Is It Really Genetic? ….Should Your Bloodline End Now?

reply to post by Phage


RE: Gene variations do not come anywhere near explaining the vast array of individual difference.

According to whom?

J. Craig Venter for one - just after he sequenced the Human Genome. 'Course everyone banking on genetics being the be-all-and-end-all bailed on him right quick after that tasty little quote.

Meagre numbers raise genome questions

….“The discovery of our meagre gene numbers,” wrote McKie, “reveals that environmental influences are vastly more powerful in shaping the way humans act.” An accompanying editorial emphasised and extended the conclusion. “There simply aren't enough genes… to have one each for all the characteristics that have been associated with them, from alcoholism to criminality and intelligence.”

I wonder, if all our genes are the same. How can an individual be identified by their DNA?

Thing is, 99.9% of DNA sequences are the same in every person - the variable 0.01% involves sequences that are highly variable - but the vast majority of individual differences are epigenetic, not genetic.

….99.9% of human DNA sequences are the same in every person, (but) enough of the DNA is different to distinguish one individual from another…

…DNA profiling uses repetitive ("repeat") sequences that are highly variable,[2] called variable number tandem repeats (VNTRs), in particular short tandem repeats (STRs).

What is genetic testing?

Genetic testing is a type of medical test that identifies changes in chromosomes, genes, or proteins. ….

…Biochemical genetic tests study the amount or activity level of proteins; abnormalities in either can indicate changes to the DNA that result in a genetic disorder.

Forensic testing
Forensic testing uses DNA sequences to identify an individual for legal purposes.

...variations caused by epigenetics are still based on genetics. Your OP says that they aren't. Your OP says that they are based on "how the cell utilises energy."

"Genetic" refers to DNA - by definition, "epigenetic" refers to heritable changes that do NOT change DNA. The key point is that epigenetic changes -even inherited epigenetic mutations- are reversible.

….The source article describes the 2nd law of thermodynamics and environment as epigenetic mechanisms. Sorta like DNA is the mechanism for genetic inheritance. Point being epigenetic inheritance, unlike genetic inheritance, is reversible and impermanent.

reply to post by soficrow

J. Craig Venter for one - just after he sequenced the Human Genome.

Then why did you not provide a statement from him to that effect? But you know your quote from McKie is about behaviour, right? I would agree that not all behavior can be exclusively tied to genetics. Otherwise identical twins would act exactly the same.

but the vast majority of individual differences are epigenetic, not genetic.

Opinion? If not I'd like a source for that statement.

The source article describes the 2nd law of thermodynamics and environment as epigenetic mechanisms.

No. It doesn't. It discounts the role of both genetics and epigentics, talking about role of the "environment" in the ultimate formation of proteins.

This process consumes energy and is therefore governed by the 2nd law, but also by the environment in which the folding takes place.

phys.org...

Point being epigenetic inheritance, unlike genetic inheritance, is reversible and impermanent.

Yes. And the further point being that epigentic inheritance operates by influencing the expression of genes. Your OP says that genes don't have anything to do with it.

reply to post by Phage


As I recall, it was Venter who said in his editorial, “There simply aren't enough genes… to have one each for all the characteristics that have been associated with them, from alcoholism to criminality and intelligence.”

Your OP says

I trust you are referring to the source article? Which focuses on mechanism to explain process - not define it or redefine it, as you are trying to do. True, your argument is all over the place - it's not quite clear whether you're trying to redefine genetics, epigenetics, both or just to promote the Eugenics-Genetics agenda by any means possible. As it stands though, genetics and epigenetics are different, and defined as follows:

genetic:

Of or relating to genetics or genes.
Affecting or determined by genes: genetic diseases.

genetic: Related to genes. A gene is a sequence of nucleotides coding for a protein (or, in some cases, part of a protein); a unit of heredity.

genetics: The study of genes and their relationship to characteristics of organisms.

genetic code: The code relating nucleotide triplets in the mRNA (or DNA) to amino acids in the proteins.

