Epigenetics. "What if everything you knew about evolution is wrong"?

[Rrose Selavy]

I'm not sure what to make of this and maybe it's not news to some but here goes, the full article linked below has much more stuff:


What if Darwin's theory of natural selection is inaccurate? What if the way you live now affects the life expectancy of your descendants?



One study, again from Sweden, looked at lifespans in Norrbotten, the country's northernmost province, where harvests are usually sparse but occasionally overflowing, meaning that, historically, children sometimes grew up with wildly varying food intake from one year to the next. A single period of extreme overeating in the midst of the usual short supply, researchers found, could cause a man's grandsons to die an average of 32 years earlier than if his childhood food intake had been steadier. Your own eating patterns, this implies, may affect your grandchildren's lifespans, years before your grandchildren – or even your children – are a twinkle in anybody's eye.

http://www.guardian.co.uk/science/2010/mar/19/evolution-darwin-natural-selection-genes-wrong

[themusicteacher]

Sounds to me like yet another misinterpretation and misapplication of "natural selection."

[NavyPack]

Epigenetics is too new to fully comment on, but basically, there's a whole other layer of control/regulatory mechanisms on the larger 3-dimensional nature of the chromosome; it's ability/frequency to be transcribed.

Darwin was unaware of DNA, was evolution wrong then?

No, whatever new wonders we learn from epigenetics, it will still conform to darwinian selection.

[BobTheDonkey]

I'm just going to throw this out:

correlation =/= causation


There are so many variables that cannot be controlled for in this study...I don't see how we can reasonably draw any worthwhile conclusions.

But, that's probably just my own $0.02

[shadron]

Epigenetics is the study of how DNA is controlled in actual use. The ease with which DNA can be unwrapped in order to make a tRNA copy of a strand is affected by how tightly it is bound to the substrate of histone proteins it is wrapped around in the first layer of twisting that DNA goes through to enable its orderly storage. That tends to be controlled by a series of additional methyl groups that assist the binding. How exactly this is effected, and how it is controlled to effect certain outcomes by making DNA unavailable for copying is still being studied. There are many articles about it; it is definitely science. Here is one:

http://www.pbs.org/wgbh/nova/sciencenow/3411/02.html

It certainly does have an effect on gene expression, and it is commonly invoked to show how a pair of twins can "grow apart" into differing individuals. This:

What if Darwin's theory of natural selection is inaccurate? What if the way you live now affects the life expectancy of your descendants?is typical hysterical newspaper grandstanding, turning what should be a feature story in the science section of the paper into a screaming headline, just like the New Scientists rag did to Darwin on its cover a couple of years ago.

[Wowbagger]

I don't know enough about epigenetics, yet, to fully comment on how much it renders natural selection inaccurate. But, I would have no problem with it, if it did. Much of the material I have read, so far, sounds reasonably plausible, at least.

Remember:
Epigenetics does not completely replace natural selection. It just adds some "corrections" to it, to render the evolutionary system more accurately. (This is similar, in some ways, as to how relativity added corrections to gravity, without completely replacing it.)

It's good to see biologists trying to "take it to the next level" of understanding. Time and further study will tell us if this approach is a good one.

[AlBell]

What epigenetics seems to do is add a mechanism for teleology, a word that really doesn't fit well in current Theory.

[Dymanic]

The part I find most pertinent is this bit:

"What all this evidence shows is that we need a much more subtle and nuanced understanding of Darwinism and natural selection," Shenk says. "I think that's inevitably going to happen among scientists. The question is how much nuance will carry over into the public sphere."

I for one will not be holding my breath where the second of those is concerned. As for the first, I think Shenk may be (perhaps deliberately, for the purpose of selling more books) underestimating the degree to which that more subtle and nuanced understanding already exists among scientists, and even to some degree among non-scientists. I mean, the notion that way you live now affects the life expectancy of your descendants can be treated as trivially obvious; so much so that it easily finds its way into discussions on various aspects of social, economic, and environmental policy. It may be true that the high school students to which Shenk refers may not all have a deep appreciation for, say, how the histories of cell lineages may influence gene expression and how this in turn percolates up to the level of the phenotype upon which selection acts -- but it's certainly not a breakthrough concept to the leading theorists.

A lot of misunderstanding arises out of the somewhat unfortunate metaphor "blueprint for life", and anything that helps to straighten that out is good. It's just too bad that it seems that the only way to do that in "the public sphere" is to come out honking horns and banging drums.

[Wowbagger]

A lot of misunderstanding arises out of the somewhat unfortunate metaphor "blueprint for life", and anything that helps to straighten that out is good.Bingo!

Richard Dawkins always prefered the "recipe" analogy, and I agree, although it is still not perfect.

If epigenetics is true, it shows us that genes are even more "like a recipe", and much less "like a blueprint". (For what it's worth, this also implies that epigenetics would be an assault to the core Intelligent Design ideal that "DNA is information".)

[macdoc]

I do think this is a hierarchy issue.....

In some ways an in utero response to external conditions....

