March 29, 2015 The focus of life science from ancient Greece to the early 20th is on animals and plants. The development of the microscope brought microorganisms into the picture during late 17th century. Botany Zoology and Geology ruled the study of life until the laws of Genetics were discovered by Mendel and much later Thomas Morgan. The 20th century was the age of genetics, cell biology, biochemistry and informatics. We are now entering the age of biophysics where most significant science will be explored in the realm of quantum effects. The locus of action goes further beyond the realm of molecules far into forces at the quantum level.
Ancient Greece - early 20th C……..Botany, Zoology
21st Century………………………….Quantum physics
Important explorations of the nature of life will be inside the atom and close interaction with sources at quantum level. See: Luca Turin on olfactory mechanism.
"The Central Dogma" of molecular biology, which states that biological information is transferred sequentially and only in one direction (from DNA to RNA to proteins).
The ramification of buying into the central dogma is that it leads to belief in absolute determinism, which leaves you utterly powerless to do anything about the health of your body; it's all driven by your genetic code, which you were born with.
However, scientists have completely shattered this dogma and proven it false. You actually have a tremendous amount of control over how your genetic traits are expressed—from how you think to what you eat and the environment you live in.
You may recall the Human Genome Project , which was launched in 1990 and completed in 2003. The mission was to map out all human genes and their interactions, which would then serve as the basis for curing virtually any disease. Alas, not only did they realize the human body consists of far fewer genes than previously believed, they also discovered that these genes do not operate as previously predicted.
In the featured article, Eriksen describes the experiments of John Cairns, a British molecular biologist who in 1988 produced compelling evidence that our responses to our environment determine the expression of our genes. A radical thought, for sure, but one that has been proven correct on multiple occasions since then. - Dr. Mercola
“...So, information flows in both directions, from DNA to proteins and from proteins to DNA, contradicting the "central dogma." Genes can be activated and deactivated by signals from the environment. The consciousness of the cell is inside the cell's membrane. Each and every cell in our bodies has a type of consciousness. Genes change their expression depending on what is happening outside our cells and even outside our bodies." - Konstantin Erikson
“ plants don't age in the way that animals do and similarly plants have a way of being able to produce germ cells from their stem cells throughout development and that's another key thing. So plants are much more sensitive to the environment, and the environment might even have genetic or epigenetic effects on the germ cells. This is almost heresy! This is like Lamarck …” -Robert Martienssen
Eva Jablonka (personal
communication) writes: “We have good reasons to believe
that epigenetic marks can be inherited between generations,
including marks that affect gene expression patterns
in the nervous system. Of course, we need evidence that
this actually happens in the case of human PTSD, but
we do know that the effects of psychological stress are
inherited in mice and rats. It would therefore not surprise
me if we find out that the disposition to PTSD is inherited
via an epigenetic route, and that traumatic experiences
of parents lead to extra-sensitivity to traumatic inputs in
offspring, and this may linger for some generations. If the
effects of trauma are inherited we shall have to find out
for how many generations (this may vary, depending on
genetic background, type of trauma, and the persistence
of traumatic experiences) and whether the effects make
the descendants more prone to develop PTSD. -
- Eva Jablonka via Natan Kellerman -”Israeli Journal of Psychiatry”
I just finished reading your paper "Can A Child Remember....." March 28, 2015
It is an excellent summary of current thinking on heritable emotional characteristics.
I am perplexed by two entirely ( vastly) different mechanisms at work under the rubric "epigenetics" and this confusion appears to saturate the field, leading to confusion. Without proper language there can be no understanding for hardcore scientists or any enthusiasts. At present the language of epigenetics is clouded, clotted, inky, obscured, confusing - perhaps it's just me.
In one sense (appearing to be the most broadly established in the traditional scientific community detailed in countless papers published in respected scientific journals in a dozen fields of bio-science during 15 years of hardcore research ) -To this community of scientists, the word epigenetic refers to a vast realm genetic modifications during the single life of a single, specific individual organism plant or animal, bacterium, virus, fungus that cause a particular gene to become expressed one of many possible chemical responses as a result of life encounters with specific phenomena Allow me to call this LIF( for lifetime)-Epigenetics -LIF Epigenetics
The second realm of epigenetics involves Lamarck and the inheritance of acquired characters between two adjacent generations - parent-offspring and second, third, fourth generation expression of that acquired characteristic.
LIF-Epigenetics is a Big F-ing Deal !! It contradicts the heart of Darwinism, it contradicts the guts of Neo-Darwinian Dogma that reigned throughout the mid to late 20th Century. It contradicts Natural Selection, it contradicts Random Mutation, it contradicts Darwin's key External / Environmental causality. As you may recall, Lamarck was subject to derision throughout the 20th century for his "foolish" idea that giraffes had long necks because of his "cornball" assertion that the stretching of giraffe necks to reach high foliage was passed to offspring. Lamarck was derided in my biology textbooks as Darwin was deified.