In addition to the regulatory mechanisms of classical genetics, nearly all cellular processes can also be regulated by epigenetic mechanisms. Epigenetic mechanisms can be just as important to biological events as genetic mechanisms, and can also result in stable and heritable changes. However, the big difference between genetic and epigenetic regulation is that epigenetic mechanisms do not involve a change to the DNA sequence, whereas genetic mechanisms involve the primary DNA sequence and changes or mutations to this sequence. Epigenetic regulation involves the modification of DNA and the proteins associated with DNA, which results in changes to the conformation of DNA and accessibility of other factors to DNA, without a change to the sequence of the DNA.

….Through epigenetics, the classic works of Charles Darwin, Gregor Mendel, and Jean-Baptiste Lamarck and others are now seen in different ways. As more factors influencing heredity are discovered, today’s scientists are using epigenetics to decipher the roles of DNA, RNA, proteins, and environment in inheritance. The future of epigenetics will reveal the complexities of cellular differentiation, embryology, the regulation of gene expression, aging, cancer, and other diseases.

reply to post by soficrow

As I recall, it was Venter who said in his editorial

What editorial? Perhaps you can provide that editorial but I didn't know that Venter is an editor for the Observer so that may be problematic.

“The discovery of our meagre gene numbers,” wrote McKie, “reveals that environmental influences are vastly more powerful in shaping the way humans act.” An accompanying editorial emphasised and extended the conclusion. “There simply aren't enough genes… to have one each for all the characteristics that have been associated with them, from alcoholism to criminality and intelligence.”

www.sciencedirect.com...

I trust you are referring to the source article?

Yes. I am talking about the article linked in your OP.

Your source:

Epigenetic regulation involves the modification of DNA and the proteins associated with DNA, which results in changes to the conformation of DNA and accessibility of other factors to DNA, without a change to the sequence of the DNA.

Yes. That is what I said here and I have not said anything different. I'm not redefining anything. www.abovetopsecret.com...


A bit more from your source:

Epigenetic mechanisms can be just as important to biological events as genetic mechanisms, and can also result in stable and heritable changes.

www.zymoresearch.com...
Now contrast that to this, from the article in your OP.

This process consumes energy and is therefore governed by the 2nd law, but also by the environment in which the folding takes place. These two factors mean that there is no causal relationship between the original gene coding sequence and the biological activity of the protein.

phys.org...

If the article in your OP is correct then neither genetic nor epigenetic mechanisms have any relationship to what the proteins produced by either of them do.

reply to post by Phage

What editorial?

I said "as I recall," Venter was quoted as saying, “There simply aren't enough genes… to have one each for all the characteristics that have been associated with them, from alcoholism to criminality and intelligence.” I've used the quote numerous times on ATS but my posts have been purged. Fortunately, there are remnants of his interviews still on the net:

'We simply do not have enough genes for this idea of biological determinism to be right,' said Dr Craig Venter, the US scientist whose company Celera was a major player in the sequencing project. 'The wonderful diversity of the human species is not hard-wired in our genetic code. Our environments are critical.'

…It is only when scientists looked at the way these genes are switched on and made to manufacture proteins that they could see a significant difference between various mammalian species. The key difference lies in the manner in which human genes are regulated in response to environmental stimulation compared with other animals.

As to differences between humans, the Celera team calculates that of the three billion DNA letters that make up our genes, only 10,000 of them account for the differences between any two individuals. 'Really we are just identical twins,' Venter said. 'But like all twins and brothers and sisters, we are all really different in the way we respond to the environment.'

There simply aren't enough genes, researchers now suggest, to have one each for all the characteristics that have been associated with them, from alcoholism to criminality to intelligence.

Craig Venter, whose company Celera raced the publicly funded sequencing consortium to the finishing line, was the only one to read the implications correctly. The number of genes is far less than needed to support the extravagant claims throughout the past decade that individual genes not only determine how our bodies are constructed, what diseases we suffer from, but also our patterns of behaviour, our intellectual ability, sexual preference and criminality.

"We simply do not have enough genes for this idea of biological determinism to be right," said Venter. "The wonderful diversity of the human species is not hard-wired in our genetic code. Our environments are critical."

Cool genetics story:

…Venter and his team of researchers, having studied preliminary results of sequencing data, decided to downgrade the number to around 80,000.

