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'Epigenetics' Ooh! La! La! Lamarck?

Cochise said:
I've never quite understood why the 'orthodox scientific community' is so violently opposed to the Lamarckian extension to Darwinism? Obviously his postulate lacked a mechanism at the time, but so did Darwinism?

If evidence is now coming to light that there _is_ a mechanism for post-natal influences to create genetic change which can in turn be passed on to the next generation, what's wrong with that?
Science (in the West at any rate), wasn't so much, 'violently opposed' to Lamarckism, as totally unpersuaded that there was any evidence for a mechanism, where by Lamarckism, the passing on of acquired traits from one generation to the next, could be shown to be a factor in biology. Lamarckism notably lost a great deal of respectability, after one famous case, involving a species of midwife toad, where fraud was allegedly discovered.

Evolutionary theory, after Darwin, based on the natural selection of random genetic mutations, through interaction with environmental factors, offered a much better explanation, which was backed by the evidence.

Of course, epigenetics may offer just such a mechanism, whereby acquired traits can be passed on to the next generation, so the name of Lamarck, whose work and theory pre-dated Darwin's, has been mumbled in connection, but the jury is still out. It is science's natural caution, not to jump to conclusions, so Lamarck's official return to the scientific mainstream may take some time.
 
The sins of the father visited upon the children
(apparently)
similar to a post on page 1 i seem to have read that when the brains of rats that have been exposed to certain 'finding your way round a maze for the reward' type problems are then turned into gruel and fed to untrained rats, these will take less time than non brain fed rats to solve the problem.
As looking for a ref involves searching through about 25 books i will add 'allegedly' for now pending more vigorous looking.
fascinating stuff.
 
jacolantern said:
The sins of the father visited upon the children
(apparently)
similar to a post on page 1 i seem to have read that when the brains of rats that have been exposed to certain 'finding your way round a maze for the reward' type problems are then turned into gruel and fed to untrained rats, these will take less time than non brain fed rats to solve the problem.
As looking for a ref involves searching through about 25 books i will add 'allegedly' for now pending more vigorous looking.
fascinating stuff.

I wouldn't mind seeing that article. I also wouldn't mind knowing how they got Home Office approval or the equivalent for such a gruesome set of experiments.
 
well i'm still leafing through dusty tomes...
dont know that it was an experiment from this country though all i can remember is the gist due to the gruesomeness of it and reading the worm post on p1 nudged a neuron or two.
 
Evolutionary theory, after Darwin, based on the natural selection of random genetic mutations, through interaction with environmental factors, offered a much better explanation, which was backed by the evidence.

But its not an 'either/or', is it? Both could happen, with Darwinist evolution being the more significant of the two.

Lamarckism was apparently around before Darwinism, so I suppose the Darwin supporters felt thay had to trash it to get credibility, but as we've now realised that just about everything is vastly more complicated than anyone thought, so maybe we ought to be more open minded about more thna one mechanism operating. In fairness I suppose that is what is happening.
 
The experiment you talked about with the rats, I think that might have been flatworms it was done with.

Lamarckianism might have been around before Darwin, but my impression is it never caught on. So in that way, there was nothing to really oppose. Except of course creationism.
 
Creationism then was somewhat different to creationism now, though. For a start, far fewer people believe in it now, even among Christians. And the alternatives are much better attested.
 
I think you're right about the flatworms, spent a couple of evenings trying to find said experiment and failing miserably-i did find reference to the worm experiment and also one to an experiment with mice brains in 1972-apparently they were able to observe restructuring of the cells of ground up mice brains when placed in test tubes. :shock: so i probably conflated the two. :oops:
However an interesting article here about generational DNA mutations involving (yet again) mice.

http://www.scientificamerican.com/artic ... se-genomes
 
Inherited Epigenetics Produced Record Fast Evolution
http://www.sciencedaily.com/releases/20 ... 091844.htm

A brown Polish frizzle chicken, one of many varieties of domesticated chickens. The domestication of chickens has given rise to rapid and extensive changes in genome function. (Credit: © msibley / Fotolia)

ScienceDaily (Feb. 29, 2012) — The domestication of chickens has given rise to rapid and extensive changes in genome function. A research team at Linköping University in Sweden has established that the changes are heritable, although they do not affect the DNA structure.

