Thursday, April 21, 2016

Mexican Researchers Observe Self-Governing Control of Scale Insects

Biologist Juan Manuel Vanegas-Rico
This will be a reprint of an article Entomology Today April 6 2016, which I bookmarked for later use. The fascinating subject is about that common white scale insect (Dactylopius opuntiae) which feeds on Prickly Pear Cactus. This insect turns blood red when you mess with it. I've really only ever found it on the common Cactus Plantation cultivators brought up from Mexico, (Opuntia megacantha) when I live in California, but often encountered it in the urban commercial landscapes I once maintained in and around San Diego, California. My way of control was using a high pressure washer with a water wand setting at a low volume, but high powered action. Even then those little buggers were tough to detach from the cacti pads.

Photo by J.A. Cruz-Rodríguez

 A prickly pear plantation in Axapusco,
Estado de México, México.
Entomology Today:
"Scale insects known as cochineals are major pests of prickly pear in Mexico, and pesticides are often used to control them. However, one prickly pear farmer has been controlling them without the use of insecticides since the year 2000."
"The farmer tipped off a team of scientists from the Universidad Autónoma Chapingo, and he told them that other insects were feeding on the scale insects. The researchers decided to investigate, and they found that the farmer was right. During the entirety of the research, the abundance of scale insects never reached pest status. Furthermore, when populations of scale insects increased, populations of predators increased at the same time, therefore regulating the growth of the scale insect populations. Their observations are described in an article in Environmental Entomology 
Did you take special note of a few key points in the article ? First the farmer of this plantation has been controlling the white scale insects without pesticides since the year 2000. He contacted researchers about predators doing the job for him. Now pay close attention to this single sentence from that second paragraph below here:
"During the entirety of the research, the abundance of scale insects never reached pest status."
The Scale insects never reached "pest" status ??? That would lead one to believe that the white scale is not all that evil when it is in balance. This is true of most all insects, even things we consider weeds in the plant world. Humans tend to judge things in Nature on human terms. Even Darwin did this when he wrote that letter to a minister named Asa Gray in 1860, where he referenced the example of a parasitic wasp which lays eggs on a caterpillar for the expressed purpose of it's young feeding on their host while going through a life stage development. To Darwin, this was absolute  proof that there could not be an omnipotent benevolent God. But exactly how did Darwin arrive at that conclusion ? He was a scientist right ? So what experiment or testing did he use to arrive at such a conclusion of what an intelligent entity which he said never existed, would or wouldn't do and can this experiment be repeatable for any one of us to arrive at the same conclusion ? Today Darwin's staunchest and most diehard defenders use these same fallacy arguments by using untestable metaphysical statesments for their scientific worldview. That's not to say that any of these questions are not legitimate ones, they definitely are. But they are religious questions, not scientific ones. Even the conventionally religious people cannot draw on any conclusions about why their God would do things in such and such a way through any experimentation. This doesn't mean they can't believe or have a faith in a certain way, but using science to test the whys and/or hows of creation by means of scientific research and writing a paper about it are near impossible. Take the origin of liffe experiements, both sides lose here. No one can prove by science how life emerged on Earth by experiment to create life. To be totally fair, this conclusion wasn't Darwin's fault either. Darwin like all of us was a human being on Earth who judged Nature on the basis of human concepts of good, bad, righteous, evil, etc. But still today, we all do this. Even myself at times. Hence when farming, landscaping, gardening or anything else, we all tend to judge any pests as an evil that needs to be obliterated from off the face of our own little world. Then we turn to industrial science for the poisons they manufacture to provide us relief. But it's not just the average person who reasons this was, highly education individuals with alphabet soup initials after their names on a business card follow this same flawed human reasoning as well, see the example here (Scientists Justify Mosquito Extermination from Earth)  Okay, let's continue:
"The farmer originally thought that ants were controlling the cochineals, but it turned out to be other insects. Six known predators of cochineals were found on the plantation, including different species of beetles, moths, lacewings, and flies — but no ants."
"This finding is important because the two most common ways to control scale insects in prickly pear in Mexico are 1) to use organophosphates, a class of insecticide that Mexican regulatory agencies do not recommend for this use, or 2) to knock the insects off of the plants using mechanical brooms. This study suggests there might be an alternative: natural control as a result of biodiversity, also known as autonomous self-governing control."

Photo by J.A. Cruz-Rodríguez

Colonies of scale insects (Dactylopius opuntiae)
 on fruits of a prickly pear (Opuntia megacantha)
"However, Dr. J. A. Cruz-Rodríguez, an author on the paper, warns that this method of control isn’t necessarily one that can be applied at will to other plantations or crops."
"Autonomous biological pest control cannot be considered a technology that is applied or not depending on the level of the pest,” he said. “It is a process that is established and maintained if the agroecosystem retains structural complexity and diversity of species."
"In other words, a lot of conditions must be met in order for autonomous self-governing control to be viable."
This is where people need to sit back and ponder, meditate and slow down and reason on any action to be taken with regards any possible biological controls and not automatically dismiss the idea that it cannot be done under every situation. While the researchers say the success the Mexican cacti plantation farmer had cannot be replicated for other crops, their next statement gives clues as to the error in their judgement on this:
"Autonomous control requires an ecological infrastructure that supports a network of interactions that limit the explosive growth of herbivores,” Cruz-Rodríguez said. “Intercropping, agroforestry systems, non-use of biocidal products (or its more rational application) — they all contribute to the formation of the biotic network that prevents the development of pests.This study shows that if the conditions are right, farmers can potentially use natural predators for autonomous control."
This last paragraph really says it all and actually allows for the door for biocontrol for other crops to remain open. Not only scientists, but anyone should proceed and experiment on their own as a sort of what is being called a "citizen scientist" and share successful results with others. Believe it or not, professional researchers learn very much from people considered layman who have a natural passion for a specific phenomena found in Nature. Remember, even in healthy forested environments where all vegetation looks perfectly healthy, the insects and plants otherwise considered pests or weeds are still present, but their numbers are kept in check through a complex infrastructure of biological controls. Learning what those are can be fun and rewarding. Now let's look below at some information about this white scale insect you probably never knew. Did you know that in many places around the globe like Mexico and Iran, they are farmed for their red dye ingredients potential for the fabrics industry ? Below is a photo of an Iranian Cacti  plantation which has these little baskets attached to prickly pear pads. Click on the link below the photo of an Iranian website in English which goes into great deal on how this so-called pest is an income earner for some Iranian Farmers.
Farming Cochineals scale insects (Dactylopius opuntiae), for their raw material for the manufacture of Red dye
"Cochineals are farmed in the traditional method by planting infected cactus pads or infecting existing cacti with cochineals and harvesting the insects by hand. The controlled method uses small baskets called Zapotec nests placed on host cacti. The baskets contain clean, fertile females which leave the nests and settle on the cactus to await insemination by the males. In both cases the cochineals have to be protected from predators, cold and rain. The complete cycle lasts 3 months during which the cacti are kept at a constant temperature of 27 °C. Once the cochineals have finished the cycle, the new cochineals are ready to begin the cycle again or to be dried for dye production."
"To produce dye from cochineals, the insects are collected when they are approximately ninety days old. Harvesting the insects is labor-intensive as they must be individually knocked, brushed or picked from the cacti and placed into bags. The insects are gathered by small groups of collectors who sell them to local processors or exporters."
Wasn't that a fantastic explanation on a subject most of us had no clue existed or could even imagine possible ? You'll find similar circumstances with many other plants and insects throughout the world. Believe it or not, most people in the industrial countries are often totally ignorant of the reality of the natural world around them and the potential for ecologically viable business possibilities. Finally one last look at that website and a quote about other nation economies who make a living with this, *cough-cough*,  Pest.
"As of 2005, Peru produced 200 tonnes of cochineal dye per year and the Canary Islands produced 20 tonnes per year. Chile and Mexico have also recently begun to export cochineal. France is believed to be the world's largest importer of cochineal; Japan and Italy also import the insect. Much of these imports are processed and reexported to other developed economies."