'The day after we published I got this call from the head of a leading biotechnology company,' says Venter. 'He was cursing and swearing and using all sorts of obscenities about my company and about myself.'

Venter calmed him down and asked the company chief's problem. 'You've just announced there are only 80,000 human genes, and I've just done a deal with SmithKline Beecham. I've already agreed to sell them 100,000 genes - where I am supposed to get the rest, you bastard.'

The biotech chief has since died, which may be fortunate - for the news that the researchers have now reduced that number even further to around 30,000 would have probably turned him to violence.

RE: "there is no causal relationship between the original gene coding sequence and the biological activity of the protein."

If the article in your OP is correct then neither genetic nor epigenetic mechanisms have any relationship to what the proteins produced by either of them do.

Not at all - they're saying that "phenotypes are emergent properties of their systems" - the 2nd law and the environment (epigenetics) determine the protein's biological activity - not the genetic code. Here's the article abstract:

Genes without prominence: a reappraisal of the foundations of biology

Abstract

The sequencing of the human genome raises two intriguing questions: why has the prediction of the inheritance of common diseases from the presence of abnormal alleles proved so unrewarding in most cases and how can some 25 000 genes generate such a rich complexity evident in the human phenotype? It is proposed that light can be shed on these questions by viewing evolution and organisms as natural processes contingent on the second law of thermodynamics, equivalent to the principle of least action in its original form. Consequently, natural selection acts on variation in any mechanism that consumes energy from the environment rather than on genetic variation. According to this tenet cellular phenotype, represented by a minimum free energy attractor state comprising active gene products, has a causal role in giving rise, by a self-similar process of cell-to-cell interaction, to morphology and functionality in organisms, which, in turn, by a self-similar process entailing Darwin's proportional numbers are influencing their ecosystems. Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype. In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.

reply to post by soficrow

Here's Venter's complete statement from 2001:

"The small number of genes has tremendous implications, and you should be asking the question: why is the small number of genes surprising? I think it happened for several reasons. The fruit fly genome has 13,000 or so genes in it, and everybody was thinking we are so much bigger and smarter on average than fruit flies that we should have a lot more genes. Then look at our everyday language," said Dr Venter.

"People talk about you got the gene for this from your mother and the gene for that from your father, and so if you think that we are hard-wired and that everything is deterministic, there should be a lot of genes, because we have a lot of different traits. So I think a lot of people were expecting that to be the case."

www.theguardian.com...

That was a statement about early ideas that each gene has a unique function. It was known at the time that was not the case. It was also known that genes affected other genes and that variations within genes affected other genes and their function.

But here's something a bit more recent from Venter regarding the amount of variation found, after mapping his own genome.

The new genome, Dr. Venter’s team reports, makes clear that the variation in the genetic programming carried by an individual is much greater than expected. In at least 44 percent of Dr. Venter’s genes, the copies inherited from his mother differ from those inherited from his father, according to the analysis published in Tuesday’s issue of PLoS Biology.

www.nytimes.com...

Not at all - they're saying that "phenotypes are emergent properties of their systems" - the 2nd law and the environment (epigenetics) determine the protein's biological activity - not the genetic code. Here's the article abstract:

I was referring to the article you linked in your OP. But lets look at the abstract:

In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.

All that says is that everything (the environment) affects the way an organism develops. That's not unreasonable. Now, the sentence before that:

Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype.

It's saying that genes just make polypeptides, they don't have anything to do with making more complex proteins. After that, it's a matter of (luck) that the proper proteins form? That's exactly what the article in your OP says that the paper says. And like I said, it's an interesting hypothesis. The phenotype is determined by the phenotype? Huh? It is was it is because that's what it is?

And, like I said, it removes both genetics and epigentics from any role in biology other than just producing the raw materials. It also provides no means for inheritance of epigenetic traits. It really doesn't make much sense to me. I'll be interested to see what those in the field have to say about it.

reply to post by soficrow


S&F ... the thoughts of possible long term outcomes truly terrifying if the linkage between DNA and epigenetics and healthcare services given. Should be a positive one to be honest, however based on the financial greed in this world it most likely will produce negative outcomes for all.