Humans kept Red Junglefowl as livestock about 8000 years ago. Evolutionarily speaking, the sudden emergence of an enormous variety of domestic fowl of different colours, shapes and sizes has occurred in record time. The traditional Darwinian explanation is that over thousands of years, people have bred properties that have arisen through random, spontaneous mutations in the chickens' genes.

Linköping zoologists, with Daniel Nätt and Per Jensen at the forefront, demonstrate in their study that so-called epigenetic factors play a greater role than previously thought. The study was published in the journal BMC Genomics.

They studied how individual patterns of gene activity in the brain were different for modern laying chickens than the original form of the species, the red jungle fowl. Furthermore they discovered hundreds of genes in which the activity was markedly different.

Degrees of a kind of epigenetic modification, DNA methylation, were measured in several thousand genes. This is a chemical alteration of the DNA molecule that can affect gene expression, but unlike a mutation it does not appear in the DNA structure. The results show clear differences in hundreds of genes.

Researchers also examined whether the epigenetic differences were hereditary. The answer was yes; the chickens inherited both methylation and gene activity from their parentages. After eight generations of cross breeding the two types of chickens, the differences were still evident.

The results suggest that domestication has led to epigenetic changes. For more than 70 % of the genes, domesticated chickens retained a higher degree of methylation. Since methylation is a much faster process than random mutations, and may occur as a result of stress and other experiences, this may explain how variation within a species can increase so dramatically in just a short time.

Nätt and Jensen's research may lead to a review of the important foundations for the theory of evolution.

The above story is reprinted from materials provided by Linkoeping Universitet, via AlphaGalileo.

Journal Reference:

Daniel Natt, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Belteky, Leif Andersson, Per Jensen. Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens. BMC Genomics, 2012; 13 (1): 59 DOI: 10.1186/1471-2164-13-59
 
Breakthrough announced in ageing genes study
John von Radowitz Friday 20 April 2012

Four "Father Time" genes that help determine how fast we age have been uncovered by scientists.
The ageing genes are switched on or off by environmental and lifestyle factors such as diet, and may be programmed from an early age.
Knowing how the genes are altered could pave the way to new generations of anti-ageing drugs, researchers believe.

Scientists already knew that "epigenetic" changes - chemical alterations to DNA made by external factors in the environment - are important to ageing.
The new research goes some way towards solving the riddle of how and when these effects occur.

Dr Jordana Bell, from King's College London, one of the study authors, said: "We found that epigenetic changes associate with age-related traits that have previously been used to define biological age.
"We identified many age-related epigenetic changes, but four seemed to impact the rate of healthy ageing and potential longevity and we can use these findings as potential markers of ageing.
"These results can help understand the biological mechanisms underlying healthy ageing and age-related disease, and future work will explore how environmental effects can affect these epigenetic changes."

The scientists, whose work is reported in the online journal Public Library of Science Genetics, first looked for epigenetic changes in the DNA of 172 twins aged 32 to 80.
Twins are often used in such studies because identical pairs share exactly the same genes, making it possible to tease apart genetic and environmental effects.
If one identical twin displays very different characteristics from the other it means the cause cannot be genetic.

Analysing the changes in relation to chronological age, the researchers identified 490 age-related epigenetic changes.
Matching these to specific age-related traits highlighted four genes displaying changes linked to cholesterol levels, lung function and maternal lifespan.

Further research showed that many of the epigenetic DNA alterations were also present in a group of 44 younger twins aged 22 to 61.
This suggests that while many age-related genetic changes caused by environmental factors occur throughout a person's life, some might be triggered early on.

