Thursday, June 1, 2017

Epigenetic Modification or Transhumanist Synthetic Biology: Which one Biomimics Nature ???

The key to answering the question is finding out what motivates both sides. One respects Nature and finds beauty in it's constructed complexity & sophistication, while the other worldview prosyletizes Nature is flawed, Imperfect & Badly Designed & only the collective self-promoting genius of Scientists can fix these flaws. So who's side right ?
Image - New Scientist

The emerging field of the synthetic biology (otherwise known as the GMO movement) which started with the primitive introduction of a foreign gene by means of an agrobacterium into another completely unrelated organism has now advanced. Because we now have the much touted more accurate (almost invincible if you believe some of the hype) CRISPR cas9 gene editing tool. Not surprisingly, the motives behind this movement are goals like creating life from scratch in a Lab (using intelligence of course), to improve the quality of life by correcting nature's perceived flaws and to make the job of a Biotechnician easier when it comes to re-engineering any organism. But the biggest problem with this technology is the flawed belief system behind their scientific worldview which is shackled to this idiocy of nature being flawed, imperfect & badly designed. In their worldview, nothing other than dumb luck copying errors chosen by some blind animist god-like force which appears to be omnipotent and omnipresent in all physical things like rocks, dirt, water, chemicals, electricity, weather, climate, etc, etc, etc, otherwise known by it's better known common name, "Natural Selection." (most often described as a sort of animist Tinker Bell with magic wand whom most Scientists are oblidged to do obescience to without question) is responsible for all life as we know it. But the problem with natural selection is that this blind unintelligent force (whatever that is) is incapable of  knowing anything about about scientific methods, optimization, or guidance. Yet when scientists experiment, they often claim that their intervention, manipulation and tweeking of an experiment for a purposed outcome is in mimicry of what natural selection does in Nature. In essence, when these researchers experiment using their intelligence and ascribe it to natural selection have in actuality  rigged process and proved nothing. Often times you'll hear of a scientific genetics experiment which results in speeding up a process for obtaining a finished product. In the research paper credit is often given to evolutionary forces like "natural selection." The reason is there is an unspoken rule that such credit must be referenced to be taken seriously or receive further funding. But if any researcher guides or selects for the outcome in any way, it's not “natural selection,” it's artificial selection done by the intelligence of a scientist. Especially where a technology is said to be an improvement and/or shortcut of how they assume nature would have done something, this is where that dogma of "Argument from Poor Design" is most damgerous, especially with genetic engineering where a gene is placed inside an Agrobacterium and a randomness of sorts takes place as to where exactly this specific gene from one organism is tossed into the air like dice ending up somewhere in the DNA strand of it's foreign host. Remember, whatever that gene from one organism is and does is specific only to that organism and works in context with other genes from that organism for which it recognizes. Now with Scientific assumptions about dice theory, all that respect for organization and order in the genome goes out the window. The problem is respect for the informatioanl content of DNA. Take a break here and watch this 4 minute promotional public relations plug for synthetic biology where it's describe as nothing more than simple legos.