Worst case scenarios:
- forced abortions (reminds me of one child policy and the drive for male off-spring)
- increased taxes to 'financially support' your future disease
- insurance companies refusing to insure for x or y potential disease
- development of a class system, not through money but based on DNA mutations and epigenics differential expressions
- may affect lifestyle, housing, work etc

You are right though, like the smoking and obesity propaganda for example, people are often blamed for a myriad of diseases (HT, HD, cancer etc). So many cigarette smokers or obese people who have the so-called myriad of diseases are literally being told that their medical problems are based on smoking or overeating. I can't tell you how many times I have been told by a person who has lung cancer or is obese, state 'I did it to myself though smoking/overeating - the doctor said'.

I have for a long while been keeping track of the research on various area's of epigenetics in the hope that some day it will turn the medical model upside down to be reinvented to improve human quality of life.

You may already have been to this website:
Science Daily - Up to date Epigenetics Research

reply to post by soficrow

FYI

DNA contains all the instructions for building all the parts of the body. But DNA is only half of the story. The DNA in our bodies is wrapped around proteins called histones. Both the DNA and the histones are covered with chemical tags. This second layer of structure is called the epigenome. The epigenome shapes the physical structure of the genome. It tightly wraps inactive genes, making them unreadable. It relaxes active genes, making them easily accessible. Different sets of genes are active in different cell types. The DNA code remains fixed for life, but the epigenome is flexible. Epigenetic tags react to signals from the outside world, such as diet and stress. The epigenome are just specific genes in our genomic landscape in response to our rapidly changing environment.

Therefore signals from our environment can work through the epigenome to change a cell's gene expression. In order to stabilize gene expression, the epigenetic tag records the cell's experiences on the DNA. Each signal shuts down some genes and activates others as it nudges a cell toward its final fate. A different experiences origin is dependent on the epigenetic profiles of each cell type to grow increasingly different over time. In the end, hundreds of cell types form, each with a distinct identity and a specialized function. Gene regulatory proteins also recruit enzymes that add or remove epigenetic tags. Enzymes also add epigenetic tags to the DNA or the histones, or both. Therefor epigenetic tags give the cell a way to "remember" in the long-term.

It is understood that the epigenetic marks can be passed from both maternal and paternal to its offspring in a way, that completely bypasses the sperm or egg, thus avoiding the epigenetic eradication that occurs in the course of early embryo development.

Most of us were taught that our traits are hard-coded in the DNA that passes from parent to offspring. Emerging information about epigenetics may lead us to a new understanding of just what inheritance is.

My interest is specifically around methylationcan proteins role in epigenetic memory, DNA methylation in several aspects of physiology and development - preferably around memory, learning, fear formation and neurogenesis.

Text…to assume that genes are unavoidable influences on our health and behaviour will distract attention from the real causes of disease, many of which arise from our environment;

the current strategy towards basing healthcare on genome-wide sequencing, so called "personalised healthcare", will prove costly and ineffective.

reply to post by soficrow


Did you put this part in?
I believe it has equal advantages to disadvantages.
Yet it is frightening to think of this being used for the wrong purposes, like things in Psi-fy such as cloning with a time limit, making deliberate mutation like killer soldiers that only know killing, no fear, & totally lacking any empathy & mores & values, then be killed b/c they can't be in society.....
I guess I'm ambivalent to the idea....

Nice find. Thx for sharing, S&F....

reply to post by SLAYER69


Extremely valid....nice to see someone's glass at least .75% full......

reply to post by Phage


The proteins are energy that can bind also …the process of changing into amino acids, which is an integral part of DNA/RNA.... you really know your stuff

reply to post by rickymouse


An instance to that would be;
Asians. Any blood lines considered Asian, Eskimos, Inuit, Native Aborigines, etc, have still not caught up to Caucasians like the Norse for example.... The Asians have smaller Pancreases which break proteins down into amino acids into Kilajoules which is energy & they have smaller livers & kidneys that filter unnecessary proteins leading to more diabetics, gallbladder issues, etc....their blood vessels & intestines are also smaller, leading to high cholesterol problems, heart disease & stomach diseases most specifically Cilliacs.
Thus, the changes in Asian's diets especially from he 1950's are still causing these problems even in those that are say, .24% Asian, sometimes less.
But it sounds like the OP is saying that that's what makes the mutated genetics or they want to use proteins purposely to change DNA genetics which has been occurring for a long long time already so it's hard to distinguish what his point is exactly....I think lol! It's hard to tell.

reply to post by Phage

Here's Venter's complete statement from 2001:

Venter gave lots of interviews following his sequencing of the Human Genome - he didn't make just one statement - everyone wanted to talk to him. It was an exciting discovery. His interviews tended to reflect the content of his official statement of course, but the phrasing was often different.