Professor Tim Spector, director of the Department of Twin Research at King's College, said: "This study is the first glimpse of the potential that large twin studies have to find the key genes involved in ageing, how they can be modified by lifestyle and start to develop anti-ageing therapies.
"The future will be very exciting for age research."
Gene experts at the Wellcome Trust Sanger Institute in Hinxton, Cambridgeshire, played a key role in the study.

Sanger scientist Dr Panos Deloukas pointed out that the research was still at an early stage.
"Our study interrogated only a fraction of sites in the genome (genetic code) that carry such epigenetic changes; these initial findings support the need for a more comprehensive scan of epigenetic variation," he said.

http://www.independent.co.uk/news/scien ... 64529.html
 
Epigenetics posited as important for evolutionary success
Environmentally modified genes could factor in the success of invasive species.
http://www.nature.com/news/epigenetics- ... ss-1.12179
Sujata Gupta
09 January 2013

Environmental factors may have given invasive house sparrows a genetic leg up in Kenya.
AINARS AUNINS / ALAMY

Two things are thought to be crucial for evolutionary adaptation: genetic diversity and long periods of time, in which advantageous mutations accumulate. So how do invasive species, which often lack genetic diversity, succeed so quickly? Some ecologists are beginning to think that environmental, or ‘epigenetic’, factors might be modifying genes while leaving the genome intact.

“There are a lot of different ways for invasive species to do well in novel environments and I think epigenetics is one of those ways,” says Christina Richards, an evolutionary ecologist at the University of South Florida in Tampa.

Although biomedical researchers have been investigating the links between epigenetics and human health for some time, evolutionary biologists are just beginning to take up the subject. Richards, who helped to organize a special symposium on ecological epigenetics at a meeting of the Society for Integrative and Comparative Biology (SICB) in San Francisco this month, says that the field has the potential to revolutionize the study of evolutionary biology.

The nascent field of ecological epigenetics has plenty of challenges standing in its way. The genomes of most wild animals and plants have not been sequenced so ecologists can’t pinpoint which genes have been modified. And, because they tend to work outside of controlled laboratory conditions, researchers have trouble linking those gene modifications to behavioural changes.

Invasive potential
Even so, there are hints that epigenetic diversity could be helping invasive species to thrive. For instance, Andrea Liebl, a fifth-year doctoral candidate at the University of South Florida, studies house sparrows (Passer domesticus) in Kenya, which, as descendants from a single group, have very little genetic diversity. But when Liebl combed the genomes of the birds to look for parts that had methyl groups attached — a key epigenetic marker — she found a high level of variability across populations. Similarly, in the invasive plant Japanese knotweed (Fallopia japonica), Richards found that genetically identical plants — knotweed reproduces clonally — have different leaf shapes and grow to different heights depending on where they live. Like the sparrows, the knotweeds exhibited high epigenetic diversity. Cristina Ledón-Rettig, a molecular biologist at North Carolina State University in Raleigh, who also helped organize the symposium, says that mapping the level of epigenetic modification may reveal “whether a population is going to tank or survive”.

Some critics aren’t ready to accept the links between epigenetics and invasive species. Jerry Coyne, an evolutionary geneticist at the University of Chicago in Illinois, says their success can be explained by well-established evolutionary theories. Sometimes a species moves into an unoccupied niche, and sometimes a small amount of genetic diversity goes a long way. “It doesn't have to have a lot of variation to evolve,” he says. “We have perfectly good other reasons, which are based on more solid premises, on why invasive species succeed.”

But with the cost of gene sequencing dropping, symposium organizers predict that research into ecological epigenetics is poised to take off. There could be several powerful studies coming out that show “how gene expression changes if the environment changes”, says Aaron Schrey, a population geneticist at Armstrong Atlantic State University in Savannah, Georgia.

