Tuesday, April 26, 2016

Epigenetic Mechanisms Defined & Illustrated

Image: langology.org
This post is yet another piece of the Epigenetics puzzle for which I am separating from my main post over on "Earth's Internet" so as not to clutter that post with more material than the average modern reader can tolerate. I can start by comparing genetic information and it's communication as similar to that of intelligent human beings, but on a far higher & grander scale. As we know, all languages have rules, regulations and laws which govern them irrespective of the language spoken. And the interesting thing is, of the more than perhaps 7,000+ languages around the globe, they all have the same identical rules, irrespective of the seemingly obvious outward differences. But communicating the idea of DNA being a language  has traditionally been a challenge to most intellectuals claiming to speak for Science. Historically speaking, they've never been good communicators when it comes to informing the common man on matters of great importance. It is hoped here that I can with simplicity teach by means of illustrations taken from life's familiar situations just how epigenetic mechanisms work on the informational content of DNA. As Allan Alda once pointed out Scientists are by nature horrible communicators because of the way they've been trained  Alan Alda Center for Communicating Science 

Nath Institute of Computer SScience N.I.C.E.

There is an interesting comparison to be drawn when looking at all human languages and the genetic language content of DNA. In the early 1960s, in one of the landmark advances in 20th-century science, Noam Chomsky , often referred to as "the father of Linguistics" revealed that all human languages share a deep invariant structure. As he called it, a universal grammar. This on the surface seems odd to most of us since not only are the world's various human languages on the surface so radically different from one another depending on what parental family they come from, but also the writing symbols and characters just seem to scream out unrelated. Not even close. But never the less, what he says is essentially true. 
"Despite the obvious outward difference of "surface" grammars, they all share a deep set of syntactic rules and organizing principles. All have rules limiting sentence length, structure and all exhibit the phenomenon of recursion, which is the embedding of one sentence in another. Chomsky had postulated that this deep "universal grammar" is innate and is embedded somewhere in the neuronal circuitry of the human brain in a language organ. Children learn [human] languages so easily, despite a "poverty of stimulus,"1 because they possess innate knowledge of the deep rules and principles of human language and can select, from all the sentences that come to their minds, only those that conform to a "deep structure" encoded in the brain's circuits."
(Source: Wikipedia - Chomsky - Universal Grammar)
From almost the very beginning of the theory of evolution being created by Darwin, evolutionary biologists have tried to provide  examples of so-called primitive languages ​by asserting that the earliest human language started with simple grunts, tonal sounds, whistles, and barks which would be similar to animal sounds. One recent example I read last year listed the Bushmen language from Southern Africa as a primitive example. But nothing could be further from the truth. Personally I think it's a white intellectual thing, but whatever. Interestingly an article in Science Illustrated of July 1948 stated:
 “Older forms of the languages known today were far more difficult than their modern descendants . . . man appears not to have begun with a simple speech, and gradually made it more complex, but rather to have gotten hold of a tremendously knotty speech somewhere in the unrecorded past, and gradually simplified it to the modern forms.”
As a fun learning tool to illustrate on just how complex many of these non-white European origin early proto-languages which have been asserted to be primitive for the obvious ideological reasons which liken them to caveman holdovers, here is a funny video of five languages thought to be primitive, but in actuality are highly complex with all the universal grammatical rules that go along with all the other languages. 

My main point here is while reading all of this over the past year, it suddenly struck me that the incredible complexity and sophistication inside the vast informational storage compression mechanisms we call DNA are really similar in comparison. It has a universal language rules and regulations for which all the world's biotechnology corporations take advantage of. If the genomes of all organisms were as radically different as asserted based on the shapes, patterns of the creatures and lifeforms we all see on the outside, then it would be almost impossible for them to take one single gene of information one any single lifeform and insert it into the genome of a totally unrelated radically different lifeform. Once again however, many evolutionists have resisted and demanded that we not use such comparisons of human language and communication when referencing biological information. But there is no other way for human beings to make sense of it. 