Tuesday, April 19, 2016

Random Mutations-Natural Selection & it's Copying Errors Legacy Illustrated

 "New mutations don't create new species; they create offspring that are impaired."
 National Academy of Sciences Lynn Margulis
 (Photo: T.A.Mousseau & A.P. Møller )

Fallen trees in Chernobyl's infamous Red Forest.
Previously in Smithsonian Magazine, Dr Timothy Mousseau explained highlighted the bizarre phenomena of the dead plant litter not breaking down as it normally would in most healthy forests elsewhere around the globe. Hence we see the photograph above of large trees barely touched by the useful bacteria, fungi, insects and other small organisms which are generally great recyclers. Here is that article from 2014:
Forests Around Chernobyl Aren’t Decaying Properly
The article shines a spotlight on something most everyone else was totally neglecting to see. It wasn't just people, animals and trees that were affected by radiation exposure at Chernobyl, but also the decomposers: insects, microbes, and fungi. But Mousseau and his research partner Möller have certainly had their (Critics) . Below here is the latest update mainly focusing once again on the microbiological component which is what I am interested in anyway. This will be evident with my second part below this one.

Timothy Mousseau is a professor of biological sciences at the University of South Carolina-Columbia. He has published more than 90 scientific papers about the effects of radiation on wildlife with his research partner, Anders Møller of the CNRS, the largest government science agency in France. Mousseau has visited Chernobyl dozens of times. He believes the "traditional radiation community has been slow to acknowledge the ramifications of nuclear accidents for wildlife." 
 Kim Hjelmgaard, USA TODAY
How "Dice Theory" works in the wild with irradiated DNA which provide raw material Random Mutations for the environment to work with like Potter's Clay 
Here are Dr Tomothy Mousseau's own words, edited and condensed for clarity: 
My first visit to Chernobyl was in 1999. One of the first things I noticed was that many of the trees that had been killed during the disaster 15 years prior were lying on the ground still relatively intact. Meanwhile in the forests, there were very few spider webs clinging to our faces as we cut through the brush looking for birds. Birds seemed less numerous than in nearby areas relatively unaffected by the radioactive contaminants.
Through a long series of experiments over many years, we learned that this dead organic matter — the trees and leaves — was decomposing at a much slower rate because the radiation was affecting the growth of bacteria, fungi, worms and insects that normally turn wood to sawdust.
We learned that this accumulation of radioactive litter posed a serious threat to surrounding areas in the event of forest fires, which have been increasing in frequency and severity as a result of climate change in the region.
The trees in Chernobyl were also growing more slowly, most likely because of radiation and reduced nutrient cycling. We discovered that the spiders were far less abundant, as were butterflies, dragonflies and grasshoppers. Many species of birds were all but missing.
Pausing here to interject some thoughts. Unlike the fluff and gloss picture going around the media today about the reappearance wildlife (which btw I think is great), the media has been attempting to put a happy face on Chernobyl with articles like this in Science Daily:
30 years after Chernobyl, camera study reveals wildlife abundance in Chernobyl Exclusion Zone 
Dr Timothy Mousseau has been focussing on the hidden under world of the microbiological one. The tell tale signs of the stunted Scotts Pine as seen in the photo below which shows 20 year old trees looking more like bushes, provide evidence that the symbiotic relationships present from the very beginning of life are no longer  functioning normally here in Chernobyl. This is the point made by his experiments and observations of logs, branches and leaves not decomposing, which in turn exposes that the recycling program is not fully functional. Hence we get stunted Bonsai looking trees.

 Current state of the Red Forest. Even 15-20 years after planting, these pine trees grew in height only by one and a half – two meters.
Keep in mind, the animals that were in the danger zone when the reactor mishap took place actually died or had deformed offspring, many of which were fortunately sterile. This is different than healthy populations of wildlife moving in from the outside. But to continue on.
One winter we decided to determine whether the mammals showed any effects of the radiation by tracking and counting footprints in the snow of the dozen species active this time of the year. It became clear that for the species with relatively small territories, there were significantly fewer animals in the more radioactive areas, although the top predator in the system, the gray wolf, appeared to come and go seemingly unaffected by the radiation. This was an unexpected finding and went against the prevailing wisdom at the time, which was that Chernobyl's plants and animals were thriving because of the lack of human activity, and that by implication, the radiation effects must be low to none.
We discovered that many of the organisms in the region had suffered genetic damage, and as with survivors of the atomic bombs of Hiroshima and Nagasaki, the birds and mammals had cataracts and smaller brains as a direct consequence of exposure to ionizing radiation in the air, water and food. As with some cancer patients undergoing radiation therapy, many of the birds had malformed sperm and in the most radioactive areas, up to 40% of the male birds were completely sterile. Tumors were obvious on some of the birds in areas of high radiation, as were developmental abnormalities in some plants and insects.
The traditional radiation community has been slow to acknowledge the ramifications of nuclear accidents for wildlife.  As with any science field, it was difficult to prove with 100% certainty that all of the abnormalities we had found were the result of radiation alone. In Chernobyl, there are other contaminants that could also negatively impact plants and animals.   
For this reason we repeated many of our studies in Fukushima, Japan, site of a nuclear plant accident after a tsunami in March 2011, and attempted to precisely estimate these doses. We found very similar patterns of declines in abundance and diversity in a manner that is nearly identical to Chernobyl.

Well that was an example of Random Mutations by Irradiation & Natural Selection in the wild, but what about Random Mutations caused by Irradiation and Artificial Selection in the Lab ???  
This takes me to the main issues I have with the dogma of random mutations & natural selection being the drivers of life and the failed historical experiments, especially with plants, that have not promised what was hoped for as far as a satisfactory explanation without the need of blind un-questioning faith. random mutation were said to be mistaken copying erorrs for which some mutations turned out to be rare, but lucky. The blind force called natural selection however knew just what to do with them. But today, we now have many more details available to us about the reasons for the great variety found in the Earth's plants and animal which are determined by the instructions contained within their genetic codes. Specific blueprints and schematics for differing unique organisms that are wrapped up in the nucleus of a cell. But for a long time now, scientists have been under the assumption that random mutations are what create these wonderful changes to the genetic code and have produced all the alterations we find in the descendants of plants and animals. Hence, at one time it was believed that radiation may have spit out all those copying erorrs, some of which were beneficial and kept for later innovations in the development of life. In 1946, Hermann (X-Ray Mutagenesis) Muller, who founded the study of mutation genetics, especially in the use of x-rays for creating mutations deliberately to test the prevailing "Dice Theory" concepts, said this: 
“Not only is this accumulation of many rare, mainly tiny changes the chief means of artificial animal and plant improvement, but it is, even more, the way in which natural evolution has occurred, under the guidance of natural selection.”
(Source: Herman J. Muller - Nobel Lecture)
Well there you have it. He made a bold faith affirmation and others ran with it. Scientists worldwide became so intrigued, that they launched well-funded research programs, using the irradiation methods for mutating DNA in hopes of speeding up evolution by means of artificial selection [intelligent selection by humans]. After more than 40 years of intensive research here is what biologist, Peter von Sengbusch of the University of Hamburg stated
“In spite of an enormous financial expenditure, the attempt to cultivate increasingly productive varieties by irradiation, widely proved to be a failure.” 
From the Max Planck Institute for Plant Breeding Research, Geneticist Wolf-Ekkehard Lönnig said this:
“By the 1980’s, the hopes and euphoria among scientists had ended in worldwide failure. Mutation breeding as a separate branch of research was abandoned in Western countries. Almost all the mutants exhibited ‘negative selection values,’ that is, they died or were weaker than wild varieties.”
(Source of both quotes: Mutation breeding, evolution, and the law of recurrent variation)
Wow, that agrees with what happened in Chernobyl in real time observation and sadly continues. This is where epigenetics is a far better explanation, but I'm formulating a post now for this subject. I only came here to write on this subject matter to avoid overcrowding my Epigenetics post. But something more is needed here to define. 
How exactly does one go about defining what "Natural Selection" really is ?
For me the definition on this has always been vague and depended on who your were talking with. To define the original term, you would have to go back to Charles Darwin who popularized the term "natural selection" where he described natural selection as analogous to artificial selection, a process by which animals and plants with traits considered desirable by a human breeders who systematically select organisms which have those favoured traits for reproduction of superior plant or animal. While I always found Darwin's term for the blind un-directed natural selection vague, Alfred Russel Wallace had a much deeper thought on the idea or concept of the environment's influence on change. While Darwin emphasized competition between individuals of the same species to survive and reproduce (Survival of the Fittest), Wallace emphasized environmental pressures on various species which forced them to become adapted to their local environment. But in both definitions and aside from the comparisons to artificial selection by intelligent humans in terms of breeding, "Natural Selection" has always been looked upon as some mystical force of nature, which although blind, without thought, goals, plans or ideas, nevertheless has similar qualities personal attributes like some type of animist nature god. As time goes on, Scientists and journalists have taken liberties in utilizing personification analogies, almost giving life to this mysterious force. For me watching the Scientific world attempting to make war on the idea that human beings are not exceptional and nothing more than animals equal to all other animals on Earth, has anyone noticed that the same movement is making "Natural Selection" more like a living person ??? Take a look at some of the latest philosophical views being spewed out there by some ideologues in this recent PhysOrg article at the end of last year on December 15th 2015:
"If evolution can learn from experience, and thus improve its own ability to evolve over time, this can demystify the awesomeness of the designs that evolution produces. Natural selection can accumulate knowledge that enables it to evolve smarter. That's exciting because it explains why biological design appears to be so intelligent."
PHYS¤ORG: Is evolution more intelligent than we thought ?
Retired Geneticist, Wolf-Ekkehard Lönnig, from the Max Planck Institute for Plant Breeding Research in Germany has a nice page on the history of  the term "Natural Selection", it's problems and attempts at finding a more viable alternative for the outdated terminology in view of latest modern scientific discoveries.