Nature doi:10.1038/nature.2013.12179

Related stories and links

From nature.com
Job swapping makes its mark on honeybee DNA
16 September 2012
Neuroscience: In their nurture
08 September 2010
Genomics goes beyond DNA sequence
10 May 2010

From elsewhere
Ecological Epigenetics symposium
 
Chemical defects ‘last generations’

Scientists believe they have shown exposure to certain chemicals in the womb can cause changes that are passed through generations.
There is no firm evidence of this in humans, but Washington State University research showed a clear effect in rats.
They isolated defects linked to kidney and ovary disease and even obesity.
The work implicates a class of chemicals found in certain plastics, as well as one found in jet fuel.

The idea of "epigenetics" - that parents do not just pass their genes to their children, but subtle differences in the way those genes operate - is one of the fastest growing areas of scientific study.

The work of Dr Michael Skinner centres around the effects that certain chemicals can have on these processes, if the female is exposed at key points during pregnancy.
So far they have documented measureable effects from a host of environmental pollutants including pesticides, fungicides, dioxins and hydrocarbons.

However, they stress that the results are not directly transferable to humans yet, as the levels of chemicals used on the rats were many times more concentrated than anything a person would experience in normal life.
There is no data on even how an animal would respond at different doses, and no clues as to how the chemicals are causing these changes.

The studies, published in the journals PLoS One and Reproductive Toxicology, looked at the impact of phthalates, chemicals found in some forms of plastics, and a substance called JP8, found in jet fuel.
Rats exposed to phthalates had offspring with higher rates of kidney and prostate disease, and their great-grandchildren had more disease of the testicles, ovaries and obesity.

Female rats exposed to the hydrocarbon JP8 at the point in pregnancy when their male foetuses were developing gonads had babies with more prostate and kidney abnormalities, and their great-grandchildren had reproductive anomalies, polycystic ovary disease and obesity.

Dr Skinner said: "Your great-grandmother's exposures during pregnancy may cause disease in you, while you had no exposure.
"This is a non-genetic form of inheritance not involving DNA sequence, but environmental impacts on DNA chemical modifications.
"This is the first study to show the epigenetic transgenerational inheritance of disease such as obesity."

Andreas Kortenkamp, professor of human toxicology at Brunel University, said the results were "potentially very interesting", but much more work would need to be carried out before any impact on humans could be considered.
He said: "This is an exploratory study, but the authors themselves are clear that the data do not allow the possible risk to people to be assessed."
"There is a currently a lack of information about the dose-response relationship, and at this stage we are very unsure about the mechanisms that are involved."

http://www.bbc.co.uk/news/health-21202026
 
The old bones are yielding new evodence of the effects environment had on evolution.

Historic human remains yield epigenetic tags
http://www.newscientist.com/article/mg2 ... -tags.html
18 April 2013 by Sara Reardon
Magazine issue 2913.

DIET, disease and climate moulded human evolution not only by driving gene selection, but also by changing which genes were switched on or off. Such epigenetic changes have now been directly detected in ancient human remains for the first time.

Major environmental factors can affect which specific genes are expressed – or switched on or off. For example, the pattern of methyl groups on DNA bases can be altered, affecting expression without changing the genetic code. If this happens in sperm or egg DNA, the changes can be inherited.

Last year, a team found evidence of DNA methylation in the bones of a 26,000-year-old bison, but it wasn't clear whether it was a fluke. To find out, Rick Smith of the University of Texas in Austin, and colleagues, collected samples from 30 different human remains, ranging from 200 to 6000 years old. They were treated with a chemical that revealed where the methyl tags were when the DNA was sequenced. Comparison of the methylation patterns with modern humans yielded similarities in 27of the samples. Epigenetic changes should therefore be detectable in other ancient remains, says Smith, who presented the findings at the American Association of Physical Anthropologists in Knoxville, Tennessee, last week.

It should one day be possible to determine which environmental factors influence traits such as disease susceptibility. But because methylation patterns differ between organs, and only bone is preserved, it will never be possible to reconstruct the full "epigenome" of long-dead individuals, says Adrian Briggs at Harvard University.
 