As we know, there is now a great deal of hard science published in respected journals that supports the notion of heritable traits. Allow me to call this realm of epigenetics INH( for inherited)-Epigenetics - INH Epigenetics.
LIF epigenetic gene expression-specialization is common in all tissues -ovary, testes, retina, brain, heart, liver, kidney, pancreas, adrenal gland, epithelium and LIF-Epigenetics has its own TWO LEVELS hierarchical levels of causation (LIF- ONE: embryonic stem cell differentiation-expression) and (LIF- TWO): specific gene regulatory events during organism lifetime stimulated by specific environment) Organism genes have the potential for a wide vocabulary of potential expression-regulation. Environmental conditions, psycho-social events initiate and lock a certain switching pattern ( methylation, phosphorylation, etc.) i.e. differential expression not only at level of organ system during embryonic development but within a specific organ system say Hearing - cochlea-auditory neurons types I and II and the audio cortex are subject to culture-specific epigenetic modification.
Example One Lif-Epigenetics: The auditory cortex of a Chinese person is patterned to enjoy 5 tone music, the Persian ear-24 tones, the Western ear - 7 tones from early lullabies to pop music in each region, these musical patterns are epigenetically developed in the types I and II auditory neuronal pathways at the auditory cortex i.e. a Chinese baby if it heard western music from birth would have the 7 tone system epigenetically imprinted.
Your papers cite many examples of INH-Epigenetics.
I find the two papers you have written fascinating. The entire realm of epigenetics, either LIF or INH variety, is intensely interesting and INH epigenetics is a paradigm shifter that may replace Darwin on his pedestal with Lamarck. Epigenetics frightens people. It frightens scientists. Any scientist who develops a case that calls Darwinism into question scares themselves and colleagues. It took Stephen Jay Gould 1,300 pages of hemming and hawing and pussyfooting to suggest that Darwin's favored level of continuous, gradual causation for natural selection- the individual organism, might be replaced by Gould ( and Niles Eldredge) idea of punctuated equilibrium at the species or clade level, not the individual level. Dissing Darwin is dangerous - it can derail serious careers - put a person in the realm of nutcases.
This fear of contradicting Neo-Darwinism infects epigenetic science and the reason my two distinct realms are now always piggybacked - one ( INH) is wild-ass career wrecker and one(LIF) makes perfect sense and has been experimentally proven for decades. To separate epigenetics into my two distinct realms LIF ( OK ) and INH (hmmm-this guy/gal's eccentric).
It boggles me that we still have only one word for these two realms of genetic modification. Each with vast implications - as vast as Darwinism itself in the Mid-Late Victorian era and to this day. There is a lot at stake here.
Your papers mix and match the LIF and INH very freely thus, though deeply compelling, still carry the common confusion. This confusion saves careers in science and the professions so it is understandable though lamentable in the spirit of truth and clear thinking.
At this point, there is too much hard science to support your strong thesis for heritable nightmares and you use a towering, indisputable example in the Jewish holocaust. To support your assertions you could very easily include 2,000 years of Jewish persecution - a long trail of heritable genetic modification.
If you have not read "The Structure of Evolutionary Theory" by Stephen Jay Gould I strongly suggest it. You are on the verge of your own Evolutionary Revolution and a bit of background on others in your position during the past 150 years will be helpful. Hang on - it's going to be a bumpy ride.
A few editorial items:
- " past ( passed) their 60s..."
2."seeing a tattoo remind(S) them..."
- No "ed" at manifest - the "ed" is implied in my experience here in U.S.A.
- You use the word "coating" in both papers as in "Chromosome coating" to describe causality for inherited emotional trait - the word coating implies that the entire gene ( 35 cm long DNA molecule) or the entire chromosome has been covered in some sort of chemical syrup thus modifying it. I suggest a different word that might more easily convey that just a single gene or small group of genes are participating in this epigenetic trait i.e. a few hundred thousand base pairs not 171,115,000 base pairs as are present on say chromosome #6. Perhaps " tag" or "mark". There may be a specific term from genetics for this.
- "allusive" i.e. alluding to - perhaps "illusive" ( involved in illusion - misreading)?
- Might re-think the "DNA genotype as hardware and RNA phenotype as software"-Maybe OK for high school analogy. there are so many organelles and molecules involved in phenotypic expression that to single out RNA appears dicey - not up to standard of thought-knowledge in rest of paper. i.e. If an amateur like myself can see that it's shaky then your scientist audience may have issues. Sometimes a small detail like this would cause a realm of influencers to shake their heads. Histones, ribosome and RER chemical composition and timing may have more to do with phenotypic expression than RNA.
