually means. Discussion then generally sink to a low grade misinformation debate which employs the use of definition shell games and when asking for further clarification by use of questions to better understand their position, all one ever receives are insults, derogatory language and personal attacks. Okay, first off I get it, the very idea that genetic information as having a comparison to real intelligent communications system as we know it, is clearly repugnant to the Science side because of the religious issues. I get it. However, these newer proposed metaphysical religious explanations by individuals claiming not to be religious simply don't cut it either. Faith statements dogmatically defended don't justify bad Science. There is clear evidence that the encoded information within DNA operates almost identically to the way the famous American Mathematician, Electronic Engineer and Cryptographer who worked for Bell Labs, Claude E Shannon proposed in his "Information Theory" (1948). Despite where one positions themselves on this debate as to origins, the fact remains that the genetic information within DNA behaves identically to any other communication system employed by humans. In actual fact however, it is truly superior to anything humans have devised. 
The arguments given in the form of definition shell gaming have followed like this. The absurd explanations of what the word information means by virtual Science Geeks (actually a collection of philosophers and other countless anonymous Ideologues out there on the internet) have gone like this. "Patterns of Snowflakes are information" , "Pebbles randomly strewn along a beach after a storm are information" , "Rocks randomly crashing down from a landslide are Information". And this asinine absurdity never quits. I can tell you that such idiotic explanations in no way help a geneticist in their personal research. If these absurdities were true, then why in the world would Scientists who actually study and decipher the meaning and understanding of DNA, why do they employ something called Linguistic Analysis ? Why is DNA looked upon as an encoder, RNA as the digital messenger and the Ribosome as the decoder of that information ? 


Funny, your computer runs on a similar messaging mechanism called the ASCII system, which is a character encoding scheme which was originally based on the English Alphabet. Press your keyboard's English Roman letter "A" and it is digitally transferred by a number code scheme of "1s" & "0s". In this case, the capital letter "A" is coded as "1000001" - "B" is encoded as "1000010" and so forth. This digital code of "1s" & "0s" are then instantaneously translated by your computer monitor the moment you touch any particular key to create the appearance on the screen for what ever letter you chose. Interestingly DNA originates the info, RNA digitally messages and the Ribosome translates and obeys instructions. For the Ribosome to do that requires it also has a in depth understanding of this genetic language. But DNA is far more complex than any of our human communications systems and does what it does at far faster than supercomputer speeds. And all of this before humans thought they knew better. 