Before I analyze how the word/term 'epigenetics' is being used by scientists in understanding however, it’s necessary to explain briefly what epigenetics is. To put it simply & succinctly (I know, a difficult and rare thing for me), epigenetics is the study of heritable traits that do not depend upon the primary sequence of DNA. So the information within any organism basically stays the same, but multiple environmental cues can effect the ways in which various parts of that DNA (individual Genes) are expressed in a context with other genes for a specific purposed outcome. Especially is this the case with single expression where certain switches are being either turned on or off. Any specific gene having a gene turned on could lead to a certain regulated specific outcome. But being turned off could have an opposite effect. I'll provide more examples of this in action in the main post over at my other blog called "Earth's Internet." I'll provide some links and videos at the bottom of the post which will further illustrate how epigenetics work. First a word of caution before going further.
“Teleological thinking has been steadfastly resisted by modern biology. And yet in nearly every area of research, biologists are hard pressed to find language that does not impute purposiveness to living forms."
 Timothy Lenoir
Okay, with this statement from Science Historian, Professor Timothy Lenoir, I shall proceed to follow the traditional example of biologists now and use massive amounts of teleology, metaphors and other words which will imply intentionality, functionality, strategy, and design in biology. So I won't apologize for something that just cannot be avoided.
Can we really compare DNA to the Language of Communication used by Humans ? If so, how is it possible for us to use illustrations from everyday familiar situations which could be understood logically speaking ? And what role do environmental cues play in the way genetic information is expressed ?

Illustrative animation from chronotext.org

Before we can understand epigenetics, we need to understand what all those genes within the DNA helical structure really are. That would be a massive library of informational content inside the tiniest known storage compression component mechanism known to mankind. And this informational content is truly composed of not only real language, but a language and communication infrastructure of the highest order. But we need to understand that this language in a sense also has rules of universal grammar, despite the fact that many of the living organisms which are also made up of DNA are run radically different from one another. Hence the extreme differences from one organism to another. But again, the genetic code is pretty much universal. Science has only barely scratched the surface of understanding the complexity of the genome and how the natural world's microbiological infrastructure actually works. To better help them to understand, they have assigned DNA code  four-letter alphabet, and structures very similar to words, sentences and paragraphs. One internet Adwords professional describes DNA by likening it to the English language in the following way,  Nucleotide = Character, Codon = Letter, Gene = Word,  Operon = Sentence, Regulon = Paragraph, etc. We should also note that environmental cues also play a major role in how the various genes within the genomes of all lifeforms have their encoded information expressed under any given change of environmental circumstances. 

Take close special note of the illustrative gif above. I love these illustrative shadowy fingers moving words & Letters around into differently expressed sentences GIF above when I first discovered it on Google+. The creator of this GIF had no intention of the meaning that I will attach to it here. But see if you can possibly see what I saw when I first laid eyes on this Gif. For me the shadowy fingers were representative of the numerous environmental cues found out there in the natural world around us which influence the triggering of either on or off of epigenetic switches. (some examples) In order to fully appreciate how the environment can influence changes, you must first remove the idea of natural selection as some sort of Tinker Bell with a magic wand forming clay like some Potter creating vessels. These environmental cues have no intelligence whatsoever. The finger merely are representative of the triggering effect upon the DNA within any organism. There is no omnipresent animistic god-like intelligence there in the environment, just physical effects which trigger the informational content within all living lifeforms which appear to have a programming sense that was designed to respond within reasonable circumstance any the organism may encounter. It's almost as if the author [who or what anyone wishes to believe] when writing life's programmed software seemed to anticipate each and every single possible future environmental scenario. Of course there this program has limits and always remains ordered.  Otherwise we'd all be living in kooky bizarre Sci-Fi world. For example, a Banana tree will never adapt to the present environmental conditions which exist above the Arctic circle with it's extreme cold. Likewise, a Bristlecone Pine will never adapt to living in the middle of  Sahara Desert under extreme heat. Epigenetic mechanisms are not a magical Genie in a bottle. 

Adaptation has Boundary Limits
This Gif above merely allows us to use our imagination of the unseen example of the written encoded language of DNA being triggered by various external components of the physical world which influence the way an unseen biological computer simulation rearranges what takes place in real time before our very eyes. But the information, letters, words, sentence meaning, paragraphs, etc are all being rearrange to fit into a new set of environmental circumstances in which the gene's present meaning is being triggered to be expressed differently for a purpose. The biological sensors of all organisms detect any external or internal change, send a message or signal to the right sector and the effect is the turning 'On' or 'Off' of various genetic switches which cause specific information to be altered for a specific purpose. Whether that purpose is to withstand drought conditions better, kick up the immune system response a few notches, etc, etc, etc, enough necessary changes to the genetic text are undertaken to accomplish a purposed goal for survival or any other purposed outcome encoded within the original programming. Interestingly, unlike the dogma of  (Random Mutations) a change which is irreversible, and typically harmful, epigenetic change can be reversed to the plant's [or any organism's] original program. So once again, files can be opened or closed, functions turned on or off. Many researchers know that in working with the subject of epigenetics in plants, they have found that they carry a back-up copy, or alternative version, of their DNA. Much the way you could restart or resubmit your backup copy of Microsoft to your computer. These alternative sequences may not have been present in the chromosomes of either parent organism, so this is not a case of recessive genes. These are essentially throwback genes present in ancestral generations, held in trust in case the parents’ genes don’t work out. 