But here's the problem, messing with DNA is not as easy as playing with Tinker Toys or Legos as promoted by those with a investment interest want you to believe. This is the same stunt pulled by Rob Fraley and Alison Van Eenennaam in that infamous "Intelligence Squared Debates"  where they gave an irresponsible simplistic description of their gmo technology saying:
"We're just talking about genes, genes are genes, you take one gene one thing and you put it with some other genes"
Or how about Canadian  geneticist, David Suzuki, whose colleague geneticists replied to his concerns: 
Listen Suzuki, we're just talking about DNA. DNA is DNA,  what difference does it make what organism it comes from?"
So in defense of the Biotechnology business model, their public relations departments have played the definition shell game card as to what exactly consitutes genetic modification. For example, how often have you heard this, "We've been genetically modifying crops since the dawn of agriculture." Usually they provide a reference like Teosinte found in the wild and cross breeding domestication of maize done by humans, much like the example in the photo on the right. In their minds this is merely a loophole explanation which is neither black nor white, wrong or right. They thrive in a definitions world with 50 legalese shades of gray which is where they like it. In their worldview Natural Selection modified everything in the wild and that's all they are doing with genetic engineering in the Lab. Everyone, including the Biotechs, knows full well that traditional conventional breeding which created all the various cultivators, breeds and/or hybrids are not the same as manipulating genetic material between two unrelated foreign organisms inside of a sterile Lab. But once again this is all about a business advertising and justification scheme. The justification is Nature is a flawed & badly designed the natural world and only their intelligence can fix these imaginary flaws. It's true, I admit it, I quite often bring up and harshly criticize this irresponsible "Argument from Poor Design" dogma as being the main problem with the way Science is conducted and practiced today. But if you think I've over blown this and exaggrated, take a look at how the World Transhumanist Association's, Humanity Plus, magazine which fiercely promotes Synthetic Biology, telling everyone that Synthetic Biology is mankind's only hope as saviour below:
"Once we recognize that the current species are flawed, we will see that only by designing and introducing new species can suffering, poverty and the depletion of natural resources be stopped. Once we look at this option, we find already a perfect and ultimately moral solution to the threats of climate change, disease, overpopulation and the terrible scarcity giving rise to endless injustice and retaliatory terrorism."   
"The perfect solution could only be brought to the world by a heroic worker in the fields of biotech and synthetic biology. Indeed, this revolution may already be possible today, but fear is sadly holding back the one who could make it happen."
(Source)
Now we have CRISPR cas9 on the GMO scene. The world has been informed that all the potential for danger and harm which the earlier GMO technology brought to the table has now been eliminated. In fact so confident that the Biotechs right about this technique, they have even gone ahead and pressured the USDA not to regulate their precious CRISPR cas9 gene editing tool technology. In a letter released to the Public back in April 2016, the US Department of Agriculture said that they wouldn't regulate the mushroom that had been gene-edited to prevent it from turning brown. What this means is that anything they wish to do from a gene editing standpoint on any organism would receive no regulation, because according to the officials who bought their story hook, line and sinker, this was NOT GMO. That would be GMO in the traditional sense of introducing new foreign gene into an unrelated subject host. Now there have been a number of other consumer crops which have gone under the CRISPR cas9 knife to eliminate that evil browning gene from things like Mushrooms, several varieties of Apples, several varieties of Potatoes, etc. Why ??? Because we have all been conditioned or brainwashed over the years into believing that white is superior to brown. That's also why we have white as opposed to brown wheat flour and white instead of brown sugar. After all, science has been telling us for 150+ years that white is superior to brown. So it's now a part of our cultural mindset. The problem though is that this particular edited gene which causes the browning also produces something very important which naturally occurs in nature called Polyphenol oxidase (PPO) which you may read about (HERE). It's loss on down the road may have unintended immune system cobsequences in both plants and mammals. 

But then low and behold, later on something else terrible was reported on about the no regulations CRISPER cas9 in the News Media. A pharmaceutical company, Alnylam Pharmaceuticals & it's RNAi drug Revusiran created through CRISPR cas9 gene editing technology for a new experimental drug which actually caused the death of many patients on the experimental drug. They really don't know what went wrong. But they discontinued the drug. Now before I leave this subject here of Alnylam Pharmaceuticals, Tranhumanists and the subject of Science vrs God, there is one more thing. I'm not the one always bringing this subject of God up. These Scientists are always brining it up. But what in the world does God have to do with Science ? Nothing! So why do they keep bringing it up ? Because their obsession is not with actual science, but rather God & Religion. Here is something the arrogant CEO of Alnylam Pharmaceuticals had to say exactly one month before they pulled the plug on their CRISPR created wonder drug, "Revusiran."
“I assure you, God didn’t create RNAi to make drugs out of it,” said John Maraganore, CEO of Alnylam Pharmaceuticals, which is working on RNAi in Cambridge, Mass. “We had to figure that out.”  (Source: Stat News)
Both their worldview & greedly impatience for profit is why we get horrible mistakes in scientific innovation as a result of pure materialist ambition. Monsanto and other Biotechs also have huge monetary plans for similar new CRISPR cas9 inspired RNAi technology pesticides in their future planning. Could there also be potential for danger if the subject here in question is not for humans ? You bet & lookie here what the news has once again brought us just a couple days ago.
CRISPR gene-editing tool causes unintended genetic mutations
(Credit: lightsource/Depositphotos)