ENCODE Statistics .org
This is what is baffling about the Science community's insistence on definition shell gaming genetic information. Recently however, I believe September actually, there were 440 scientists from 32 Labs with published years of collaborative research, went far deeper into the human genome than ever before. You may have read in the News about a project called ENCODE which is attempting to publish an encyclopedia of DNA. This is quite interesting since many years ago it was said by many well known scientists like Richard Dawkins and even the Encyclopædia Britannica which boldly stated that even in the DNA of the most primitive Amoeba, there is enough information contained therein to fill a small library with 1000 books with 600 pages each. Thus far the conclusion of the scientists at ENCODE has been that the religiously motivated term "Junk DNA" is now an obsolete term. Now sadly, instead of applauding the genuine efforts being made by these scientists for acknowledging Science does not know what all of the genetic code is about, but that they are going to study and research and get back to you on this, they have instead been attacked by well known academic Ideologues who claim to represent all of science on this matter. And that's really too bad. An interesting update on the complexity of life being define by the information which drives it as opposed to the environment destroying life is nothing more than an arrangement of Chemicals. The Guardian News in the UK reports on the dilemma scientists have with these debates: (see also footnote reference)
"Most research into life's murky origin has been carried out by chemists. They've tried a variety of approaches in their attempts to recreate the first steps on the road to life, but little progress has been made. Perhaps that is no surprise, given life's stupendous complexity. Even the simplest bacterium is incomparably more complicated than any chemical brew ever studied."
"But a more fundamental obstacle stands in the way of attempts to cook up life in the chemistry lab. The language of chemistry simply does not mesh with that of biology. Chemistry is about substances and how they react, whereas biology appeals to concepts such as information and organisation. Informational narratives permeate biology. DNA is described as a genetic "database", containing "instructions" on how to build an organism. The genetic "code" has to be "transcribed" and "translated" before it can act. And so on. If we cast the problem of life's origin in computer jargon, attempts at chemical synthesis focus exclusively on the hardware – the chemical substrate of life – but ignore the software – the informational aspect. To explain how life began we need to understand how its unique management of information came about."
Despite the origin of the Information contained within DNA, nevertheless, it truly is real coded information within the most complicated communication compression system mankind has ever known. Dismissing this has lead to horrible technologies like the release of Genetically Modified Organisms which should never have been produced without a full understanding of the information contained within DNA. Not to mention the fact that they were never necessary in the first place if people would have originally researched and found out what nature's too-box actually contains for any given situation. Saying that 90% of DNA is junk for no other reason than you cannot read it's function and purpose is clearly irresponsible. This is also why such terminology like "Vestigial Organs" (outdated evolutionary organs with no function) came into play, why ? Because some ideologically driven intellectual at some time in the past didn't actually know the function and purpose of certain parts of the human body like as an example Tonsils or Appendix. I had my own Tonsils taken out when I was a kid because the belief at the time was they served no important function to the human body. Well low and behold years later that has been debunked and immune system function has been discovered. So this idea that genetic information is not really a language is equally ridiculous and has brought us terrible consequences. It would be like me saying that the only real spoken and written language for humans is the English Language with it's Roman characters. Take an example of this sentence in English.
"What is the definition of information?"
Now because I know what the pattern of the English language characters are, then I also understand instantaneously the meaning of the sentence. This is true of all information. All information known to us have different patterns, but not all patterns in nature contain information, But now what if I translate this same sentence into say, the Arabic or Chinese pattern of characters ?
ما هو تعريف المعلومات كلمة؟
信息的定義是什麼
Would it be logical or even reasonable for me to say that those are only meaningless patterns which contain no information whatsoever, for no other reason than I am incapable of understanding those specific patterns and spoken languages of both Arabic and Chinese ? It would clearly be absurd and asinine for me to insist upon such a reasoning or explanation. And yet this is exactly what the scientific world has in effect done when it comes to releasing GMOs into the wild. They won't recognize it as a true language with rules or laws and believe they are only connecting simple Lego or Tinker toy patterns from other organisms together. There is far more information in that BT Cry Gene than mere simple instructions for manufacturing a toxin. Not all scientists are on board with this. Many like Geneticist David Suzuki, recognize that we don't understand enough about genetics to be toying with it's makeup. But big business commercial interests in bed with politics has given this world a newer tool for the natural world's degradation. This is only the first part in a series of posts I'll do on this. While I don't agree with GMOs, I am also not on board with many of the Anti-GMO sites which rather than having their facts straight, tend to run on emotion and that ultimately hurts their cause. The main scientific GMO defenders swallow much of the above philosophy and label anyone who doesn't approve of GMOs as being Anti-Science. This couldn't be further from the truth. People from all backgrounds and beliefs simply want responsible science and the destruction of our natural world is proof that the last 150 years of intellectual enlightenment has been an environmental disaster, despite the many conveniences we all enjoy and use. I'll post a link later below.

image: agriculturedefensecoalition.org
While this photo is comical and funny, it never the less illustrates people's disgust with industrial agriculture. Only a month ago people thought they could get labeling laws passed, but it failed. The reality of course is that such laws would never have been any guarantee that such GMO contamination has not happened anyway. We all are well aware what happens when news laws are created, proposed and passed. They become newer opportunities for corruption and loopholes. GMO Biotech Companies and their Industrial Brand Food allies spent millions of dollars in defeating it. The biggest problem with GMOs is the attitude referenced above, that THEY more than anybody else know what they are doing. Clearly there have been enough studies and results which show otherwise. But it's the disinformation - misinformation public relations marketing campaign that has damaged the most and I'll deal with some of these next time. Bottomline here for the defenders of GMO technology, irrespective of how you think the brilliant complex and sophisticated genetic information within DNA came to arise and appear which resulted in Life on Earth, it never the less is as real information. But it's actually superior to anything intelligent humans have ever invented or ever will. The arrogance and irresponsible conduct of Industrial Science is killing our Natural World for nothing more than power and wealth. The we just want to feed the world chant is just a cloak to justify their business model. There is no way to reverse the genetic pollution these people have put out there in the world. It's there to stay and what consequences come as a result are just now revealing their ugly heads.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
Further Reading References and News Updates:
Top US Healthcare Giant - Kaiser Permanente: GMOs Are Devastating Health
Biotech Scientist: It’s ‘Awesome’ That GMOs Cause Infertility, Death (Video)
ASCII Code Chart
The secret of life won't be cooked up in a chemistry lab Life's origins may only be explained through a study of its unique management of information

Thursday, December 27, 2012

Who Knew ? "Even in same vineyard, different microbes may create variations in wine grapes"