Like the written punctuation characters we call commas, exclamation point, colons, semi-colons, question marks, etc to convey purposeful meaning of real world written  text, so these epigenetic switches act as a sort of biological rule like the punctuation in written human language which help clarify meaningful specific expression of any coded text within the double helix strands of the lifeform's genome to be expressed in a beneficial way for the good of the host. But the reverse could also be true if these switches are influenced by negative factors. But even then it would be possible for epigenetic correction by means of backup files based on the original programming. 

Now pay close attention to yet another incredible illustrative GIF as compare to the Crick/Watson science  (scientific icon)  above. This moving image below is truly  (iconoclastic)  in that it's effect will cause major rethinks of everything many thought they knew about DNA's childlike understanding of the double helix. This makes more sense. Think of this as epigenetic gene expression mechanisms all working in a complex ordered fashion. You must also need to keep in mind that this Gif, while wonderfully illustrative, is extremely slowed way down from the faster than supercomputer speeds at which epigenetics actually operate within any cell in real time. If not slowed down, it would simply be a blur and all understanding to the average human being would be lost and not understood.

Episode 5: Everything you thought you knew about the shape of DNA is wrong
Below is a wonderful video from the link above narrated by Carl Zimmer.
Can we further slow things down and illustrate epigenetics even more ? Sure!
Let's consider an even further slowed down simplified version of illustrative example where following the rules of grammar and translation can be altered radically by the placement of punctuation of any sentence. Word of caution here, I'm going to provide a glaring example of  a commonly mistranslated Greek text from the biblical Scriptures, but this is not a promotion of religion, but rather an exposure of an error which has never been corrected. An error that was the result of ignoring the rules of translation which grossly ignores the surrounding context.  Unfortunately from a translation and gramatical standpoint, most of the well known translations in English get this wrong. Again, this is only for illustrative purposes regarding grammar, punctuation & context which dictates the true meaning.   
Text Image - International Bible Society
Take the example of written Greek text above with ancient Greek writing with all it's grammatical rules. In many ancient Greek manuscripts of the biblical New Testament, all the words ran together without chapter or verse numbers, punctuation, or even spaces between words. Now if we were to translate word for word and follow the same rules as those ancient Greeks in the manuscript into English, very few English speakers would understand an article written in such a way. Below is an example of a simple single sentence of biblical text where almost every single translator has ignored the rules of translation and a speech quality known as  "proper sense stress" where a public speaker emphasizes words or phrases to effect the correct meaning by the author. This is where punctuation placed properly in written text is a wonderful guide. Now all the while, try and compare this simple single sentence of text to a single strand of DNA. Here is that verse by two different translators: (Luke 23:43)
43 And Jesus said unto him, "Verily I say unto thee, Today shalt thou be with me in paradise." (King James Version)
43 And he said to him: “Truly I tell you today, you will be with me in Paradise.” (New World Translation)
Can anyone see the difference in placement of the comma before and after the word "today" in bolded red ? Can anyone see the major difference this has in the meaning of the verses' content of either translation ? The King James Version implies that the criminal would go to heaven that very day when he died which is what the comma placement before the word 'today' is meant to do. The New World Translation provides the actual meaning of the criminal being brought back to life again on the Earth at some future date when God's Kingdom was established at some far off future time. This is also what most of the Jews back then understood anyway about the word paradise which always referred to the Earth and never Heaven.  Hence the comma placement is after the word 'today.' There are only three other English translations which render this verse correctly as the New World Translation does. The Rotherham and Lamsa in English, the version in German by Reinhardt and W. Michaelis, as well as the Curetonian Syriac of the fifth century C.E. All of the other translations [100+ Versions] render it as the King James Version. But Why ??? They ignored the context, and in this case the entire biblical context should dictate how the translators should all render that verse. 