The problem for Science is that the usuage of such vague terms as  blind, undirected, purposeless, pointless, unguided, etc offers no satisfying understanding to the average person they are trying to convince of the complex world we all see around us. So the attempt is made to apply personal human attributes to inanimate objects or concepts. Origin of life researcher Gerald Joyce is good for this when he often describes early primitive molecules self-assembled themselves into proteins, or analogies are made about evolution which tinkers and cobbles things like some potter does with clay. I believe Native Americans also use such personification when describing the personalities of Mother Earth and Father Sky. Is there really a difference between these cultures who believe in animistic forces of nature as gods and modern science today ? Hence we get such explanations as in the above paragraph becoming more and more common in the scientific literature and especially science journals. This is something that use to be forbidden in the past by a staunch scientific orthodoxy. Still others just can't get past this warm and fuzzy Victorian Era commitment for tradition when defending their beliefs regarding this subject despite all the modern day advances in genetics and now especially with epigenetics which gives a far more satisfying  understanding of how the mechanisms for change actually work in real time observation. 

Sarah Scoles at the Smithsonian Magazine (April 19, 2016) wrote an article on the cupcake story of multiverse and the problems with  lack of hard evidence not being a problem for it's promoters. Mostly because there is no real hard evidence for the imaginary fable fabrication going around the online News feeds about this theory. In one paragraph she makes an analogy of online dating sites where gullible people are time and again taken in by bogus dating profiles which lack hard face to face evidence.

Actress Keira Knightly
"As physicists spelunk deeper into the heart of reality, their hypotheses—like the multiverse—become harder and harder, and maybe even impossible, to test. Without the ability to prove or disprove their ideas, there’s no way for scientists to know how well a theory actually represents reality. It’s like meeting a potential date on the internet: While they may look good on digital paper, you can’t know if their profile represents their actual self until you meet in person. And if you never meet in person, they could be catfishing you. And so could the multiverse."

The spooky reality with a dating site is that a guy who imagines he is head over heels for a person claiming to be actress Keira Knightly is in reality taken in by what truthfully amounts to false unproven information provided in the fake profile. If the guy who was taken in by the bogus profile were to ever actually have a face to face meeting with the person behind the profile, the reality of hard evidence would expose the would be catfisher who they really were. You could get someone like this Finnish guy, KimmoKM, whose poster child image is often depicted in countless internet troll and nerd memes. This is the same with the made up terms like, "random mutations" & "natural selection" which are nothing more than vague terms inserted where no real viable explanation based on hard evidence that can accurately account for change in question. These terms  are writing default expressions inserted here and there in the text of a scientific paper or science journal. But apparently lack of hard evidence is no problem as many researchers have come up with another solution in answering those critics who demand the hard etched in stone evidence. The article from Smithsonianmag continues:
"Other scientists say that the definitions of “evidence” and “proof” need an upgrade. Richard Dawid of the Munich Center for Mathematical Philosophy believes scientists could support their hypotheses, like the multiverse—without actually finding physical support. He laid out his ideas in a book called String Theory and the Scientific Method. Inside is a kind of rubric, called “Non-Empirical Theory Assessment,” that is like a science-fair judging sheet for professional physicists. If a theory fulfills three criteria, it is probably true."
Ah yes, if the long time historical definition of the word, "evidence," is against your pet theory, then let's just redefine the word/term "evidence" by means of definition shell games. The strategy is make the definition muddled, murky, fuzzy or gray and somehow we can smokescreen our pet theory as fact. She continues:
"First, if scientists have tried, and failed, to come up with an alternative theory that explains a phenomenon well, that counts as evidence in favor of the original theory. Second, if a theory keeps seeming like a better idea the more you study it, that’s another plus-one. And if a line of thought produced a theory that evidence later supported, chances are it will again."
"Radin Dardashti, also of the Munich Center for Mathematical Philosophy, thinks Dawid is straddling the right track. “The most basic idea undergirding all of this is that if we have a theory that seems like it works, and we have come up with nothing that works better, chances are our idea is right,” he says. But, historically, that undergirding has often collapsed, and scientists haven’t been able to see the obvious alternatives to dogmatic ideas. For example, the Sun, in its rising and setting, seems to go around Earth. People, therefore, long thought that our star orbited the Earth. More."   
Smithsonian Magazine

What's always fascinated me about people who are confronted with hard evidence to the contrary, they still cherish the imaginary worldview provided by the beloved theory. It's sort a worldview security blanket they can't let go of despite the hard evidence of fraud and they just simply want to hold onto and cuddle it forever. That paragraph above from the article in PhysOrg attempted to personify Natural Selection, but in doing so they throw confusion in anyone being able to differentiate Natural Selection from Walt Disney's "Tinker Bell" character who makes miraculous things happen with just a twinkle of her magic wand. The scientific descriptions of 'Natural Selection' remind me of when I was a kid in the early 1960s with adults around me trying to convince me there was a magical  character who knew when I was sleeping or knew when I was awake and even know if I was being bad or good. Otherwise known as Santa Claus who we all later found was not so real. Does it seem to anyone else that Natural Selection is often being described in these journals as a sort of animistic nature god who is also omnipotent, omnipresent and omniscient ? So this is where I'll leave it for now. At least I will not have to apply and explain this faith-based baggage over in my other post on Epigenetics. 