Credit: Wikipedia
"Depending on location in the picturesque rolling hills within a vineyard, the amount of sunshine or shade and a large host of other factors which effect microbial growth and association, differing species may effect taste and flavour of your flavourite wine. There clearly is more to choosing the best wine than knowing it's vintage and the Chateau it came from."
There was an incredible article or paper published recently which came out and revealed that different yeast species (microbes) may cause difference in wine batches even though they may be from the  same identical grapes grown out of the same vineyard. Incredibly as many of us know, any type of farming of crops, be they grains, vegetables or even orchard crops will be different depending on the growing conditions experienced even withing the same geographical area. Crops grown on a southern exposure will be different than those on a northern exposure and so forth. Microbe species apparently are no different, we just simply don't see them and never give thought nor attention for no other reason than out of sight out of mind. They clearly are effected by the geography and micro-climates of a given area. Many and most red wines for example do better in a warmer or even hot climate. White wines do better where the climate is more northern and cooler than others. We all understand how specific areas of the world are better for growing wine grapes than others and there are any number of physiological variables which influence this. Now we know that microbes are no different.
Photo Credit: Wine and Moore
"That white chalky looking substance on grapes is where the yeast lives which creates that fermentation of wine grapes. Not commonly known to many, almost all most fruits have the same colonization of microbial species living on the outer skin layers of their fruit skins."
Credit: The Wine Educators Toolbelt
"The tiny, single-celled fungi (I’ll spare you the bad joke) known as yeast are responsible for creating wine; without them, it would merely be grape juice. Simply put, the yeast consumes glucose and fructose in grapes, converting the sugars into alcohol and carbon dioxide. The resulting product is much more complex and interesting than if the yeast had not intervened (thanks yeast!). These organisms exist throughout nature and are found on the skins of grapes (not a bad place to hang out if you’re looking for a free lunch), among other places."
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Eureka Alert source:
"In the wine industry, the fungal communities on grapes are especially important. The microbial species present on the berry may contribute to the fermentation process, and therefore the aromatic properties of the resulting wine", the authors explain. For this study, the researchers sampled grapes from different vines in three well-established commercial vineyards, each of which used a different farming system - organic, traditional or biodynamic- to cultivate the grapes."
"Across the three cultivation practices, they found that the same yeast species dominated in all vineyards, but the least treated vineyard had more variety of fungal species than the other two. They also found that within a single vineyard, small differences between vines, such as in temperature or sun exposure, could significantly alter the composition of the fungal community on grape surfaces. Setati adds, "Our findings could help viticulturalists and winemakers plan microharvest better, and implement better wine blending strategies to ensure consistency."
I especially loved one particular sentence in the paper. After listing the three types of vineyards - Traditional approach (those that employ the more conventional Industrial Agricultural approach by use of chemical fertilizers and Pesticides) - Biodynamic approach (those that employ many of the organic practices, but controversially will also spray with various herbal and mineral potions on the plants to control pest, plus may even employ mystic beliefs such as grinding up quartz and packing it into cows horns to attract cosmic forces to enhance growth. Many other oddball practices as well, but you get the idea) - Organic approach (the practice of replicating nature for natural biological controls, such as planting of roses, lavender and/or other flowers that attract and benefit predatory wasps and other beneficial for pest control. The use of sheep for grazing weeds and other grasses between the rows. Even employing a method of Agroforestry around the vineyard to create a beneficial micro-climate) - Now look at the photo below and that last line in the report.