But here's something a bit more recent from Venter regarding the amount of variation found

After Venter said "We simply do not have enough genes for this idea of biological determinism to be right," he lost his funding, support and credibility. Then he went back to the dark side - and its cash - and back to looking for proof of genetic determinism. From your source:

…Dr. Venter believes strongly in ….personalized genomic medicine.

…Another reason for his success has been his skill at raising private finances to achieve research goals after being denied support from the National Institutes of Health.

RE:

In such natural processes, everything depends on everything else, and phenotypes are emergent properties of their systems.

All that says is that everything (the environment) affects the way an organism develops. That's not unreasonable.

Nope, it's not - it's systems theory.

RE:

Thus, genes are merely a means of specifying polypeptides: those that serve free energy consumption in a given surroundings contribute to cellular phenotype as determined by the phenotype.

It's saying that genes just make polypeptides, they don't have anything to do with making more complex proteins.

Polypeptides can be considered small proteins - eg., The enzyme (protein) lysozyme is made of just one polypeptide. ….The evidence shows that a gene initiates the process of protein production (making polypeptides), then 'epigenetics' takes over to complete the production process, which may result in changes (overrides) to the original "code."

After that, it's a matter of (luck) that the proper proteins form?

No, not luck - systems biology. Not your single-cause-and-effect dogma, but valid. However, I can see why you're uncomfortable with it.

…it removes both genetics and epigentics from any role in biology other than just producing the raw materials. …

Not at all - it describes the epigenetic process in the context of systems theory - and yes, relegates genetics to the role of "producing the raw materials." Which I quite enjoy and which clearly antagonizes you.

I'll be interested to see what those in the field have to say about it.

Me too. Given the role of the mitochondria in health and disease (specifically proteinopathies), this hypothesis seems to provide a defensible "unifying theory" resulting from the now-requisite inter- and multi-disciplinary collaboration in systems biology.

lonewolf2
reply to post by soficrow

 

S&F ... the thoughts of possible long term outcomes truly terrifying if the linkage between DNA and epigenetics and healthcare services given. Should be a positive one to be honest, however based on the financial greed in this world it most likely will produce negative outcomes for all.

Thanks. S& back atcha. The terrifying outcomes rely on the Eugenics-Genetics camp appropriating epigenetics and defining it as "genetic." It's not - but the appropriation forms the foundation for "personalized genomic medicine" based on out-dated and disproven notions of "genetics." ...The idea is that genetic analysis will result in personalized medicine targeted to individual "genetic susceptibilities." Won't happen of course - we'll all find our insurance doesn't cover health problems resulting from "genetic inferiority." As you say, "insurance companies refusing to insure for x or y potential disease." And btw - it already happens in the form of 'unwritten policies.'

And the facts remain, epigenetic processes override the genetic code and most "modern" disease results from the epigenetic response to environmental assault.

You may already have been to this website:
Science Daily - Up to date Epigenetics Research

Thanks for the link - I keep losing/forgetting about the darn things. Did you catch this one?

Revolutionary new view on heritability in plants: Complex heritable traits not only determined by changes in DNA sequence
Date: February 11, 2014

Summary:
Complex heritable traits are not only determined by changes in the DNA sequence. Scientists have now shown that epigenetic marks can affect traits such as flowering time and architecture in plants. Furthermore, these marks are passed on for many generations in a stable manner.

Here's a journal you might appreciate:

Epigenetics: official journal of the DNA Methylation Society (Epigenetics )

lonewolf2
reply to post by soficrow

 

DNA contains all the instructions for building all the parts of the body. But DNA is only half of the story.
.....Most of us were taught that our traits are hard-coded in the DNA that passes from parent to offspring. Emerging information about epigenetics may lead us to a new understanding of just what inheritance is.