Here is a prime example today posted in Science Daily
Consider this for it's mere entertainment value
Researchers achieve a first by coaxing molecules into assembling themselves 
Concerns on Biotechnological Innovations based on the flawed concept of Random Mutations, otherwise known as "Dice Theory" 
Jose A. Bernat Bacete/Getty Images
 common white button mushroom (Agaricus bisporus)has been modified to resist browning
Well, the controversy has been all over the news across the Internet. The FDA will not regulate the genetically engineered white button mushroom which has been modified not to turn brown. This is yet another produce item which, like the apple and potato, has been messed with to prevent browning. Here is the story from Nature. 
Nature: Gene-edited CRISPR mushroom escapes US regulation
So because the fungus was engineered with the CRISPR–Cas9 technique, it can be cultivated and sold without further oversight. The argument given for this decision is that unlike other GMOs, this GMO did not have an unrelated foreign gene from another organism inserted by means of a viral vector. Instead they altered and shut down the gene which causes the browning. Paul Stamets wrote an excellent opinion on this and provided viable concerns based on his own research regarding this gene's other potential functions within the fungus. This is where epigenetics comes in and they clearly are aware of how the informational content can be expressed depending on it's influence from external sources and working together with other genes in a context. Here is what Paul Stamets wrote on his concerns.
Note: Although heralded by some scientists as a breakthrough, re: “The research community will be very happy with the news,” says Caixia Gao, a plant biologist at the Chinese Academy of Sciences’s Institute of ‪‎Genetics‬ and Developmental ‪Biology‬ in Beijing."
I am one researcher who does not agree. I strongly recommend caution. Using ‪#‎Crispr‬ gene editing, scientists interfered with polyphenol oxidase (tyrosinase) production to produce a button (Agaricus bisporus) strain that does not brown. What these researchers apparently did not know is that my research has found that this pathway is responsible for many novel antivirals. Research paper: "Antiviral Activity from Medicinal Mushrooms and their Active Constituents"
‪Mushrooms‬ have developed novel antivirals that protect them, and by extrapolation us. By interfering with this polyphenol pathway, I am concerned that they have defeated the endogenous natural antiviral defenses. What does this mean? Time will tell. I hope this does not lead to new reservoirs of hyper-viruses that can now emerge unchecked by the natural genome. In scientific terms, this could be a big "OOPS" ! The hubris of scientists playing with such powerful technology without consideration of downstream consequences is potentially dangerous. Genes code for many activities. Defeating them for one purpose may cause unforeseen consequences far more important than creating cosmetically beautiful mushrooms that will sell longer in the grocery stores.
I have questions and concerns of my own. I love to cook with fresh ingredients, but now how will I be able to determine how old these newer improved non-browning mushrooms will be when I look for them in the supermarket ? Will I need to look for them to be shriveled from age to understand how old the white button mushrooms are now ? The browning always allowed me a choice for freshness and how badly I wanted them for cooking. Given the fact Biotechs have had a hard time containing GMO seeds and pollen from escaping into the wild, how will they contain these GMO spores from escape and mixing these new traits with wild mushrooms ? Have any of these researchers even looked at the possible benefits the natural browning are in the wild ? How would this effect the ecosystem if this trait was let loose in the wild ? Will it in any way effect spore reproduction ? Does the silencing of this gene shut down any other epigenetic switches either on or offf as a result of the manipulation and is this either good or bad ? How real are Paul Stamets concerns regarding this gene's ability to stimulate an immune response in plants and antiviral activities ? Again, the Biotechs feel they are under no obligation to explain themselves. After all, they are only following the lead of what the prevailing evolutionary biologists insists. Nature is viewed as flawed, inefficient, inept and badly designed and only intelligent people in Lab Coats can correct the flaws and mistakes. And the degrading health of our natural world is a testament as to their own flaws and imperfections. So when Biotechs go OOPS, then we will all pay for their religious errors.

Concluding thoughts and Comment 

(Photo: Kim Hjelmgaard, USA TODAY)
All present Scientific Roads lead to Chernobyl

Dr Timothy Mousseau
How many Scientists were there in the past 20th century who were led down the wrong Yellow Brick Road, pinned their hopes and dreams on those lucky “beneficial random mutations” thought to generate novelty, for which natural or even artificial selection would strain out all the precious gems in its sieve, leading to the wondrous variety of adapted life around the Earth ??? And how truthful and factual is their research which was based on all this less than honest belief system ??? This hasn't exactly been seen or observed in and around Chernobyl. But one thing is clear, these so-called iconic evolutionary mechanisms [random mutation & natural selection] have failed miserably.  These so-called beneficial mutations which should have resulted after the Nuclear Power Plant's reactor irradiated everything actually created instead a stampede of a  mutational arms race at Chernobyl which undermined Natural Selection's power and authority, instead triggering a mutational meltdown, sending whole populations of living organisms over the cliff of extinction. While many environmentalists have cheered with Ecological cheerleading pom poms the surprising increase in some wildlife populations, this had nothing to do with Chernobyl's radiation. These creatures moved in from outside the zone with the absence of human presence. Many of the same troubling environmental factors still remain as Dr Timothy Mouseau has proven. It's amazing that under such negative environmental circumstance where rare lucky mutations are supposed to provide wonderful raw building materials, all we've seen in real time are more mistakes and lingering deadly ones on a grand scales. So do random mutations really happen ? Sure, but such circumstances for the newer appearances of random mutations to occur have been brought about by human ignorance and stupidity, especially with regards to their interactions with various environments in the natural world. In truth, most of these mistaken random mutations have brought about sickness, diseases, cancers, death and extinction. That is hardly something to cherish and celebrate, but the dogma still gets hallowed status in science. Insisting upon random mutations and natural selection are like saying that random acts of terrorism are the only way to bring about a civilized society. How much good clean viable science and ecological innovation has been held back from our world because of this celebrated consensus worldview ?
“Men only care for science so far as they get a living by it, and that they worship even error when it affords them a subsistence.” 
 Goethe, from "Conversations of Goethe with Eckermann and Soret"
This now really frees me up to conclude my other post
"Epigenetics: Sophisticated Complex Mechanisms for Change vrs Dumb Luck in a Pointless Universe" 
Stay Tuned! In the mean time, you may enjoy this on epigenetic mechanisms and how those amazing Environmental Cues  trigger incredible changes in gene expression which not only help organisms to survive, but provide great biodiversity for all of us to enjoy out there in Nature
 Pay close attention to this Gif illustration and link below

Epigenetic Mechanisms Defined & Illustrated

Thursday, April 14, 2016

How common everyday unexceptional human beings teach Intellectuals to more fully appreciate Nature

“When I say, ‘Trees suckle their children,’ everyone knows immediately what I mean.” Peter Wohlleben
Gordon Welters for The New York Times

This was a nice article when I first read it back in January 2016. Unfortunately, the Elites of this world's leadership throughout history have always had issues when it comes to communicating to the masses of humanity. And this is irrespective if the higher authority is a politician, clergyman or scientist. They are all on equal footing and that footing has always been on shaky ground. By nature, an intellectual talks down to people, often in condescending tones if the elite feels the audience being addressed is beneath them on an educational level. Once again, it makes absolutely no difference whatsoever if that Elistist happens to be a politician, clergyman, businessman or even scientist. I've always observed intellect-speak purposefully used to make a subject matter incomprehensible to the average person, which I would assume is to stifle any questioning of their authority. The individual above in the forest photograph is, German Forester, Peter Wohllebenwho not long ago wrote a book which was meant to help the average person  more fully appreciate the uniqueness, complexity and sophistication with which nature is put together, irrespective of how anyone believes it originally got that way. He has taken flack from several intellectual Biologists for his usage of several simple common everyday words and expressions where using them as metaphors is meant to teach common folk, otherwise viewed as non-relevant by the present "Human are Non-Exceptionalism Movement." Seriously, you think I'm kidding ? Take this one paragraph about how unexceptional the human brain is from the journal Science Daily
"People need to drop the idea that the human brain is exceptional," said Vanderbilt University neuroscientist Suzana Herculano-Houzel, who directed the study. "Our brain is basically a primate brain. Because it is the largest primate brain, it does have one distinctive feature: It has the highest number of cortical neurons of any primate. Humans have 16 billion compared with 9 billion in gorillas and orangutans and six-to-seven billion in chimpanzees. It is remarkable, but it is not exceptional."
Yes, every so often we are treating to something so exquisitely stupid which turns up in a science journal and told this something apparently worth celebrating by those within the Scientific Orthodoxy. Ever hear of these imbecilic worldview debates called, "arguments from poor design" ? We now have 100+ years of enlightenment and technologies based on this worldview of poor designs found in Nature are apparently proof of evolution. This flawed thinking has brought us climate change, oceans dead zones, ecosystem destruction etc and apparently some responsible researchers are taking notice. For example there is now a push by some of these scientific researchers that mankind needs to copy the designs found out in nature. Unfortunately they are going up against a powerful Scientific Orthodoxy which has been pimping otherwise. In otherwords the official view is still that nature is badly designed. Yet, some are waking up to the secular transhumanist religiosity which has infected science resulting in the ruination of Earth's ecosystems through badly designed technology under the influence of lousy bad design arguments. 
Biomimicry: Streamlining Innovation for Ecologically Sustainable Products
But oddly enough there are others who also understand the important need of not talking down to people, but rather using simple illustrations which try and elevate the average person's knowledge of our natural world. They do so with dumping the usual intellect-speak. And they are not always appreciate by the elites who insist this does nothing but dumbing people down. Here are a few selected paragraphs from the interesting New York Times article:
"Mr. Wohlleben, 51, is a very tall career forest ranger who, with his ramrod posture and muted green uniform, looks a little like one of the sturdy beeches in the woods he cares for. Yet he is lately something of a sensation as a writer in Germany, a place where the forest has long played an outsize role in the cultural consciousness, in places like fairy tales, 20th-century philosophy, Nazi ideology and the birth of the modern environmental movement."
Seriously ?  Nazi Ideology in Forestry ? Exactly & the consequences for questioning the prevailing Scientific Orthodoxy with regards to anything they establish as "Settled Science" or "Consensus" hasn't changed! 
Industrial Forestry in 1930s Germany
Created by Yesteryears Forestry Intellectuals