It is helpful for any honest translator to view the context both before and after this sentence which would have provided them  with the most accurate clue as to how the information in that sentence should be expressed. Prior to his execution, Jesus made prophetic reference comparison of his being dead in the grave for 3 days comparing it to Jonah's experience of 3 days in the belly of the whale. After this verse, the context of the account actually says he was indeed dead for 3 days and raised back to life, but didn't immediately go to heaven, as even later on the Apostle Paul referred to this as does the bible book of Acts where he is shown finally going up to heaven after 40 days on Earth. Can this verse or sentence still be rendered in the way that people have long traditionally wished it to read ? Sure, but you need dismantle much of the surrounding biblical account and remove all contrary  unfriendly biblical context, then fabricate a new storyline by inserting it to support the new context to meet your cherished belief on a concept of "Last Rites". Unfortunately you'll be violating another rule found at Revelation 22:18-19 in your cherished holy book.
18 "I warn everyone who hears the words of the prophecy of this book: If anyone adds anything to these words, God will give him the troubles written about in this book. 19 And if anyone takes away from the words of this book of prophecy, God will take away his share of the tree of life and of the holy city, which are written about in this book."
Revelation 22:18-19 - International Children’s Bible (ICB)
Really, you mean even a child get's this ? Everyone should understand that the context means everything. In the natural world the environment (is the context) with it's various pressure cue cards which set off epigenetic sensors which respond with epigenetic signaling which further triggers a specific gene (in a sentence context with other genes) to be uniquely expressed within an organism for a specific purpose or intended goal. In the light of Epigenetics, the modern scientific cult term Natural Selection becomes almost worthless. The natural world can only eliminate life by means of boundaries or limits, not create monumental engineering feats. The term "Natural Selection" was invented as a euphemism to be used by those incapable of explaining an incredible creative phenomena which brings about amazing change out in nature. When the expression or term is used in scientific research papers or science journal articles, the insertion is meant to be used as a bridge over wide canyons of understanding or plugging the gaps or holes in the lack of full explanation. Ask further question for a clearer understanding and you are mocked, called names and are the target of personal insults. Despite all that, isn't epigenetics a much more realistic educational way of how nature creates change in the context of any environment ? Isn't this really something that any normal intelligent person can grasp onto, touch, feel, smell and figuratively taste which provides a more satisfying realistic answer ? To be sure however, science is only scratching the surface of this subject of epigenetics. There are still many unknowns, possibly even unknown unknowns. Questions like, how does all this complexity accomplish accurate signalling to the right target gene ? The questions are endless.

Image by Professor Jurriaan Ton, University of Sheffield
My main interest in writing this post has almost always had to do with my love and experience in working with plant ecosystems, the microbiological infrastructure which provides the foundation for their healthy continued existence and finding ways of practical application in any human endeavour regarding plant community system maintenance. So much of what I illustrate will often be associated with plants and fungi. People should be alerted to some changes coming regarding the world's corporate run Biotechs who are changing their focus on their traditional business as usual. For example, Epigenetically Modified or Engineered Organisms are going to become the new controversy very soon. Think I'm kidding ? It's already started with silencing the gene in white button mushrooms which causes browning. They are advertising it as harmless and they've convinced the FDA to view things through their lense into not regulating this type of GMO because they say they are not inserting a foreign gene from an unrelated organism into another organism by means of a viral vector. They use the mighty CRISPR which they insist is flawless.
NATURE: Gene-edited CRISPR mushroom escapes US regulation
A fungus engineered with the CRISPR–Cas9 technique can be cultivated and sold without further oversight.
They say that it's safe and there will be no problems. Mycologist Paul Stamets doesn't think so. And proves it here.
FUNGI.NET: Thoughts on the Escape of the Gene-edited Crispr Mushroom from US regulation
The majority of those people who think genetic translation is nothing more than chemistry simply have not thought about it clearly enough. The implications frighten them and I guess we all know the why. This was a side post in defining and illustrating what Epigenetics does from a human perspective. My main post possibly in a week will be on my other blog, "Earth's Internet"
"All speech, written or spoken, is a dead language, until it finds a willing and prepared hearer."
Scottish writer, Robert Louis Stevenson (think Ribosomes ?)
Incredible Videos which further illustrate the epigenetic mechanisms within DNA which guide and instruct how the information is to be used

This final video is another fun one. It takes a subject that goes over most people's head and makes it incredibly fascinating by things humans in general are familiar with. For example he provides a paragraph example with several sentences couple with punctuation. I provided up above a single sentence to make it much simpler. But you may wish to view this a few times to pick up more and more details in your understanding of how every living lifeform's genome operates at faster than supercomputer speeds.

And another very informative website which deals with the subject of  (semiotics) , which is also helping many geneticists getting a better grip on understanding the inner workings of the genetic language is an interesting website which adds the term, Bio, in front of  the other word, semiosis, which gives us. I've only found this recently. Very kool site:
 Biosemiosis.org -->>   http://biosemiosis.org 
Further Interesting reading references for those who are hungry for more Learning!
Brave new RNA world 
Tool Module: Chomsky’s Universal Grammar

Cambridge Books Online: Noam Chomsky, The Science of Language

The Gift of Language

The Strategy of Life: Teleology and Mechanics in Nineteenth Century German Biology

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