The paper cited in the OP article suggests DNA may be less than half the story. Current research does place mitochondrial dysfunction at the center of proteinopathy pathogenesis - and the 2nd law of thermodynamics coupled with the effects of environmental perturbations certainly explains the process. Whether or not the hypothesis proves to be accurate, there is no doubt these 'mysteries' will only be unravelled with inter- and multi-dusciplinary collaborations.

reply to post by StormyStars

RE:

Text…to assume that genes are unavoidable influences on our health and behaviour will distract attention from the real causes of disease, many of which arise from our environment;

the current strategy towards basing healthcare on genome-wide sequencing, so called "personalised healthcare", will prove costly and ineffective.

Did you put this part in?

No. Those are quotes from the source article, which was/is boxed with a link (the cloud thingie in the upper left means it's an external source):

A challenge to the genetic interpretation of biology

A proposal for reformulating the foundations of biology, based on the 2nd law of thermodynamics and which is in sharp contrast to the prevailing genetic view, is published today in the Journal of the Royal Society Interface under the title "Genes without prominence: a reappraisal of the foundations of biology".

…the prominent emphasis currently given to the gene in biology is based on a flawed interpretation of experimental genetics and should be replaced by more fundamental considerations of how the cell utilises energy. There are far-reaching implications, both in research and for the current strategy in many countries to develop personalised medicine based on genome-wide sequencing.

…to assume that genes are unavoidable influences on our health and behaviour will distract attention from the real causes of disease, many of which arise from our environment;

the current strategy towards basing healthcare on genome-wide sequencing, so called "personalised healthcare", will prove costly and ineffective.

reply to post by StormyStars


Very interesting information. I know I have problems with my pancreas...It is like opening a fire hydrant. I didn't have a problem when I worked 12-16 hrs a day on construction but now that I am not doing much because of a type of epilepsy, the insulin causes a problem. I often go hypoglycemic easily. I have always had a problem with that. I am a Finn/swede/Norwegian mix. All from what they called Lapland in the past.

reply to post by soficrow



Darwin and Freud walk into a bar.

Two alcoholic mice — a mother and her son — sit on two bar stools, lapping gin from two thimbles.
The mother mouse looks up and says, “Hey, geniuses, tell me how my son got into this sorry state.”
“Bad inheritance,” says Darwin.
“Bad mothering,” says Freud.
For over a hundred years, those two views — nature or nurture, biology or psychology — offered opposing explanations for how behaviors develop and persist, not only within a single individual but across generations.
And then, in 1992, two young scientists following in Freud’s and Darwin’s footsteps actually did walk into a bar. And by the time they walked out, a few beers later, they had begun to forge a revolutionary new synthesis of how life experiences could directly affect your genes — and not only your own life experiences, but those of your mother’s, grandmother’s and beyond.


Have you ever stopped to think it isn't a case of one or the other?

reply to post by Grimpachi

Have you ever stopped to think it isn't a case of one or the other?

I got really bored with the nature-nurture "debate" about 40 years ago, and consider the polarization to be synthetic and old-school. What interests me now are mechanisms, processes and facts - interests triggered by trying to get information about my own incurable disease - fibromuscular dysplasia (in my case caused by an allergic reaction to penicillin in childhood, but considered a "genetic" disease nonetheless) - which led me to fibroblasts and prions, on to protein misfolding and proteinopathies, epigenetics and mitochondrial dysfunction. In part.

The evidence shows that epigenetic processes govern genetic activity without being themselves genetic - even when inherited, epigenetic traits are reversible. The hypothesis outlined in the source article and abstract, Genes without prominence: a reappraisal of the foundations of biology, seems to be a unifying theory worthy of consideration.

reply to post by swanne

Jeez. What a deep discussion. Creating a separate species through bloodlines has been going on for centuries (the European royal houses) with just a few throwbacks. Mates have been specifically chosen for certain traits (whether they be genetic or otherwise) but early inbreeding put their cause back a bit. This is still an ongoing program that they choose to persue though some say it's to keep the money and power in the family.