After the publication in May of Mr. Wohlleben’s book, a surprise hit titled  "The Hidden Life of Trees: What They Feel, How they Communicate - Discoveries From a Secret World," the German forest is back in the spotlight. Since it first topped best-seller lists last year, Mr. Wohlleben has been spending more time on the media trail and less on the forest variety, making the case for a popular reimagination of trees, which, he says, contemporary society tends to look at as “organic robots” designed to produce oxygen and wood.
Notice the second part of the last sentence above which reveals how most people view forests in economic terms ? " . . contemporary society tends to look at as "organic robots" designed to produce oxygen and wood." There was an article in the online journal,, titled, What’s that Forest Worth? Disaster Assistance (finally!) Takes Nature into Account , which exposes the flaw of human thinking of a forest as having no more value than it's economic short term money making potential. Often times the human choice of what is considered beautiful in nature is almost identical. Plants are selected for color and form, aside from economic value. While other plants are rejected as having little economic or eye-appeal importance from a flawed human perspective. Imperfect human beings are drawn to eye candy and like real candy, while enjoyable in moderation, isn't exactly healthy in the long run. Take the  Chaparral plant community in mediterranean climates (California). These plants for decades have been demonized for being invasive even in their own natural habitat after wildfire. Often times reforestation programs are delayed because studies need to be done first after a wildfire event. Nature doesn't do studies, it is programmed to respond almost immediately in a disturbed landscape [not years]. When Foresters finally do move in, they find chaparral has moved in and therefore label the undesirable vegetation invasive competition which needs removal prior to tree planting. In ignorance, these forestry experts ignore the fact that Chaparral actually serves not as a competitor, but as Mother or Nurse Plants to Tree Seedlings. See the example 
Adenostoma fasciculatum (chamise or greasewood): Worthless Brush or potential Nurse Plant ???
Apparently this same warped view of Forests and other woodlands is prevalent in Germany as well. 
"PRESENTING scientific research and his own observations in highly anthropomorphic terms, the matter-of-fact Mr. Wohlleben has delighted readers and talk-show audiences alike with the news — long known to biologists — that trees in the forest are social beings. They can count, learn and remember; nurse sick neighbors; warn each other of danger by sending electrical signals across a fungal network known as the “Wood Wide Web”; and, for reasons unknown, keep the ancient stumps of long-felled companions alive for centuries by feeding them a sugar solution through their roots."
“With his book, he changed the way I look at the forest forever,” Markus Lanz, a popular talk show host, said in an email. “Every time I walk through a beautiful woods, I think about it.”
"Though duly impressed with Mr. Wohlleben’s ability to capture the public’s attention, some German biologists question his use of words, like “talk” rather than the more standard “communicate,” to describe what goes on between trees in the forest."
"But this, says Mr. Wohlleben, who invites readers to imagine what a tree might feel when its bark tears (“Ouch!”), is exactly the point. “I use a very human language,” he explained. “Scientific language removes all the emotion, and people don’t understand it anymore. When I say, ‘Trees suckle their children,’ everyone knows immediately what I mean.”
"Still No. 1 on the Spiegel best-seller list for nonfiction, “Hidden Life” has sold 320,000 copies and has been optioned for translation in 19 countries (Canada’s Greystone Books will publish an English version in September). “It’s one of the biggest successes of the year,” said Denis Scheck, a German literary critic who praised the humble narrative style and the book’s ability to awaken in readers an intense, childlike curiosity about the workings of the world."

Ascension - Vibrant landscape expressive painting, looking up through
an Aspen tree forest in the mountains of New Mexico near Santa Fe
 from Johnathan Harris Fine Art 
"The popularity of “The Hidden Life of Trees,” Mr. Scheck added, says less about Germany than it does about modern life. People who spend most of their time in front of computers want to read about nature. “Germans are reputed to have a special relationship with the forest, but it’s kind of a cliché,” Mr. Scheck said. “Yes, there’s Hansel and Gretel, and, sure, if your marriage fails, you go for a long hike in the woods. But I don’t think Germans love their forest more than Swedes or Norwegians or Finns.”
 "MR. WOHLLEBEN traces his own love of the forest to his early childhood. Growing up in the 1960s and ’70s in Bonn, then the West German capital, he raised spiders and turtles, and liked playing outside more than any of his three siblings did. In high school, a generation of young, left-leaning teachers painted a dire picture of the world’s ecological future, and he decided it was his mission to help."
"He studied forestry, and began working for the state forestry administration in Rhineland-Palatinate in 1987. Later, as a young forester in charge of a 3,000-odd acre woodlot in the Eifel region, about an hour outside Cologne, he felled old trees and sprayed logs with insecticides. But he did not feel good about it: “I thought, ‘What am I doing? I’m making everything kaput.’ ”
To stop and interject a thought here, I think many people who have pursued an interest in something they loved like Forestry or even commercial landscaping like myself, have at one point questioned themselves when it came to unsustainable environmental  destroying conventional maintenance practices. I know I did when it came to synthetic insecticides, herbicides, fungicides and synthetic fertilizers. Once you discover how nature has actually operated successfully for countless 10s of 1000s of years prior to the 1950s business motivated "Green Revolution" , then you realize that something more in the way of a big change is desperately needed. 
"Reading up on the behavior of trees — a topic he learned little about in forestry school — he found that, in nature, trees operate less like individuals and more as communal beings. Working together in networks and sharing resources, they increase their resistance."
"By artificially spacing out trees, the plantation forests that make up most of Germany’s woods ensure that trees get more sunlight and grow faster. But, naturalists say, creating too much space between trees can disconnect them from their networks, stymieing some of their inborn resilience mechanisms."
Yup, sure enough. The prevailing Scientific Orthodoxy which backs Industrial Forestry and various sectors of responsible Science which discovers incredible mutualistic mechanisms are polar opposites of each other. Sadly, only one has the power and money behind them to push economic agendas and the other limps along on whatever non-commercial grant funding they can obtain from generous sources who actually care. 
"Intrigued, Mr. Wohlleben began investigating alternate approaches to forestry. Visiting a handful of private forests in Switzerland and Germany, he was impressed. “They had really thick, old trees,” he said. “They treated their forest much more lovingly, and the wood they produced was more valuable. In one forest, they said, when they wanted to buy a car, they cut two trees. For us, at the time, two trees would buy you a pizza.”
"Back in the Eifel in 2002, Mr. Wohlleben set aside a section of “burial woods,” where people could bury cremated loved ones under 200-year-old trees with a plaque bearing their names, bringing in revenue without harvesting any wood. The project was financially successful. But, Mr. Wohlleben said, his bosses were unhappy with his unorthodox activities. He wanted to go further — for example, replacing heavy logging machinery, which damages forest soil, with horses — but could not get permission."
"After a decade of struggling with his higher-ups, he decided to quit. “I consulted with my family first,” said Mr. Wohlleben, who is married and has two children. Though it meant giving up the ironclad security of employment as a German civil servant, “I just thought, ‘I cannot do this the rest of my life.’”
"The family planned to emigrate to Sweden. But it turned out that Mr. Wohlleben had won over the forest’s municipal owners." So, 10 years ago, the municipality took a chance. It ended its contract with the state forestry administration, and hired Mr. Wohlleben directly. He brought in horses, eliminated insecticides and began experimenting with letting the woods grow wilder. Within two years, the forest went from loss to profit, in part by eliminating expensive machinery and chemicals."
"Despite his successes, in 2009 Mr. Wohlleben started having panic attacks. “I kept thinking, ‘Ah! You only have 20 years, and you still have to accomplish this, and this, and that.’” He began therapy, to treat burnout and depression. It helped. “I learned to be happy about what I’ve done so far,” he said. “With a forest, you have to think in terms of 200 or 300 years. I learned to accept that I can’t do everything. Nobody can.”
Photo Image from Wikipedia
The Crooked Forest (Polish: Krzywy Las), is a grove of oddly-shaped pine trees located outside Nowe Czarnowo, West Pomerania, Poland. To an Industrial Science Forester these trees are worthless in terms of economic value. But to the average common not so exceptional human being they are brilliant works of Art.
"He wanted to write “The Hidden Life of Trees” to show laypeople how great trees are. Stopping to consider a tree that rose up straight then curved like a question mark, Mr. Wohlleben said, however, that it was the untrained perspective of visitors he took on forest tours years ago to which he owed much insight."
“For a forester, this tree is ugly, because it is crooked, which means you can’t get very much money for the wood,” he said. “It really surprised me, walking through the forest, when people called a tree like this one beautiful. They said, ‘My life hasn’t always run in a straight line, either.’ And I began to see things with new eyes.”