Our evolutionary heritage endows us with muscles that respond to stress....no stress they do not respond by growing larger ( simplistic but you get the drift)

Epigenetics puts an in womb layer to genetic expression and timing and in doing so, unlike your muscles, can impact genetic heritage in a limited manner...

The latter I understand is where the controversy or unknowns lie ....just how much can that be passed along and are gene sequences altered in response to conditions over generations...

In no way in my view does it alter natural selection...just add a layer of "response" within the individual rather than purely within a population.

It is certainly an exciting field :thumbsup:

[!Kaggen]

The OP article is about epigenetic inheritance, not just epigenetics.

This a good portal for everything epigenetics.
http://www.epidna.com/

The most important result of the study in the OP and similar ones is that it re-introduces the idea of Lamarckism in evolutionary theory.

What it does for me is question the whole concept of genetic engineering, which assumes that Lamarckism is impossible.

[Wowbagger]

The most important result of the study in the OP and similar ones is that it re-introduces the idea of Lamarckism in evolutionary theory.
A very, very limited form of it, I might add.

ETA: Lamarckism was never impossible. Just much less probable to crop up, or have any influence, than the simpler natural selection model, especially where there is a germ-line "bottleneck" involved. And, especially since the olde Lamarckian homonuculus doesn't seem to exist.

[macdoc]

What it does for me is question the whole concept of genetic engineering, which assumes that Lamarckism is impossible.

you sure it does not just add to the engineers toolbox?
might actually make some aspects of it easier.....

[Paul C. Anagnostopoulos]

Breaking news: Evolution is more complicated than we know at any given point in history.

~~ Paul

[!Kaggen]

you sure it does not just add to the engineers toolbox?
might actually make some aspects of it easier.....

Not really, since genetic engineering is completely dependent on the concept of "a clone" which can be mass produced for sale.

Now "a clone" is defined as

"a cell, cell product, or organism that is genetically identical to the unit or individual from which it was derived. "

from http://dictionary.reference.com/browse/clone

what if clones may be affected by epigenetic inheritance as the article in the OP suggests and therefore have different traits between generations although they are genetically identical?

It is a bit like buying a music CD which plays different music on different CD players.

This also contradicts an important argument of GMO pundits, that
GMO food is substantially equivalent (http://en.wikipedia.org/wiki/Substantial_equivalence) and therefore does not require labeling.

[Sideroxylon]

Is epigenetics going to be the new quantum mechanics? (for woos to weave their nonsense about).

Bruce Lipton:
http://www.youtube.com/watch?v=Y-Hh7b3Nxxc

[steve s]

The program Nova did an episode about this called The Ghost in Your Genes. The transcript can be found here (http://www.pbs.org/wgbh/nova/transcripts/3413_genes.html). And here's (http://www.pbs.org/wgbh/nova/preview/w_3413_220.html) a video preview. I don't think the entire program is available on the web. Nowhere in the show did they mention about Darwin being wrong.

The Guardian article starts with that tired old creationist claim that there's a missing day. I wouldn't put too much stock in their claim that Darwin was wrong.

Steve S

[casebro]

Sounds quite exciting. Looks like making changes doesn't really mean changing genes, but only a bit of methylation? Easier?

Though before today's discussion, like Macdoc said "Our evolutionary heritage endows us with muscles that respond to stress....no stress they do not respond by growing larger ( simplistic but you get the drift)" I figured epigenetics had a major effect on the current generation rather than something passed along.

Hmm, does epigenetics have a place in lower life forms? Plants? Or strictly on the highest forms, mammals and/or primates? Possible difference between Man and____ ?

[Dancing David]

Breaking news: Evolution is more complicated than we know at any given point in history.

~~ Paul

All hail Paul! (And many others.)

[Dancing David]

Not really, since genetic engineering is completely dependent on the concept of "a clone" which can be mass produced for sale.

Now "a clone" is defined as

"a cell, cell product, or organism that is genetically identical to the unit or individual from which it was derived. "

from http://dictionary.reference.com/browse/clone

what if clones may be affected by epigenetic inheritance as the article in the OP suggests and therefore have different traits between generations although they are genetically identical?

It is a bit like buying a music CD which plays different music on different CD players.

This also contradicts an important argument of GMO pundits, that
GMO food is substantially equivalent (http://en.wikipedia.org/wiki/Substantial_equivalence) and therefore does not require labeling.


I think clones will be more infuenced by the mitochondrial DNA, but you never know. Being that a clone is created by removing the nucleus from an egg.

And it is already well known that identical twins have different expressions of the genetics.

:)

[KingofMadCows]

This isn't exactly a new thing. The idea of psychosomatic disorders originated from the time of Freud. Stryker and Sherk demonstrated in 1975 that kittens that had only been exposed to horizontal lines became blind to vertical lines.

[Crazycowbob]

I'm just going to throw this out:

correlation =/= causation


There are so many variables that cannot be controlled for in this study...I don't see how we can reasonably draw any worthwhile conclusions.

But, that's probably just my own $0.02

I'm going to have to go with this answer too...