- The last few sentences beginning with "clearly however..." then advising skepticism about power of thought muddies your fascinating paper - no need for warnings or scolding - hey ! if a wild Darwin knee-capping idea like INH epigenetics holds water why couldn't the power of thought modify one's genome?
As for dismantling Darwin don't miss "Microcosmos" by Lynn Margulis and Dorion Sagan
Warm Regards, Jim
March 29, 2015
Thank you for your careful and very thoughtful reading of my paper "The Ugly Gene" It was refreshing to get a second opinion. Your points are excellent. I'm throwing a lot of spaghetti against a wall that may or may not be present.
Intensely interesting to think about your essay and to try to help develop a clear language so that you can keep these revolutionary thoughts in order. As for your omitting the paragraph re: TTT - only a good idea to omit because the language is still fuzzy. When you get the terms organized and ordered then certainly revisit this idea as it is at the core of your thesis
I have a suggestion that will help me to think and discuss your idea. Let us each provide a few term to this discussion of these two key pathways at the core of the matter.
TTT - Transgenerational Transmission of Trauma: DNA mutation that is heritable ( example: a germ cell chromosome in a female Buchenwald prisoner's ovum had one of 1,200 genes ( the gene that directs anxiety thresholds in the amygdala ( limbic system) undergo a post translational modification via phosphorylation while standing in line at a gas chamber. This woman's anxiety was so intense, her fear was so deep that a torrent of adrenalin flowed into every cell in her body including her gametes-ova-sex cells. This overload of adrenalin caused this woman's Amygdala Fear Response Threshold Gene ( AFRTG) to violate its rules of evolutionary conservation and three base pairs were modified when a phosphorus atom bonded with a hydrogen atom- at a base pair-at a codon on a DNA molecule ( a gene) - at a chromosome - in the DNA -in the chromatin - in the nucleus of her germ cell - Her ovum DNA has now been LIF-EPIM. ( LIFetime only-EPIMgenetic mutation/modification.) along with 37 trillion of her cells - i.e. every cell in her body was subject to adrenalin overload.
BECAUSE THIS WOMAN'S OVUM WAS SUBJECT TO MUTATION AS WELL AS COUNTLESS OTHER CELLS SHE IS NOW CARRYING A TTT-EPIM in her eggs as well as LIF-EPIMs in billions of other cell nuclei - DNA throughout her body has mutated but only the DNA in her eggs will be inherited by her children and only through the typical roulette of genetic inheritance. One of her children might inherit the gene for amygdala fear threshold regulation from a very happy father while another of her children inherits her gene carrying the trauma effects. This second child will have a mutated AFRTG and be more susceptible to anxiety throughout his life.
The Holocaust survivor is now living in Tel Aviv. It is 1950. Her ova are all carrying the TTT-EPI mutation AND all of her cortical neurons and all of her Limbic neurons and all of her 200 million gut neurons and every cell in her body is experiencing some effect from her holocaust trauma. It is only her AFRTG that is heritable. Her limbic and cortical neural pathways are hardwired with nightmare memories of Buchenwald, her reflex response to authority figures is not normal, standing in lines causes anxiety, etc. Her hormonal balance is permanently changed by her camp experience - these are her own LIF-EPI effects that will not be passed GENETICALLY to her children but may be passed on to them during their lives via LIF-EPI processes as the child senses his mother's relentless anxiety about a wide array of life experience.
To do: Follow the germ cell ( 10,000 careers in research) for "Nature" - TTT-EPIM
To do: Follow the effects of parental behavior on children ( 1,000,000 careers in research) for "Nurture" - LIF-EPIM
It appears that research the realm of LIF-EPIM is now well represented in several branches of biology -embryology, biophysics, biochemistry, cell biology, neuroscience etc.
The entire realm of Post Translational Modification is LIF-EPIM process. The word epigenetics is used freely among these scientists.
The realm of heritable traits i.e. TTT-EPIM is still a minefield.
The 800 pound gorilla in the living room here is that if any one of a person's 37 trillion cells can be affected during the individual's lifetime by the behavior of a parent by any number of post translational modifications then that person's germ cells are among those 37 trillion..... so....any LIF-EPIM via post translational modification can theoretically be passed on to one's offspring through the affected germ cells.
Our body tends to clear itself of the great majority of LIF-EPIM as cells divide. Because most neurons do not replicate and because a woman's eggs are all present at birth - these cells are different than the vast majority.
The neuron LIF-EPIM remain throughout one's life and must be addressed.