Back in the 20th Century there was another Forester from a similar cultural background as Peter Wohlleben, an Austrian Forester and self-taught physicist, Viktor Schauberger, often ran into brick walls with the prevailing intellectual elites of the 1930s German ideological mindset. Both men came to their conclusions based on observation of natural phenomena found in the great outdoors. As Viktor Schauberger experienced, Wohlleben experiences the same thing with biologists bent on demonizing anything outside of their worldview of things. So with Schauberger it was the conventional Physicist and Wohlleben it is the conventional Biologist. Many of today's modern scientists are committed to the business interests of the Corporate entities who employ them. When called on the carpet for fraud or other less than honest behaviour, most will cop out with  a good old Nuremburg Defense plea of, "We were just following orders." I live in Europe and have traveled through many forests here. Most are artficial industrial plantations which reveal little of the old natural old growth characterisitics Peter referenced in this article. Much of the diversity of life is sadly missing in most of these European areas.

I also sympathize with Peter Wohlleben's reasons for anxiety as a result of not having enough time to learn and accomplish all that he wishes to do in sustainable forestry. More people probably relate to this more than he may think, since especially outdoor enthusiasts feel similar identical feelings of aging frustration when there is so much more to life than this pathetic bubble of a lifespan of 70 to 80 years average. Add to the fact that the misuse and abuses of science and technology are actually responsbile for accelerating the reverse engineering of our natural world, time is quickly running out to reverse things. The dismantling is evident in the change and disruption of climate mechanisms all over the globe and even an illiterate person of limited education is capable of observing such disastrous changes because many are people who farm the land and dependent on stable seasonal phenomena. Incredibly many well educated university ideologues refuse to see this and claim to have the science on their side. Industrial celebrity darlings like Patrick Moore, Henry Miller and Mischa Popoff come to mind. Something is clearly going wrong with our planet's natural systems. 

For those interested, I've found an updated 2002 version on a PDF of Swedish Author, Olof Alexandersson's book on Schauberger's life and researchcalled "Living Water." It a fun read and does not seem to have the spelling errors in English that the original version.

There are a couple of major blunders Biologists (not all) have been promoting for decades which have held science back. One major flawed has been the dogma used in these stupid time wasting debates about life's origins and proof of no designer called,       "Argument from Poor Design."  This has done more harm in hindering scientific understandng and indoctrinated the average human being in the industrial world to disrespect Nature more than anything else. There is absolutely no scientific experiment to come to the conclusions these religiously driven secular ideologues insist. The has allowed a montrous Biotech Industry to redesign nature in the vision they perceive it should be corrected (for profit of course) and we are all now paying the price for this. Commercial Urban Landscaping, Commercial Agriculture and Home Gardening all should be replicating where Nature does in the wild for promoting product and at the same time creating balance in pest control. The other doctrine which has killed our general understanding of Nature have been a flawed outdated Victorian Era dogma called, "Survival of the Fittest." This was an Imperialistic 19th century concept of human society, inspired by the principle of natural selection, postulating that those who are eliminated in the struggle for existence are the unfit. The reality of course is that this religious dogma was used to justify white European nations occupying foreign soil and promoting their dominance over what they perceived as primitive inferior cultures. But it also backfired in that it provided a degraded worldview of Nature itself. Only now are many in the scientific community beinging to appreciate that all along, Nature has actually been developed and maintained through'
 "Survival of the Mutually Cooperative."              
Something horrendously catastrophic (ecologically speaking) is clearly headed this way like the proverbial asteroid hitting the Earth. Most people will be caught unaware as they take no note of the degrading conditions around them. However, there are some thing people can do. Get outdoors. Today there is loads of activism for every kind of cause imaginable, and none of it bringing any unity. Ever notice house organizations target the young people to get involved ? This is because youth are vulnerable, lack a record of good life experience and they are the most impressionalbe. That doesn't necessarily have to be a bad thing, only if the people pushing the cause are credible adults as well as their cause. Parents should be well aware of this and if school systems are unwilling to teach young ones appreciation for the natural world, then it's the parent's responsibility. Of course how well has that been working for us ? Once grown up and older, even former activists become burned out and apathetic. As individuals everyone has free choise to decide for themselves which direction they will take for themselves and their children. On that note I'll leave here on a bit of a humorous note below.

It's ultimately a parents job to instruct kids about morality and being good land stewards regading Nature. Not the State. 

Saturday, April 9, 2016

Synthetic Nitrogen's effects on the symbiosis between Legumes and their microbial partners

"Soil microbes known as rhizobia supply much-needed nitrogen to legumes such as clover (Trifolium species). In return, legumes shelter the rhizobia in nodules on their roots and provide them with carbon." - University of Illinois
 (Graphic by Julie McMahon)
Another excellent article by some researchers from the University of Illinois on the negative effects Synthetic [science-based] Fertilizers are actually found to hinder the epigenetic mechanisms for which instructions for signaling symbyosis are being switched off by the overwhelming concentration of synthetic nutrients. This has been going on for some time however, because there are now many cultivators of crop plants which are no longer mycorrhizal. Now you know why Monsanto blames failure of productivity for their seed if the farmer doesn't purchase the synthetics they were engineered to work with. They have either deliberately engineered this shutdown knowingly or it's happened by accident as a result of industrial practices influencing epigenetic changes within the DNA of the plant itself. So here below are the findings in the article published by the University of Illinois.

Plant biologists at the University of Illinois have pinpointed the area of genomes within nitrogen-fixing bacteria in roots, called rhizobia, that’s being altered when the plant they serve is exposed to nitrogen fertilizer.
The study, published in the Royal Society journal Proceedings of the Royal Society B, deepens the understanding of an Illinois study last year that indicated rhizobia—which are particularly beneficial to legumes such as clover, beans, peas, soybeans, lentils, and others—are less beneficial for plants when they are exposed to nitrogen fertilizer.
“This is one of the first times we’ve found at the genetic level the basis of an evolutionary change in mutualism,” said Katy Heath, professor of plant biology and one of the study’s authors, referring to the mutually beneficial relationship between rhizobia and plants that has evolved over millions of years. Rhizobia receive sugar from the plant and in turn provide the plant with nitrogen.
Again, I loved this article and the shedding of light on a subject close to my own heart, but there is a need here to clarify something stated in the above paragraph. Here it is below with one slight, but very important alteration or correction:
“This is one of the first times we’ve found at the genetic level the basis of an evolutionary change "epigenetic change" in mutualism”
Of course for some of you folks reading here, you might consider this to be an unacceptable major alteration of the text on my part. Hardly, it has more relevance than you realize. But there is a huge reason why I insist on this. Because it offers nothing in the way of value in actually trying to understand this incredible natural phenomena from an actual mechanisms viewpoint which the authors are describing to us here and I'll explain the why below in the footnote. Just follow the red single star (*) at the bottom of this page. Now back to the article's text.
Heath conducted the study with Christie Klinger, a researcher at the Beckman Institute for Advanced Science and Technology who was a graduate student in Heath’s laboratory for this work, and Jennifer Lau, a plant biologist at Michigan State University. The researchers also conducted last years’ study revealing that human-made nitrogen fertilizer altered the relationship between rhizobia and plants.