It's not hyperbolic to say that the CRISPR-Cas9 gene-editing technique has been a revolutionary breakthrough, allowing scientists the ability to quickly, easily and precisely edit sections of DNA. But questions over how precise the CRISPR tool is have been raised in a new study from Columbia University Medical Center, which shows this gene-editing technology can introduce hundreds of unintended mutations into the genome. 
CRISPR has sparked a flurry of new avenues of research around the world, from targeting cancer to HIV, with the first human trials involving CRISPR-edited cells already underway in China and a US trial slated for 2018. But this new study urges caution moving forward, suggesting we are still yet to understand the greater genomic effects of the tool. 
The team of scientists involved in the study had previously been working with the CRISPR tool to treat a serious eye disease called retinitis pigmentosa, which leads to blindness. They decided to examine the entire genome of the CRISPR-treated mice from their previous experiments, looking for any potential mutations, even those that altered just a single nucleotide.   Generally, when scientists are trying to identify whether a CRISPR edit has resulted in an off-target mutation or deletion they use computer algorithms to identify areas most likely to be affected and focus their attention on those.   
"These predictive algorithms seem to do a good job when CRISPR is performed in cells or tissues in a dish," says co-author of the study, Professor Alexander Bassuk, "but whole genome sequencing has not been employed to look for all off-target effects in living animals."   
In examining the entire genome from the CRISPR-treated mice, they found that the tool had successfully corrected the specific gene they were targeting, but it also potentially caused a great deal of other genetic changes. In two CRISPR-treated animals, more than 100 large gene deletions or insertions and over 1,500 single-nucleotide mutations were identified. 
"Researchers who aren't using whole genome sequencing to find off-target effects may be missing potentially important mutations," says co-author Dr. Stephen Tsang. "Even a single nucleotide change can have a huge impact." 
The team is still upbeat about CRISPR technology, but they caution other scientists to more closely study the off-target effects of any gene-editing that is undertaken. They especially note that whole-genome sequencing is vital in developing more accurate ways of using the CRISPR tool. 
Now get a load of this last paragraph. Does this statement remind you of anything you might have heard before ? 😬
"We're physicians," explains co-author of the study Dr Vinit Mahajan, "and we know that every new therapy has some potential side effects but we need to be aware of what they are."  (Source)
Remember in the film Jurassic Park and that lunch room debate between John Hammond and Dr. Ian Malcolm ???  😯
John Hammond: "All major theme parks have delays. When they opened Disneyland in 1956, nothing worked!" 
Dr. Ian Malcolm: "Yeah, but, John, if The Pirates of the Caribbean breaks down, the pirates don't eat the tourists."


Illustration - Nature Methods

If you recall the original Biotech advertised hype, this CRISPR-cas9 editing system was supposed to target precise gene sequences and removes, adds to, or change them with the help of two components: an enzyme called Cas9 and guide RNA (gRNA). The Scientist could aim his/her gene editing arrows with pinpoint accuracy, much like a flying military Drone targeting a terrorst camp with deadly accuracy. But like the real life military Drone miscalculations, there apparently has been some unintended collateral damage with the CRISPR cas9 gene editing tool. These  unintended mutations will most likely bring problems later on down the road in the form of the wrong kind of epigentic gene expression. Then every so often on the horizon we get a glimmer of hope when something more biomimetic comes along.
First Step Taken Toward Epigenetically Modified Cotton
Image - Kimberly Vardeman.

