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.

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