Photo Credit: Luis Felipe Edwards Wines

Photo Credit: King Estate Vineyards, Eugene, Oregon
The family winery has been producing wine for over two decades southwest of Eugene, Oregon. They are dedicated to certified organic and sustainable farming methods and they specialize in producing Pinot Gris and Pinot Noir as well as a small amount of Chardonnay. Take note of the rows of Lavender shrubs bordering the exterior of the Vineyard itself. Such plants will attract predatory insects to keep pests under control where pesticides won't be necessary anymore.
Photo Credit: Patianna Organic Vineyards using Chickens
And I really loved the last line in that report. 
"Across the three cultivation practices, they found that the same yeast species dominated in all vineyards, but the least treated vineyard had more variety of fungal species than the other two."
Can you guess which one ? No kidding ? For those who have an interest in further reading of more in depth material and don't mind a lot of  "Intellect Speak" , here are the further deeper reading of the study below.
PLOS-ONE.org: "The Vineyard Yeast Microbiome, a Mixed Model Microbial Map"
ABSTRACT:
Vineyards harbour a wide variety of microorganisms that play a pivotal role in pre- and post-harvest grape quality and will contribute significantly to the final aromatic properties of wine. The aim of the current study was to investigate the spatial distribution of microbial communities within and between individual vineyard management units. For the first time in such a study, we applied the Theory of Sampling (TOS) to sample gapes from adjacent and well established commercial vineyards within the same terroir unit and from several sampling points within each individual vineyard. Cultivation-based and molecular data sets were generated to capture the spatial heterogeneity in microbial populations within and between vineyards and analysed with novel mixed-model networks, which combine sample correlations and microbial community distribution probabilities. The data demonstrate that farming systems have a significant impact on fungal diversity but more importantly that there is significant species heterogeneity between samples in the same vineyard. Cultivation-based methods confirmed that while the same oxidative yeast species dominated in all vineyards, the least treated vineyard displayed significantly higher species richness, including many yeasts with biocontrol potential. The cultivatable yeast population was not fully representative of the more complex populations seen with molecular methods, and only the molecular data allowed discrimination amongst farming practices with multivariate and network analysis methods. Importantly, yeast species distribution is subject to significant intra-vineyard spatial fluctuations and the frequently reported heterogeneity of tank samples of grapes harvested from single vineyards at the same stage of ripeness might therefore, at least in part, be due to the differing microbiota in different sections of the vineyard.
Now just some concluding comments about this phenomena of microbial species living on the skins of fruits. This is of course true of most any fruit or berry, even in the wild. No doubt fermentation processes were discovered thousands of years ago by accident. Further trail and error brought us many of the countless varieties of fermented beverages we all enjoy today. No doubt some have also been lost and buried along with their inventors. But consider how these differences in microbes species can influence differences in wines are very much like the differences in tastes of cheeses. Cheddar, Blue Cheese, etc etc etc, all get differing unique flavours from different yeast species and practices. But somewhere back in time by chance someone discovered somewhere something unique which made the difference. Take the chaparral plant community. There are countless berries from the Manzanitas, Lemonade Berry and others with a sticky tart substance on their fruit skins which can be utilized in similar ways.

Ben Larios Jr
Back when I first moved to Anza California, I befriended the Ben Larios family whose father worked for Jim Minor of Agri-Empire based in San Jacinto California. Originally Ben & Berta Larios were from a farming area of the state of Sonora Mexico and knew many traditional ways of food preparation and foraging for wild foods. In the early days, there were no grocery stores, which the exception of a Circle-K and a small old time market next to Frank Demartino Realty Office. There was no Mexican Foods to be bought, so most of the Farm Workers who worked for Agri-Empire went to the Larios family's old adobe home to purchase homemade (actually made by hand) flour and corn tortillas. They were wonderful. One day the mother, Berta Larios offered me to try her goat cheese. I never had goat cheese before and knew I didn't really like goat's milk, but I tried it. It was okay, but I wasn't crazy about it. Today however is a different story as I love both goat and sheep cheese and have it once or twice a week. She told me however that she didn't use the modern Rennet from the store to curdle the goat milk, she used instead dried Manzanita Berries which had substances on them for curdling the milk for making cheese. How cool was that ? I never knew that before. It's sad to say, but in this age of "Scientific Synthetic Artificial Biology", much of the old natural ways have been forgotten and most younger ones have been indoctrinated enough through consumerism marketing into not bothering with understanding how nature truly works, Big Corporations can provide convenience. The newer generations also have no clue as to how much better those foods also tasted way back when.


Can you imagine what a human being could learn and accomplish through a healthy type of trial and error ? I mean if they were able to live forever on this Earth there would be no end to what they could learn and do ? Think of all the perfected wine vintages, beer recipes or what ever an individual's heart desired to perfect. Of course, this devising and planning could be applied across the board for any practical worthwhile venture. The possibilities are endless!

Wednesday, December 19, 2012

An Icon of the Old West, Sagebrush (Atermisia tridentata) is Still Demonized as a Competing Invasive in it's Own Native Habitat


Photo By Michael L. Charters

http://www.calflora.net/recentfieldtrips/index.html
California State Route Hwy 74 running through Garner Valley in the San Jacinto Mountains of Southern California. Hwy 74 is to the left of the photo and heading west towards Lake Hemet, Idyllwild and beyond. Numerous Jeffrey Pine Reforestation tree planting projects have taken place on the south side of this Highway which would be on the left-hand side of this picture. In an effort to achieve plantation success, Authorities in charge have often mistakenly eradicated most all Chaparral (with the exception of a few large Scrub Oak specimens) believing the pseudo-science   view that Chaparral (which includes Big Sagebrush) is an invasive predator and competitor of forest movement, development, growth and maintenance for survival. However, modern day research and understanding of Artemisia tridentata (& other Chaparral), proves that these species of plants actually assist and promote young forest growth and development. Yet, despite all the good encouraging research papers currently available, which shed light on the truth of Chaparral benefits, old die hard ideological and economic agendas of business/political entities still pervades.