Images: Edalat Sowda Trading Company, Iran

Images: Edalat Sowda Trading Company, Iran

Whether applied using industrial technology or simply spreading it by field hand workers as traditional peasant farmers do in the world's poorer countries, both techniques and practices will kill the soil's microbiobome and shut down the symbiosis between host plants and micro-organisms. Why is this ? Epigenetic shut down of the switches for symbiosis signaling. The plant will stop signaling for cooperation and the fungi will detatch. Amazing how the natural plant world thrived long before the Green Revolution in what was nitrogen poor wild soils. This is because the micro-organisms were the work horses of acquiring nitrogen from the atmosphere and feeding it to their host plants. Back then soil was very aggregated, porus and breathing capability was at it's highest in allowing the atmosphere to infiltrate soils. But over time from the 1950s onward these epigentic switches for the instructions within crop plant DNA regarding symbiotic cooperation have been turned off. This has created a perpetual dependencey on crop plants for all Agro-Chemical company's manufactured synthetic inputs as a life-support system. So with modern GMO seeds, they fail unless otherwise fed a synthetic junk food diet.
“Humans are dumping fertilizer everywhere,” Heath said. “And so one thing we were interested in asking is whether long-term nitrogen additions would disrupt this long, many tens of millions years old symbiosis that is pretty important to the ability of legumes to compete in natural ecosystems.”
By studying legumes at the W.K. Kellogg Biological Station in Michigan, site of a long-term ecological research site created by the National Science Foundation in part to study the effects of nitrogen fertilizer on plants, the researchers determined last year that in fact fertilizer caused rhizobia to become less beneficial to the plants they served. The new study was launched to determine why that was so.
“This new study is extending that work with whole genome sequencing of the bacteria,” Heath said. “We sequenced our samples from our control group and from the nitrogen-fertilized group, and we located this key region on the genome that appears to be differentiated between those two groups.”
They found the difference in an area called the symbiosis plasmid, which is an area of extra chromosones in rhibozia that enables them to be mutually beneficial with the plants—it’s where the gene is located that actually breaks the bond between nitrogen molecules and the air to “fix” it into ammonium that the plant can use.
“We see that at that region of the genome there’s differentiation suggesting that the effects of the nitrogen fertilizer were to make these less beneficial rhizobia different than the controlled rhizobia at that location,” Heath said. “In the rest of the genome they’re interchangeable. But when you look at that one region they all start separating. That basically means that selection has changed something in that region.”
Heath said that they are continuing to study the topic. She believes that the findings have significant implications as societies deal with a changing environment. 

(Photo by L. Brian Stauffer.)

University of Illinois plant biology professor Katy Heath and her colleagues pinpointed the area of genomes within nitrogen-fixing bacteria in plant roots that’s being altered when the plant is exposed to nitrogen fertilizer. 
“Why does it matter if we can synthesize nitrogen and dump it on fields anyhow?” Heath said. “It matters because we’re looking for more sustainable solutions. I think we’re looking to not add tons of human-fixed nitrogen, which is a super energy-intensive process. Rhizobia are really special because they can do it themselves.”
Similar article from South Dakota State University on mycorrhizae's effect on plants and the potential for dumping all synthetic inputs (April 8, 2016)
South Dakota State University: "Microbiologists unravel relationship among plants, mycorrhizal fungi" 

If you've got the time, take a look at what the Food and Ariculture Organization of the United Nation (FAO) says about the need for increased synthetic inputs for feeding the world. They insist that synthetic fertilizer use will surpass 200 million tonnes in 2018. And yet this manufacture process for nitrogen is extremely energy intensive to produce. Phosphates are mined which also means intensive energy usage through strip mining which also destroys the landscape. Both of these together require major transportation for distribution points, then trucked to the farm and later heavy agricultural machiney is required for field application which requires even more fossil fuels. This all contributes to climate change, but the industry helped smoke screen all of this months before the last climate convention in Paris. (See "Get-Out-of-Jail-Free-Card")  Take note of some thought meditations that Darwin expressed to a minister named Asa Gray which I actually find to be a legitimate question by any intelligent human being, but it's just not a scientific one: 

(Darwin to Asa Gray, [a minister] May 22, 1860)
But again, such metaphysical reasonings question beg, where do these industrial scientists get their warped view of nature being flawed, inefficient and so badly designed that they feel they are in a better position to use all their collective intelligence and make shortcuts towards biological  perfection by means of biotechnology & synthetic chemicals ? This ongoing need to reference evolution in research papers and journals is key here to understanding what motivates and influences industrial scientists to push their view of the world into their less than ecologically responsible innovations. Because they are influenced by many of theory's well known proponents and ideologically driven philosophers who are constantly writing about some imagined proofs out there which reveal flaws in design everywhere in Nature and how some intelligent designer wouldn't have done it that way. Such metaphysical reasoning cannot be scientifically tested or experimented for and therefore should have nothing to do with science. But theoretical dogma are however used by profit driven industrial business models in rejecting other specific scientific findings on how nature actually works and mutualistic symbiotic functions within all ecosystems for balance and stability. Therefore these intelligent men and women reason and rationalize that they know better than Nature on how to improve upon Nature's flaws. You know the reality is, Nature has never been so flawed and out of balance since the past 100+ years of enlightenment took over running things.  

For me, it still just boggles the mind how these folks arrived at such conclusions and as I've stated previously, what science experiment did they use to conclude this ? Truthfully, None! We never hear of a single one, hence the need for promoting their own version of religious metaphysics which actually requires unquestioned blind faith. Take for example, this religiously driven ideologue below. Here is what evolutionary biologist Jerry Coyne thinks. It's illustrative of why Nature and then mankind take a hit when it comes to quality of life.

"Evolution is the greatest killer of belief that has ever happened on this planet because it showed that some of the best evidence for God, which was the design of animals and plants that so wonderfully matched their environment could be the result of this naturalistic, blind materialistic process of natural selection."
Okay, so all plants, animals, birds, fish, reptiles, amphibians, microbes etc and the ecosystems they create are basically flawed, badly designed and that is proof positive Jerry's worldview is true  ??? Problem is many agricultural researchers have either knowingly or unconsciously bought into this pathetic religious  dogma which has resulted in a globally ruined landscape all across our once beautiful planet which is now a mirror image of their degenerate worldview of things. But there is further evidence of their flawed thinking and it's effect on biotechnology today.    
" . . the universe and life are pointless....Pointless in the sense that there is no externally imposed purpose or point in the universe."
 Does anyone remember when the Biotechs came out with those stupid scientific studies about anti-gmo people being religious nutcases who took their anti-gmo stance because they believed the Earth actually had purpose ? Seriously, that's what they insisted and they told us the research was science-based. Remember the science paper that was published and reported on by Science Daily and other science journals ? Psychology of the appeal of being anti-GMO Not only did the researchers poke fun and accuse all anti-gmo people for believing in what they viewed as a stupid idea of the Earth having a purpose, but with their mocking and insults they also exposed the opposite view that pro-gmo, pro-biotech & pro-agro-chemical people mostly likely believe as Jerry Coyne does, that Earth doesn't have any purpose and that life is basically pointless. You'd think this would strike a nerve in many pro-gmo people, many of whom are heavily committed environmental activists. But guess what folks, you never hear a peep out of any them because they fear the peer-pressure from colleagues who may label them as being, *cough-cough*, " Anti-Science " and what an embarrassing shameful heretical thing that would be. Pathetic really. But wait, there is even more gems. Jerry says he and his kind are their own gods and make up their own rules on moral question of what is right and what is wrong.
"As atheists this is something that is manifestly true to us. We make our own meaning and purpose."
Jerry Coyne actually believes that his modern day enlightened worldview and philosophical takes on life are based on modern day rational free thinking, but they are in fact nothing more than an old tired recycled belief system stated way back many many centuries ago recorded in some ancient manuscripts. Genesis 3:5 - Douay-Rheims 1899 American Edition  and there is this rendition from another version Genesis 3:5 - Amplified Bible   Okay let's move along here. Take a long look below at the infamous legacy that the more enlightened version of industrial science has thus far provided for mankind and our planet's natural environment with their version of how agriculture should be practiced. Now remember folks, this is science-based stuff here and if you dare criticize what you see below, you run the risk of being labeled an anti-science Luddite. Okay, I'll admit it. If this is really "THE" Science, than yeah sure, I am a Luddite.