While the cotton referenced here in the article, the real story is the eipgenetic modification. Really, it's epigenetic modification as opposed to a mythical unknown force of natural selection which does most of the workhorse engineering for change. Nothing random, no copying errors, no dumb luck, nothing to do with "Stuff Happens or Dice Theory", just an informational storage component interacting with nano-nmachines responding through environmental cues through a sophisticated sensory network system which guides, regulates, directs, etc with a goal oriented outcome. This new field of epigenetics takes a fascinating look at the chemical modifications that take place within DNA, known as epigenetic markers, that influence which genes are expressed where and/or when to be turned on or off. Some epigenetic markers stay switched in place throughout the life of an organism, but others may be added or removed in response to environmental factors such as diet (you are what you eat), disease, climate change, etc, etc, etc. Keep in mind that the field of genetics and epigenetics are really one in the same, with epigentics taking a closer look at what makes the genetic mechnisms tick. 


Image - TopSpeed
Simplistic view of the word/term Genetics by itself would be like havind a simplistc view of an automobile as a means of transportation for humans from point A to B. But epigentics would be like going even further than outward appearances by opening up those car doors and observing the dashboard control panel with it's various guages, steering, levers, switches, pedals for braking, shifting or regulating the cars speed. Or even going further and deeper by opening up the hood, viewing the engine and all it's various mechanical parts and how they all contribute and interconnect, what each part's contribution is to moving the vehicle, etc, etc, etc, right down to the sophisticated on built-in computer systems with it's climate and other control sensors which regulate and adjust the engine timing when various changes are detected in physical conditions which effect the engines perfomance regarding fuel economy, pollution control, etc. And that is how genetics should be viewed through a lens of epigenetic components. Fortunately, some responsible researchers are now taking a closer look at an idea called epigenetic modification with regards to breeding for better breeding the real way nature actually works. 

In recent decades, scientists have discovered that many traits in living things are controlled not just by their genetics—what’s written in the code of their DNA—but also by processes outside their DNA that determine whether, when and how much the genes are expressed, known as epigenetics. This opens up the possibility of entirely new ways to breed plants and animals. By selectively turning gene expression on and off, breeders could create new varieties without altering the genes.    
In this latest study, the researchers identified more than 500 genes that are epigenetically modified between wild cotton varieties and domesticated cotton, some of which are known to relate to agronomic and domestication traits. This information could aid selection for the kinds of traits that breeders want to alter, like fiber yield or resistance to drought, heat or pests. For example, varieties of wild cotton might harbor genes that help them respond better to drought, but have been epigenetically silenced in domesticated cotton. 
“This understanding will allow us to supplement genetic breeding with epigenetic breeding,” says Chen, the D. J. Sibley Centennial Professor of Plant Molecular Genetics in the Department of Molecular Biosciences. “Since we know now how epigenetic changes affect flowering and stress responses, you could reactivate stress-responsive genes in domesticated cotton.”    
The researchers discovered changes in DNA methylation occurred as wild varieties combined to form hybrids, the hybrids adapted to changes in their environment and finally, humans domesticated them. One key finding is that the change that allowed cotton to go from a plant adapted to grow only in the tropics to one that grows in many parts of the world was not a genetic change, but an epigenetic one.   
The researchers found that wild cotton contains a methylated gene that prevents it from flowering when daylight hours are long—as they are in the summer in many places, including the United States and China. In domesticated cotton, the same gene lost this methylation, allowing the gene to be expressed, an epigenetic change that allowed cotton to go global.  
I haven't quoted some of the paragraphs, only the relevant ones and I've also omitted paragraphs which dealt with evolutionary assumptions which added zero of understanding to the subject of epigenetic change. But one of the last paragraphs here should give us some pause as to how they should move forward with this research information. Take note of the highlighted wording here:
Chen says modern breeders can modify gene methylation with chemicals or through modified gene-editing technologies such as CRISPR/Cas9. These methods could allow breeders to make targeted changes to a plant’s epigenome and create new breeds with improved traits. Epigenetic breeding could be applied not just to cotton but to many other major crops such as wheat, canola, coffee, potatoes, bananas and corn.
(Source: University of Texas - Austin)