Photo by Michael L Charters

Sagebrush (Artemisia tridentata)
Garner Valley, California
Though commonly thought of as a dominant species of the Nevada Great Basin and other interior mountain states, Artemisia Tridentata is closer to home than most Southern Californian's think. Often past by on a road trip and never given a second look for no other reason than it's viewed as mundane and boring to the uninformed car passenger, this plant among other important Chaparral Plant Community species, is so foundational to it's native habitat, that it's absence can lead to other critical environmental problems because unseen to many, it actually performs an amazing service to everything else around it.  This service of course is known as Hydraulic Lift & Redistribution . This is where a particular plant has the ability with it's deeper root system to actually pump water up from within deeper moisture rich soil layers and bring them vertically to the surface and then redistribute this water through it's horizontal lateral roots to other plants by means of an interconnecting mycorrhizal fungal grid network between differing plant species. The knowledge of this Chaparral species ability facilitate water transport from deeper subsoil layers to surface topsoil and sharing it with others in the plant community has been known since the 1980s. (See footnote references)


For the moment, let me review a few points from a USDA report written about some of the misinformation on Big Sagebrush and it's management or mismanagement. The paper is authored by Bruce L Welch  and Craig Criddle who authored the book, "Countering Misinformation Concerning Big Sagebrush" (July 2003) - Rocky Mountain Research Station (Fort Collins, Colorado). It deals with 8 commonly believed Axioms, which for those unfamiliar with the term, an Axiom could simply be described as a self-evident truth that requires no proof. Frankly there are many such Axioms in other areas of science, but let's focus on this one regarding Artemisia tridentata. I loved this read. It illustrates how bad science can be at times when biased and/or prejudiced by economic, political, religious or other ideological or philosophical motivations. They clearly expose the traditional long held pseudo-scientific flaws in the view of Artemisia tridentata and it's imagined damage to Livestock performance success. Keep in mind as you read the link to the study how this flawed thinking is also what drives the demonization of other plant species around the globe.
Countering Misinformation Concerning Big Sagebrush
Abstract:
"This paper examines the scientific merits of eight axioms of range or vegetative management pertaining to big sagebrush.  These axioms are: (1) Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) does not naturally exceed 10 percent canopy cover and mountain big sagebrush (A. t. ssp. vaseyana) does not naturally exceed 20 percent canopy cover; (2) As big sagebrush canopy cover increases over 12 to15 percent, bare ground increases and perennial grass cover decreases; (3) Removing, controlling, or killing big sagebrush will results in a two or three or more fold increase in perennial grass production; (4) Nothing eats it; (5) Biodiversity increases with removing, controlling, thinning, or killing of big sagebrush; (6) Mountain big sagebrush evolved in an environment with a mean fire interval of 20 to 30 years; (7) Big sagebrush is an agent of allelopathy; and (8) Big sagebrush is a highly competitive, dominating, suppressive plant species."
I going to touch on just a few of the Axioms which are pertinent to my own experience, but they are all clearly outstanding in their assessment by the authors. I also love the sarcastic sense of humor by the Authors in questioning some of the long held stupid ideological scientific beliefs motivated by money making ventures conducted on public and private land holdings. You may even see some similarities to the much demonized Mesquite in the southwest which has spread as a result of lousy land management and overgrazing.
Axiom Number 1
"Wyoming big sagebrush (Artemisia tridentata ssp wyomingensis) does not naturally exceed 10 percent cover and mountain big sagebrush (A. t. ssp. vaseyana) does not naturally exceed 20 percent cover."
"This axiom is best verbalized by Miller and others (1994, p. 115): “In the early to mid 1800s, much of the sagebrush steppe was probably composed of open stands of shrubs with a strong component of longlived perennial grasses and forbs in the understory … Shrub canopy cover probably ranged between 5-10% in the drier Wyoming big sagebrush (Artemisia tridentata ssp. wyomingensis) communities ..., to 10-20% on the more mesic sites, occupied by mountain big sagebrush.” Speaking of the present, they noted (p. 119): “Wyoming big sagebrush cover has increased from less than 10% to 20%, and mountain big sagebrush cover from less than 20% to 30% and 40%.” All due to overgrazing."
The authors then go on to ask a series of logical question that should have been asked in the original studies and observations. The then proceed to ask three very important questions.
"First, what do the wild animals which are adapted to this type of Big Sage Brush habitat suggest to us concerning this canopy cover ?" 
This first question is important in that how does the rest of natural world like animals, interact with such Big Sagebrush habitat which has been around for thousands of years and worked perfectly well ?
Second, what are the Big Sage Brush canopy cover values found in undisturbed relics and kiputkas  (undisturbed wildlife habitat islands left untouched by urban growth) and what do we observe from these semi-pristine islands ?
This is another very important question, as even southern California in Chaparral country still has some wildlife islands, but they are dwindling fast. Still they provide a far better observational venue than modern day disturbed sites which have been thrashed and forced to heal over and over countless times in just the last 150 years of human intervention and disruption of natural processes. It is almost impossible to study how things actually work in a pristine environment anymore. Mission Valley in San Diego has north and south facing examples which may yet reveal important clues about old growth coastal chaparral plant communities, even Cowles Mountain among others.
Third, what is the quality of the science used to support this flawed Axiom ?
No kidding. No further input by me is necessary here! But the authors then proceed to offer numerous studies which indicate that large numbers of wildlife actually prefer old growth Big Sagebrush habitats. Again, no kidding. This is almost identical to Chaparral Plant Communities.
Axiom Number 3
"Removing, controlling, or killing big sagebrush will result in a two, three or more fold increase in perennial grass production. 
Miller (1957, p. 18) states the axiom in these words: “Spraying sagebrush on a Washington range results in a three-fold increase of grass forage.” On the surface this sounds great if you are interested in livestock grazing, but there are some problems with the science."
Wow, where have we heard this it becomes necessary to destroy before it can get better dogma before ? The authors point out the flaws of both studies of chemical spraying and the comparisons of treated and untreated big sagebrush plots which were on overgrazed land where a comparison of overgrazed big sagebrush plots to treated plots with treated plots showing a substantial gain in perennial grass production. The authors then cite their own personal observations of several pristine isolated pristine areas which were protected from fire because they were fortunate enough to be surrounded geographically by ancient lava flows which prevented much historical burn activity. What they found was an abundance of biodiversity and as the author noted,
"there seem to be the usual complement of birds, small mammals (including foxes, rabbits, and coyotes), reptiles, insects, spiders, lichens, shrubs, grasses, forbs, and biological crusts. On one kipuka I observed deer tracks."
Axiom Number 4
Nothing eats it, or as expressed by Tueller (1985, p. 29): “It is ironic that the dominant plant and highest producer on this area of 30,000 square miles is essentially unpalatable.” This subject reminds us of an old bumper sticker that reads: “Eat lamb! A million coyotes can’t be wrong!” Paraphrasing, we could say “Eat big sagebrush! 52 species of aphids can’t be wrong!”
Wikipedia