'Memories' pass between generations
By James Gallagher, Health and science reporter, BBC News

Behaviour can be affected by events in previous generations which have been passed on through a form of genetic memory, animal studies suggest.
Experiments showed that a traumatic event could affect the DNA in sperm and alter the brains and behaviour of subsequent generations.
A Nature Neuroscience study shows mice trained to avoid a smell passed their aversion on to their "grandchildren".

Experts said the results were important for phobia and anxiety research.
The animals were trained to fear a smell similar to cherry blossom.
The team at the Emory University School of Medicine, in the US, then looked at what was happening inside the sperm.
They showed a section of DNA responsible for sensitivity to the cherry blossom scent was made more active in the mice's sperm.
Both the mice's offspring, and their offspring, were "extremely sensitive" to cherry blossom and would avoid the scent, despite never having experiencing it in their lives.
Changes in brain structure were also found.

"The experiences of a parent, even before conceiving, markedly influence both structure and function in the nervous system of subsequent generations," the report concluded.
The findings provide evidence of "transgenerational epigenetic inheritance" - that the environment can affect an individual's genetics, which can in turn be passed on
.

One of the researchers Dr Brian Dias told the BBC: "This might be one mechanism that descendants show imprints of their ancestor.
"There is absolutely no doubt that what happens to the sperm and egg will affect subsequent generations."

Prof Marcus Pembrey, from University College London, said the findings were "highly relevant to phobias, anxiety and post-traumatic stress disorders" and provided "compelling evidence" that a form of memory could be passed between generations.
He commented: "It is high time public health researchers took human transgenerational responses seriously.
"I suspect we will not understand the rise in neuropsychiatric disorders or obesity, diabetes and metabolic disruptions generally without taking a multigenerational approach."

In the smell-aversion study, is it thought that either some of the odour ends up in the bloodstream which affected sperm production or that a signal from the brain was sent to the sperm to alter DNA.

http://www.bbc.co.uk/news/health-25156510

I knew it wasn't just me! I blame all my ancestors for making me so screwed up!
 
Full text at link.

Epigenetic Effects of Mom’s Diet
Molecular markers of a mother’s nutrition around the time of conception can be found in her child’s DNA.

Maternal nutrition around the time of conception can affect the regulatory tagging of her child’s DNA from the earliest embryonic stages, according to a study published today (April 29) in Nature Communications, which focused on a population of women and children in Gambia.

The West African country has distinct rainy and dry seasons that dictate its inhabitants’ diets, making nutrition easy to track. Branwen Hennig from the London School of Hygiene & Tropical Medicine and her colleagues sought to determine whether Gambian women’s nutrition at conception affected their infants’ patterns of DNA tags, or methyl groups. The researchers profiled maternal blood samples, looking for nutrients linked to methylation, and examined methylation patterns of infant hair and blood DNA, homing in on specific sites called metastable epialleles—sequences where methyl groups appear to be added randomly, compared with the more-predictable patterning of much of the rest of the genome.

Because Hennig’s team found similar methylation patterns in the blood and hair samples from the same individuals, and because these patterns varied among individuals, “the authors demonstrate that these loci properly fulfill the criteria of metastable epialleles,” Gavin Kelsey, an epigeneticist with the Babraham Institute and the University of Cambridge, told The Scientist in an e-mail. “This is clearly an interesting paper,” said Kelsey, who was not involved in the work, adding that the study extends upon previous reports linking maternal nutrition with epigenetic tagging in both mouse and human offspring.