So why the references to both 'chemicals' and 'CRISPR' in view of the negatives We've just touched on above ??? Because Science basically is shackled and committed towards making the industrial Agricultural business model more profitable. The last thing many researchers in Academia want is to kill the very generous hand of the host that feeds them. Anyone who believes science is strictly neutral and interested only in the discovery of natural wonders is fooling themselves. In this case these authors of the Cotton breeding research are trying to tweak an existing biotech or agro-chemical model just enough to make it look a little more responsible. Take chemicals for instance being used as the choice of epigenetic trigger for switching genes. Okay I get that, but as James Kohl says, life is nutrient (chemicals) dependent. Nutrients is actually a better word than the mere use of chemicals because these are structured in a form for which biological organisms can utilize for life. In nature many many chemical elements are strucutred in such a way in which such nutrients are unavailable to plants, hence that is where the mining operation of Mycorrhizal services come in. Industrial Science on the other hand prefers to synthesize nutrient inputs & chemical pest control products for profit. That's why working towards a mycorrhizal fungal and/or bacterial approached to maintaining whole plant systems (for farming, landscaping, gardening etc) is unacceptable because eventually there is no more profit. They need to manufacture a constant supply of consumable items to be sold regularly. That also leaves out the field of biocontrols with pests. A balanced natural nature inspired pest control system kept sustainable through responsible farming practices is a dead end for them. 


So the chemicals mentioned in the article on Cotton and epigentic modification would in their view be the trigger for the right switch in a gene to be switched on or off for a specific blueprint expression. Something like drought resistence or immune system ignition, etc. But how do you identify the right switch within a gene or what gene exactly and where in the gene is the correct switch to be manipulated located ??? That was basically what this research was about, but their answer for turning on or off such a specific switch is where we differ as to how to go about doing that for better breeding. One of the things that always puzzled me is why a seed breeder practices farming the old conventional method with synthetic inputs as opposed to a mycorrhizal one. Clearly the goal here was never yields, but rather a higher quality seed. the Mycorrhizal fungi already do this switching of genes on or off depending on the specific need for their host, but it's an area of science that won't get as much funding as the industrial science sector. The beneficial soil fungi will manufacture their own specific enzymes or nutrients which can trigger various responses within a plants immune system, much like researchers have found with human gut flora and our immune system. Our's is internal, but plant's microflora is external. Differing fungi can trigger different epigenetic responses. For example if one wanted to breed drought resistence varieties into a crop like Corn/Maize, you could identify specific endomycorrhizal species that would facilitate that process best. For example all Glomus species of mycorrhizal fungi are thought to be found in nearly all terrestrial habitats around the globe, which includes arable land, deserts, grasslands, tropical forests, and tundras, etc. So perhaps a choice of Glomus deserticola would be a good selection to instill drought resistence traits in a crop plant and it's future offspring which would be farmed in a hot arid type of environment. Clearly the name 'deserticola' is a give away as to it's first discovery. So perhaps if breeding plants for an farming area some where in Canada which has a Boreal ecology, maybe 'deserticola' is not a good choice. So you look for another species for that environment. But this article never covered any of this in the research, not even honorable mention. But at least dumping money into epigenetic research in identifying the mechanisms for change will help improve our further understanding of how nature really works. This may inadvertantly prove invaluable in the future to funding and improving mycorrhizal research.

Image - Scientific American
So let's recap: The Good, the Bad, & the Ugly
First, the Good. Responsible researchers are going to follow true biomimicry when it comes to breeding for superior crops by putting more attention into understanding how epigenetics actually works. And while that is good, there is caution here if using CRISPR cas9 is still an option. The article mentioned nothing about using mycorrhizal fungi and beneficial bacteria in obtaining proper epigenetic results, but it's a start. 

Second, the Bad This continued insistence on using yet another unproven safe technology which they insist is so accurate there will be no side effects is dangerous. I kid you not, despite the negative news out now about the potential for danger, they will look the other way and place a happy face over the whole thing. Anyone who still criticizes them will be labeled anti-science. 