Pronghorn Antelope
This is absolutely funny. The Mesquite get the same exact ignorant vilification because it is believe nothing eats Mesquite. The funny thing though is that countless animals, including domestic Cattle eat Mesquite bean pods as they are very tasty and nutritious. Incredibly none of the people saying these things are embarrassed as a result of saying such stupid unscientific things. For the Artemisia tridentata, Pronghorn Antelope are a prime grazer of Big Sagebrush.  Even Bison, while no preferring the Big Sagebrush do seek it out for their rich understory treasure trove of many herbaceous plants and grasses which flourish under their canopies. Despite the lies being told that this plant toxic to others. The one thing that just keeps nagging me is, what would the health of these various vegetative plant communities still be like if many of the larger wildlife numbers still existed today ? We will never know or possibly understand this as we may never again see such numbers under the present System the entire world finds itself in.
Axiom Number 5
Biodiversity increases with the removal, controlling, thinning, or killing of big sagebrush. Olson and others (1994) reported that in their big sagebrush control plots, the number of plant species increased by three to four species over untreated big sagebrush plots, but they failed to name what species of plants and where they came from. Did the new unknown plant species seeds just float in, on the wind, like musk thistle (Carduus nutans), could or develop from long-lived dormant seeds formed from plants that have been grazed out before treatment? Are their comparisons between overgrazed big sagebrush sites versus treated sites proper, or should the comparisons be between undisturbed or never grazed by livestock big sagebrush sites versus treated sites? Should the measurement of biodiversity be determined only on number of plant species present or on total number of species of all life forms? What did the rebuttal of the last axiom number 4 tell us? That a large number of species consumes big sagebrush directly and indirectly. Is this not an expression of biodiversity?
This is another hilarious report which isn't even close to being founded in reality. Compare this to the southern California Chaparral Plant Community. This idiocy of spraying to kill Big Sagebrush would be to the present stripping the land by means of fires, bulldozing, brush grinders, crushers, chains and any irresponsible chemical treatments and then justifying it by saying plant biodiversity increased, but then not listing the plants that replaced and colonized former Chaparral Habitat, because the bogus embarrassment of a list would in reality be Mediterranean Wild Mustard, Wild Radish, Star Thistle, various species of non-native Foxtails and European Wild Oats etc etc etc would be absurd and asinine. And yet that has been the reality of So-Cal Fire mismanagement in the rural areas. 
Axiom Number 6
"Mountain big sagebrush evolved in an environment with a mean fire interval of 20 to 30 years (Winward 1984), or as expressed by Winward (1991, p.4): “These ecosystems, which have developed with an historical 10-40 year fire interval, were dependent on this periodic removal or thinning of sagebrush crowns to maintain their balanced understories.”
Once again, like the Chaparral Plant community, there is a deliberate attempt as misinformation on fire ecology and the myth and fables of prescribed or controlled burn necessity. Read the entire comments from the above link by the authors. It's unbelievable. The managers insisting on burns stated that the Big Sagebrush recovers rapidly after fire and the authors questioned: "How rapid is rapid?" This is because the Artemisia does NOT recover from it's base from fire as other chaparral plants do. It has to have seed wind blown in from outside locations.  One study of an area showed that after one burned area was observed, Big Sagebrush still hadn't returned even after 11 years. 

