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"
(See http://appft.uspto.gov/netacgi/nph-Parser…)
‪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


  1. After weighting the evidence, Jenkins ruled that the fallout had probably caused the cancers in ten of the plaintiffs, and he dismissed the claims of fourteen.

    After hearing Bruce Jenkins' opinion, Udall urged the Reagan administration to accept the decision and pay for the negligence of the AEC employees. Instead, Reagan's attorneys appealed. In a replay of the Bulloch sheep cases, the Tenth Circuit Court became the Downwinders' graveyard of justice.
    I lived in the downwind area for 3 years and have had more than 30 surgeries for different types of skin cancers (only one malignant melanoma), which cannot be attributed to sun exposure or anything else.

    See also: Radiation Death and Deception


    Excerpt: "Overturning Judge Jenkins' opinion, the circuit court judges ruled that his methods of conducting the tests and the decision not to inform the maimed and dying Downwinders were policy judgments protected by the discretionary rule of the FTCA. In 1988, the Downwinders lost in the court of last resort as the U.S. Supreme Court refused to review the circuit court decision."

    1. Amazing how random mutations have not caused beneficial effects, just sickness, disease, cancer, death and extinction


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