The egg LIF-EPIM are TTT-EPI heritable genetic mutations. Women are far more likely to carry LIF-EPIM due to longevity of eggs thus to pass on a wider array of trauma by Mendelian laws of inheritance without resorting to the many ways a mother can influence a child through her behavior palette. An ovum records the blows of life for many years and may pass these effects on to children - a sperm stores experience for only 48 hours then new recruits arrive.
Have faith that NOTHING is beyond your understanding and certainly no aspect of your topic until perhaps it arrives at quantum mechanics or string theory causality. It is a complex but penetrable idea and you have expressed it more clearly than any I have read to date with your powerful and revealing subject matter - the Holocaust.
TTT turns Darwinism on its head which is VERY big deal for trained scientists and the entire educated population of the Western world. One could easily lose standing in the intensely competitive and ferociously rigorous ( to a fault) realm of traditional science by getting on board with TTT-EPI too soon. You are a brave explorer here. Feel free to invent terms that help your case - after all - throughout history that's what every pioneer has done. Stephen Jay Gould pulled "Punctuated Equilibrium" out of his *** and now it's in all the textbooks and papers on evolution.
A problem with de-throning Darwin in the U.S.A. is that it immediately opens one up to charges of being a religious fundamentalist who does not believe in evolution at all and thinks God created the world in six days 5,000 years ago - ugh. Contradicting Darwin can be a third-rail here.
I was thinking you might apply for a grant to study your thesis of TTT-EPI. Perhaps a drosophila or mouse " holocaust" with ( excuse me for making somewhat light of a subject that doesn't work too well with light) thousands of flies or mice subject to traumatic conditions then breeding and examining for inherited effects on their amygdalian / primitive fight-flight response. It seems like all lab primates experience an ongoing holocaust of sorts - perhaps compare and contrast primates from the wild with lab monkeys for AFRTG effects.
- Does all LIF-EPI end up in a woman's eggs thus become heritable?
- How does the body sort out the LIF-EPIM that will be stored in germ cells from that which is discarded.
Your idea gives rise to 1,000 avenues of experiment. Your two papers that I have read could be foundational documents for the work of a generation of bio-scientists. Your big challenge at this point is to go into this herd of ideas like a cowboy rides into a big herd of cattle and select a few cows at a time and explore, clarify for yourself to the best of your ability ( and Google). At present it is a revolutionary herd of ides that will excite a generation. You are the Darwin for a new paradigm - be fearless - in the words of American Founding Father Aaron Burr.
"The Law is whatever is boldly asserted and plausibly maintained."
All Best, Jim
Questions from notes March 23 thru March 28, 2015
- Perhaps non-coding DNA, let’s call it TUN DNA not “junk” DNA is a warehouse where 1,000,000 species of bacteria and viruses have stored their own DNA for future use in humans or elsewhere. Some of it is going to make us sick or kill us. One day, when the owner comes to collect his “stuff” from his evolutionary storage shed. In humans 98% of the DNA in our genome is non-coding. In bacteria only 2% is non-coding.
- JB neologism - HMP for Histone Modification Pathways: methylation, phosphorylation, acetylation, ribosylation, ubiquitination,citrullination etc.
- Are cilia at the tips of olfactory receptor cells dendrites?
- The neocortex evolved, increased in size in response to greater pressure for better cooperation - substitute “increased social harmony with greater capacity to endure social atonality.
- One makes a living in society by finding a gradient and reducing it.
- Is there a protein in a tree or any plant that measures strain ( deformation in inches per pound per square inch of force) under the force of gravity - compression on one side of the tree that sends a grow signal to opposite side of tree in order to balance entire mass of tree with new growth?
- Is there ribosome signal relay across the neuron soma using electromagnetic quanta effects or other cells?
- A molecule may be changed ( like anything) by addition or subtraction. A thing is very particular about what it will accept as an “add-on” but any number of forces can subtract, damage or destroy: activation by addition, activation by subtraction, damaging via bending, re-folding, breaking apart.
- Cezanne was revolutionary because he courted ambiguity in his interpretation of pictorial space.
- “There is an overload of intention in bourgeois art” - Roland Barthes
- “In bourgeois art there is intimidation by detail.” R. Barthes
- “It is by the scope of his transformations that a man measures his power.” - R. Barthes
- “The great bourgeois task: to reduce being to having.” - R. Barthes
- “On plastic: For the first time in history artifice aims for the common.” - Barthes
- JB: Duchamp and Warhol were to fine art what plastic is to material - privileging the ordinary.
- Ubiquitin irregularities - cancer etiology - must be an army on this
- See: “The Rosicrucian Enlightenment” - Frances Yates
- Do wiggling tails of sperm strike dendrites at increasing rate and force as they mature causing intensifying effects at limbic or cortical region?
- Test TTT(Transgenerational Transmission of Trauma)-Epigenetics w/ drosophila holocaust.
- 4:08 pm