Axiom Number 7
"Big sagebrush is an agent of allelopathy"

Allelopathy is where a plant utilizes chemical strategies to further it's selfish gene survival as an area's dominant species and in this case it's a flat out false statement. This is so easy to understand by doing your own personal field observation on your next hike into these areas and again you should read what they author's site as examples of erroneous testing and other flawed experiments. The understory of the old growth Artemisia tridentata has some of the richest plant diversity in it's habitat. In actual fact the rich diversity is better there than out in the open. One important point I referenced at the outset of this post is the ability of Hydraulic lift and redistribution of deep underground subsoil moisture and giving it to other shallow rooted plants. One plant, Indian Paintbrush (Castilleja coccinea) is commonly seen flowering among Artemisia Sagebrush species. Why ? It is considered a partial root parasitic plant that must colonize the Artemisia in order to thrive. Many home gardeners have a tough time growing these plants on their own. Take a look at the advertisement below.

Image by Game Warden Bill Bish
What they are not telling you here is that the Indian Paintbrush actually needs the Artemisia sagebrush as a host, aside from the fact that it makes a great companion for stunning beauty. This next and final Axiom hits real close to home.
Axiom Number 8
Big sagebrush is a highly competitive, dominating, suppressive plant species. Winward (1991, p. 5) states: “Mountain and basin big sagebrush sites in best condition have cover values between 15-20 percent. Those numerous sites that support cover values in the 30 to 40 percent category have a much restricted herbaceous production and are essentially closed to recruitment of new herbaceous seedlings. Some type of shrub removal process will be needed before understory forbs and grasses can regain their natural prominence in these communities.”
"We have found in the field the seedlings of bigtooth maple-Acer grandidentatum, box elder-Acer negundo, singleleaf pinyon pine-Pinus monophylla, and Utah juniper-Juniperus osteosperma  growing under the canopy of mature big sagebrush plants. Diettert (1938, p. 5) observed: “Not only is it of direct value as a forage crop but in many places it provides shelter for tender and perhaps more useful plants.” Drivas and Everett (1987, 1988) and Callaway and others (1996) describe the use of big sagebrush as nurse plants for singleaf pinyon (Pinus monophylla) seedlings, Patten (1969) for lodgepole pine (Pinus contorta), and Schultz and others (1996) for curlleaf mountain mahogany (Cercocarpus ledifolius)."
What more can be said on this false assertion, that Sagebrush or Chaparral hinder the growth of more desirable plants and trees ? Presently the Chaparral Institute is engaged in a legal battle over the flaws in the reforestation projects which have actually destroyed Rancho Cuyamaca State Park by their mismanagement of the natural vegetation there called Ceanothus. This is another attempt to demonize a chaparral plant said to hinder growth of Pine, Oak, Fir, Incense Cedar and other more desirable eye appealing species. You may read about it here below.

Image - Chaparral Institute
Large stands of Ceanothus cut down as well as dead tress which provide valuable habitat. The area is being prepared for a prescribed burn. See fire line to the left.
Loss in Cuyamaca Rancho State Park - California State Parks Conducting Project Contrary to the Best Available Science

In the top photos of Garner Valley, it was common back in the 1980s and maybe early 1990s to promote forest growth by the old Penny Pines plantation projects. Several planting projects were mostly done on the south side of the Palms to Pines Scenic Highway 74. In fact for all those almost 24 years of my living there, I never saw a planting project on the north side. Mostly it was meadow and grasslands. I did however see one land preparation method of old small scale Farm Caterpillars being used to pull giant chains to cut off Chaparral at it's collar and burn the residue in piles. The ground was stripped bare as it was always assumed that seedling success would only be achieved by eliminating competing Chaparral species which would crowd them out. This has been proven over the past few decades to be false and continued bad land management practices with research papers justifying these flawed antiquated outdated techniques have further proved to be an ongoing lie in favour of promoting other economic agendas. One possible reasons for the methods in this area particularly may be the maintenance agenda for promoting business along the "Palms to Pines Scenic Highway". Take note below of the map and program's link which goes into depth of their Corridor Management Planning which wants the route to continually have public eye appeal. Pines, Oaks, Cedars, etc fit that agenda, chaparral doesn't.