Third, the Ugly Every living thing is at risk now for all manner of unintended consequences. Living organisms individually, entire ecosystems collapsing, etc. Human society as a whole has degraded horribly if you've been watching the latest news reports. So it's a wait and see game. The present huge loss of bioabundance of many lifeforms around the globe may already be the result of this scientific innovation getting loose out in the wild. The misuse and abuse of intelligence most likely is the culprit. People should be  questioning who and what they have been putting their faith & trust in all these years.

So can anything be done to prevent these negative side affects from taking place ? Hardly and it's likely doubtful that any steps will be taken to regulate this industry (which historically has always resented being regulated), since it was they themselves who convinced the USDA to not regulate CRISPR cas9 gene editing tool because they were not introducing any foreign genetic information into an organism, just editing out what they considered a negative trait. And don't count on the Transhumanist Groups like the IFLscience cult to be concerned, this will be like water off a duck's back to them. When the IFLscience cult people contune to repeat the claim over and over again that people who have legitimate questions and voice concerns about GMO Techology are nothing more than Anti-Science Luddites, they demonstrate that they will never provide a mature adult response to physical evidence, thus isolating their precious theory from criticism. The real question here is “are they willing” to actually integrate the observable evidence? Thus far the answer has been “No”. In fact their response & attitude is glaringly spotlighted in an article published back in 2013 in the journal, "The Conversation," where the irresponsible attitude towards bad science was exposed.
Bankers aim to maximise profits. Scientists aim to understand reality. But Mike Peacey of the University of Bristol suggests, based on a new model he has just published in Nature, that both professionals are equally likely to conform to whatever views are prevalent, whether they are right or wrong.   
In the past decade scientists have raised serious doubts about whether science is as self-correcting as is commonly assumed. Many published findings, including those in the most prestigious journals, have been found to be wrong. One of the reasons is that, once a hypothesis becomes widely accepted, it becomes very difficult to refute it, which makes it, as Jeremy Freese of Northwestern University recently put it, “vampirical more than empirical – unable to be killed by mere evidence”.
(Source: The Conversation 2013)

Illustration by Sébastien Thibault
Perhaps there is an important lesson here to be extrapolated from the last biblical book of Revelation 22:18-19, there is a dire warning is addressed to anyone who would add or take away from the informational content of that book. The warning expressed that if someone were to add any information to the book, then the plagues mentioned within that book would be added to them. It also waned that if any information was taken away from the book, then his name would be taken away from the book of the tree of life. Could we also apply this as a warning message to all the world's White Lab Coats involved in the meddling and manipulation of the informational content of genetic material within the genomes of any and all living organisms ? Do you think this same adding or taking away of informational content from the genome of any organism for profit, especially in the light of what we now know about unintended consequences, has greatly  exposed their huge disconnect with reality and ignorant incompetence ??? So what unknown unknowns are there in the way of possible un-natural plagues that might be  awaiting to be unleased on the horizon as a consequence of adding information to the genome of something mistakenly viewed as flawed and badly designed ??? On the other hand, by taking away already proven valuable information from the genome of any living organism viewed as unnecessary junk (based on an unscientific worldview motivated by ignorance), how have scientists shortened the lifespan of many (if not all) lifeforms here on Earth as a result of not looking ahead at potential negative consequences ??? If the potential for negative side effects really do exist, then what can be done about them to reverse the negative consequences ? Off hand I'd say there is nothing humanly possible that can be done to undo the damage caused to our environment by these ideologically driven people in power, other than maybe pray - God help us! 🙏



2 comments:

  1. Thank you for trying to keep people focuses on what serious scientists know about how the epigenetic landscape must be linked to the physical landscape of supercoiled DNA via energy-dependent changes that link angstroms to ecosystems in terms that many non-academics can understand. I am reminded of what it must have been like in Biblical times for someone like Richard Feynman to link food energy to all biodiversity via the physiology of reproduction. See: Food energy https://www.youtube.com/watch?v=roX2NXDUTsM

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