“The real advance of this study is that we nailed it that these regions in the human genome are bona fide metastable epialleles,” said study coauthor Robert Waterland, a nutritional epigeneticist at Baylor College of Medicine in Houston, Texas. “Not only does [the variation] occur stochastically and is influenced by maternal nutrition before and during pregnancy, but also it occurs systemically,” throughout the early embryo, he added. ...
http://www.the-scientist.com/?articles. ... om-s-Diet/
 
Study shows how epigenetic memory is passed across generations

A growing body of evidence suggests that environmental stresses can cause changes in gene expression that are transmitted from parents to their offspring, making "epigenetics" a hot topic. Epigenetic modifications do not affect the DNA sequence of genes, but change how the DNA is packaged and how genes are expressed. Now, a study by scientists at the University of California, Santa Cruz, shows how epigenetic memory can be passed across generations and from cell to cell during development.

The study, published September 19 in Science, focused on one well studied epigenetic modification—the methylation of a DNA packaging protein called histone H3. Methylation of a particular amino acid (lysine 27) in histone H3 is known to turn off or "repress" genes, and this epigenetic mark is found in all multicellular animals, from humans to the tiny roundworm C. elegans that was used in this study.
"There has been ongoing debate about whether the methylation mark can be passed on through cell divisions and across generations, and we've now shown that it is," said corresponding author Susan Strome, a professor of molecular, cell and developmental biology at UC Santa Cruz.

Strome's lab created worms with a mutation that knocks out the enzyme responsible for making the methylation mark, then bred them with normal worms. Using fluorescent labels, they were able to track the fates of marked and unmarked chromosomes under the microscope, from egg cells and sperm to the dividing cells of embryos after fertilization. Embryos from mutant egg cells fertilized by normal sperm had six methylated chromosomes (from the sperm) and six unmarked or "naked" chromosomes (from the egg).
can't see it anymore." ...

"Study shows how epigenetic memory is passed across generations." September 18th, 2014. http://phys.org/news/2014-09-epigenetic-memory.html
 
And we have a challenger.

Epigenetics Paper Raises Questions
GENETICS publishes a commentary criticizing a Nature Neuroscience paper claiming that mice can inherit smell sensitivities that their parents acquired during life.

A commentary published in GENETICS this week (October 15) questions the results of a December 2013 Nature Neuroscience paper about how mice, when conditioned to fear odors, pass on their fears to their pups, as well as to their pups’ offspring, presumably by an epigenetic mechanism. Gregory Francis, the critique’s author and a professor of psychological sciences at Purdue University, suggests that the original paper’s statistical results are “too good to be true.”

Francis has previously written similar statistical reviews of psychology papers. His reviews are based on the theory that experiments, particularly those with relatively small sample sizes, are likely to produce “unsuccessful” findings, such as results that do not reach statistical significance (a p-value of less than 0.05), at least some of the time, even if the experiments are measuring a real phenomenon. Taking into account the researchers’ reports of the strength of the phenomena they are measuring, known as effect size, Francis calculates the probability that an entire series of experiments will be “successful.” In the case of the Nature Neuroscience study, which also showed changes in neuroanatomy and reduced methylation of the body of an odor receptor gene for the sweet-smelling chemical acetophenone in offspring of exposed parents, Francis concluded that there was only a 0.004 chance of getting their pattern of successful results. The researchers either got very lucky, he suggests, or that there was something wrong with their results. ...

http://www.the-scientist.com/?articles. ... Questions/
 
Long-term endurance training alters the epigenetic pattern of the human skeletal muscle, according to new research from the Karolinska Institutet in Sweden, published in the journal Epigenetics.

The study found that genomic regions subject to increased methylation also featured carbohydrate metabolism and adaptation of the skeletal muscle.
Epigenetics are temporary biochemical changes in the genome caused by environmental influences. The researchers behind the new study explain that if genes are the "hardware" of cells, then epigenetics are their "software."

In particular, the researchers were interested in a type of epigenetic change called methylation. In methylation, a methyl group - molecules that reside within genes - is either added to or subtracted from a DNA molecule base without it affecting the original DNA sequence.

In the study, 23 healthy young men and women performed supervised one-legged cycling, with the untrained leg acting as a control. ...

http://www.medicalnewstoday.com/articles/286929.php

Is this a balanced article?
 
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