Palms to Pines Scenic Highway Corridor Management Planning


Wikipedia

Laurel Sumac (Malosma_laurina)
When I went to school, such land clearing techniques were what i was taught as a means of the reforestation programs I personally participated in. We were always taught that if success was to be achieved in reforestation, then ALL competing Chaparral species had to be eradicated. And that's what we did. Previously I have written of my own personal experiences as a youth in experimenting on my own in establishing a Torrey Pines (Pinus torreyana) wooded area up on Rattlesnake Mountain in El Cajon California. This started in the 1970s and I cleared land to the dirt by eradicating all California Sagebrush and California Buckwheat. I grew almost 20 seedlings and nurtured and watered them for a couple of years. They did okay, but did better when I applied a heavy layer of pine mulch which shaded the ground and helped retain water which had to be painstakingly hauled straight up a mountainside by hand. To make an already told before story shorter, I later inoculated the trees with ecto-mycorrhizal inoculum and also learned at that time that in nature Nurse trees are of benefit. At first I thought this was merely a shade issue which helped establishment, but it wasn't until almost over a decade later i found out about phenomena called Hydraulic Lift and Redistribution and/or Hydraulic Descent. But luckily for what ever reason, I planted two Torrey Pines in the shelter of an old growth Laurel Sumac (Malosma_laurina). Once again out of all that time and effort, only the two Torrey Pines have succeeded where the other babied trees died. BTW, I only watered the two Laurel Sumac planted pines the first year. after the failure of the other pines (some over 6 foot tall) that same hot summer, I said forget it and later moved to Idyllwild CA in 1981. It wasn't until a little over a decade later while visiting El Cajon in early 1990s and going for a hike up there with my son that I found both trees as tall as me and without any care. The foliage was bright and healthy. Before moving over here to Sweden, I had gone to Rattlesnake  mountain again in 2004 and they were between 15 and 20 foot in height. I went back for a visit last year for a summer visit in 2011 and photographed them for the first time and below is the result.


image: Mine
Torrey Pine Tree on Rattlesnake Mountain in  El Cajon California. Last year I actually saw  the early formation of it's first pine cones. It's truly incredible how these trees which by the Scientific Native Habitat rule have no  earthly reason for succeeding here are  indeed doing so well. Update (Sept 2013): The picture of the Torrey Pine above has been cut down with a chain saw. The residents of the new housing development Sky Ranch of  Santee California were offended by it and one other tree's presence and justified cutting it down because they were said to be known to caused fire hazards, which is an idiotic uneducated comment to make. Nevertheless, the trees are now gone. But the lessons learned will last forever. Laurel Sumac makes an excellent Mother Tree or Nurse plant for the establishment of not only Torrey Pines, but also any other tree normally associated with the Coastal Sage Scrub plant community. Trees like various Oak species.

image: Mine
This second tree is lower than the upper one and nearer to the wash below the Laurel  Sumac. The foliage of the Sumac was more  vigorous down there and  it shaped and contorted the tree into more picturesque shape and form. Since then I have learned that Laurel Sumac exhibits some of those Hydraulic Lift & Redistributing abilities. No Kidding! So here is a challenge to everyone reading this post. Where ever you are on planet Earth, test out some of the amazing findings of how nature works with regards nurse trees and their incredibly sophisticated underground networks for nurturing seedlings towards mature tree establishment. Find a suitable tree known in it's native habitat in your area for qualities of exhibiting Hydraulic Lift and Redistribution and plant a tree seedling and leave it alone after inoculating with mycorrhizae. Water the first year on and off and leave well enough alone after that. For folks in Southern California's Chaparral Plant Community, prove Chaparral's worth as an important piece of the ecological puzzle.

Good Luck and success with your own Guerrilla Habitat restoration project!
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Further Reading References:
Hydraulic Lift: Substantial Nocturnal Water Transport between Soil Layers by Artemisia tridentata Roots
Hydraulic redistribution in a stand of Artemisia tridentata: evaluation of benefits to transpiration assessed with a simulation model