Lynn Betts - U.S. Department of Agriculture, Natural Resources Conservation Service
View of runoff, also called nonpoint source pollution, from a farm field in Iowa during a rain storm. Topsoil as well as farm fertilizers and other potential pollutants run off unprotected farm fields when heavy rains occur. Synthetic fertilizers close up and tighten soil pores and kill most of it's microbiology which creates an aggregated sponge which would otherwsie soak up all rains. Even many flooding downpours vertically, instead of horizontal runoff
Image: F. lamiot (own work) - Own work
Eutrophication is caused by the enrichment of an ecosystem with chemical nutrients, typically compounds containing nitrogen or phosphorus, here in a pond, with many dead leaves., under tree, in Lille (North of France). This sort of eutrophication is not abnormal if just for some days or weeks. But this also is the end result of runoff and explains the deaths in lakes, lagoons, sloughs and oceans by means of mainly agricultural pollution. You will find massive algal bloom photos everywhere in the news now all across the planet.
Now look at something Nature actually inspires some scientists and responsible companies through the practical application of biomimetics. No imaginary improvement is require, just plain ol'replication from observation of how Nature does really work. This was actually posted this morning by Mycorrhizal Application Inc's Facebook page. They are one of the companies at the forefront of valuing the Natural World and showing people how to profit off biomimicry by saving 10s of 1000s of $$$ not having to purchase Synthetic Inputs and keeping nature hygenically healthy at the same time around their farms. Apparently there are other companies and their scientists who believe the Earth does have a purpose, irrespective of what they believe about the origins debates which are mostly time wasting anyway.

Image: Mycorrhizal Applications Inc.
Mycorrhizal Applications Inc just recently completed a trial on the effects of their MycoApply Ultrafine Endo inoculant on potato yields in India. With a population of 1.2 billion to feed, this OMRI-listed bio-rational solution can feed the masses using nature's ancient programmed software of storage mechanisms of knowledge and the age-old symbiotic relationships that industrial scientists say are flawed, inept, inefficient, and badly designed. Now I have no problem or issues with companies wanting to make money. But at least when technologies based on biomimetics like that of Mycorrhizal Applications Inc make money, they don't screw up the planet for everyone else.
In a future article on Epigenetics which is really starting to explode now and revealing how change in all organisms actually takes place by means of genetic information control by sensors which trigger on and off switches in how such specific information is expressed. Understanding it is really not overly complicated and that is the beauty of this over the tired old fogma of random mutations being tinkered by natural selection, ot otherwise known as Stuff Happens. Now below here is my footnote explanation.
Footnotes Explained & My Own Conclusions

From the Footnote*, the online journal, "The - Scientist" in August 2005, Philip S. Skell (1918 – 2010), an American chemist, emeritus Evan Pugh Professor at Pennsylvania State University, and from 1977 a member of the United States National Academy of Sciences wrote an article called, "Why do we invoke Darwin." Here are three great paragraphs from Philip Skell's article which sum up micely why Darwinian evolution is not helpful in experimental biology. Professor Skell explains the deep seated reasons that the name Darwin and/or words & terms natural selection evolution, etc are used in peer-reviewed papers and journals:

"In the peer-reviewed literature, the word "evolution" often occurs as a sort of coda to academic papers in experimental biology. Is the term integral or superfluous to the substance of these papers? To find out, I substituted for "evolution" some other word – "Buddhism," "Aztec cosmology," or even "creationism." I found that the substitution never touched the paper's core. This did not surprise me. From my conversations with leading researchers it had became clear that modern experimental biology gains its strength from the availability of new instruments and methodologies, not from an immersion in historical biology."

"In reality, however, this passage illustrates my point. The efforts mentioned there are not experimental biology; they are attempts to explain already authenticated phenomena in Darwinian terms, things like human nature. Further, Darwinian explanations for such things are often too supple: Natural selection makes humans self-centered and aggressive – except when it makes them altruistic and peaceable. Or natural selection produces virile men who eagerly spread their seed – except when it prefers men who are faithful protectors and providers. When an explanation is so supple that it can explain any behavior, it is difficult to test it experimentally, much less use it as a catalyst for scientific discovery."

"Darwinian evolution – whatever its other virtues – does not provide a fruitful heuristic in experimental biology. This becomes especially clear when we compare it with a heuristic framework such as the atomic model, which opens up structural chemistry and leads to advances in the synthesis of a multitude of new molecules of practical benefit. None of this demonstrates that Darwinism is false. It does, however, mean that the claim that it is the cornerstone of modern experimental biology will be met with quiet skepticism from a growing number of scientists in fields where theories actually do serve as cornerstones for tangible breakthroughs."
This is a very logical explanation for why no value is offered in understanding what is observed in experimental biology when faith-based terminology is inserted into any science paper or journalist's article on a subject matter. In fact, Katy Heath's and her team of colleagues conclusions on effects of nitrogen fertilizer on the symbiosis between plants and micro-organisms could be summed up in Philip Skell's last paragraph he wrote to a colleague who criticized his article.

"Evolution is not an observable characteristic of living organisms. What modern experimental biologists study are the mechanisms by which living organisms maintain their stability, without evolving. Organisms oscillate about a median state; and if they deviate significantly from that state, they die. It has been research on these mechanisms of stability, not research guided by Darwin's theory, which has produced the major fruits of modern biology and medicine. And so I ask again: Why do we invoke Darwin?"
This is why I inserted in above in the paragraph the term, "Epigentic Change" which is going to be so important in the future in explaining mechanisms with which influence the natural world into adaptive change to environment, as oppose to religious speculations demanded by the Scientific Orthodoxy which run Science and determines whose career receives life or figuratively burned at the stake. And if you think this dogma doesn't harm or influence industrial science, go back up and read my observations on the industrial agro-science industry.  Oddly enough, the same Evolutionary Biologist, Jerry Coyne, I referenced above admitted this in an article published in "Nature": 

"if truth be told, evolution hasn't yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say."

You know what's really annoying for me when I read any scientific research paper or science journal article which inserts these blind faith metaphysical terminologies into their script ? Ever try and watch a Youtube video where someone has uploaded a video which contains those annoying Advertisement interruptions they try and force you to watch ? But then you get that button on the lower right side of the video with a message tells you that in 7 seconds you can click the Skip button and proceed with the viewing. So you wait through the longest 6 or 7 seconds of your life to click Skip Ad. That's what it's like when you have to skim over the gloss and fluff to get past the religiosity to appreciate the actual import of the information given on the article's subject. If there is too much insertion in the text, then like the Youtube videos, you just have to turn them off completely and move along elsewhere. So when I see science papers like the one in the recent Science Daily with the title, "The genetic evolution of Zika virus" , you find if you read the article, there was zero to do with evolution and everything to do with epigenetic change within DNA depending on which host the Zika virus was present. There was nothing that the word 'evolution' in the title that offered any value to help you understand the subject's main body of of information found in the text. It would be equally disappointing as Philip Skell explained, if other terms like God, Christ, Allah, Buddha, created, etc were inserted instead. They simply wouldn't help you to understand what was actually going on from a scientific observational mechanism standpoint. Sometimes folks, depending on who is doing the research, it's not advisable to follow the science where it leads based on the bias and motivation of the reseacher. In a worldview that claims to champion skepticism, amazing that so few actually practice skepicism. To summarize again, inoculate instead of fertilize with industrial science-based products.