I mean, if you look far enough down the road after a widespread event, you'll find another widespread event that you can claim is related because it happened in the same area. This group of people get a few years of over indulgence, and then they say that their grandchildren generally end up dying 32 years earlier than average? What was the cause of all these deaths? Did they take into account any disease? Famine? How about war? How many generations did they follow? The information presented is simply woefully inadequate in regards to drawing any conclusions whatsoever. I'd wager that another, more likely, explaination to the change in lifespan is at work here.

Quite frankly, I think it's a bit fool hardy to jump to the conclusion you've discovered something new until you've thoroughly tested and proven that existing answers cannot fit.

Edited to add: Just thinking more about this... I'd really like to know what years the "grandchildren" from this study lived in. Given an average lifespan of say 50-60 years, that would have put these grandchildren dying at around 18-28 years old, that sounds a lot like a war.

[!Kaggen]

I'm going to have to go with this answer too...

I mean, if you look far enough down the road after a widespread event, you'll find another widespread event that you can claim is related because it happened in the same area. This group of people get a few years of over indulgence, and then they say that their grandchildren generally end up dying 32 years earlier than average? What was the cause of all these deaths? Did they take into account any disease? Famine? How about war? How many generations did they follow? The information presented is simply woefully inadequate in regards to drawing any conclusions whatsoever. I'd wager that another, more likely, explaination to the change in lifespan is at work here.

Quite frankly, I think it's a bit fool hardy to jump to the conclusion you've discovered something new until you've thoroughly tested and proven that existing answers cannot fit.

Edited to add: Just thinking more about this... I'd really like to know what years the "grandchildren" from this study lived in. Given an average lifespan of say 50-60 years, that would have put these grandchildren dying at around 18-28 years old, that sounds a lot like a war.

No, you are not understanding epigenetic inheritance.

It is not a case of drawing conclusions based on correlations.

The important feature of transgenerational epigenetic inheritance described in the OP is that the 3rd generation of the male line are being affected without the environmental influence which led to the original gene expression of the 1st generation or the effect of a mother carrying the child for 9 months in her womb. Please read the abstract below.

Transgenerational effects of maternal nutrition or other environmental 'exposures' are well recognised, but the possibility of exposure in the male influencing development and health in the next generation(s) is rarely considered. However, historical associations of longevity with paternal ancestors' food supply in the slow growth period (SGP) in mid childhood have been reported. Using the Avon Longitudinal Study of Parents and Children (ALSPAC), we identified 166 fathers who reported starting smoking before age 11 years and compared the growth of their offspring with those with a later paternal onset of smoking, after correcting for confounders. We analysed food supply effects on offspring and grandchild mortality risk ratios (RR) using 303 probands and their 1818 parents and grandparents from the 1890, 1905 and 1920 Overkalix cohorts, northern Sweden. After appropriate adjustment, early paternal smoking is associated with greater body mass index (BMI) at 9 years in sons, but not daughters. Sex-specific effects were also shown in the Overkalix data; paternal grandfather's food supply was only linked to the mortality RR of grandsons, while paternal grandmother's food supply was only associated with the granddaughters' mortality RR. These transgenerational effects were observed with exposure during the SGP (both grandparents) or fetal/infant life (grandmothers) but not during either grandparent's puberty. We conclude that sex-specific, male-line transgenerational responses exist in humans and hypothesise that these transmissions are mediated by the sex chromosomes, X and Y. Such responses add an entirely new dimension to the study of gene-environment interactions in development and health.
from
http://www.ncbi.nlm.nih.gov/pubmed/16391557

also trans generational epigenetic inheritance is ubiquitous


ABSTRACT

This review describes new developments in the study of transgenerational epigenetic inheritance, a component of epigenetics. We start by examining the basic concepts of the field and the mechanisms that underlie epigenetic inheritance. We present a comprehensive review of transgenerational cellular epigenetic inheritance among different taxa in the form of a table, and discuss the data contained therein. The analysis of these data shows that epigenetic inheritance is ubiquitous and suggests lines of research that go beyond present approaches to the subject. We conclude by exploring some of the consequences of epigenetic inheritance for the study of evolution, while also pointing to the importance of recognizing and understanding epigenetic inheritance for practical and theoretical issues in biology.

from
http://www.journals.uchicago.edu/doi/abs/10.1086/598822

[Rolfe]

Look at the increase in human height (certainly in Britain) over the past 100 years or so. It's far too fast for natural selection. And yet it's too slow for an immediate effect of improved diet. People go on getting taller unto the children and the children's children of them that got decent nutrition.

Not saying I actually understand epigenetics, but that's the example I use when I try.

Rolfe.

[Estellea]

Epigenetic expression does not invalidate natural selection; I think someone here put it best by describing it as another layer. It is a fascinating field and my first exposure to it was years ago, dealing with cat coat colours. Here (http://www.lifescied.org/cgi/content/full/9/1/6) is a good primer on the subject.

Este

[macdoc]

IK
Originally Posted by macdoc
you sure it does not just add to the engineers toolbox?
might actually make some aspects of it easier.....
Not really, since genetic engineering is completely dependent on the concept of "a clone" which can be mass produced for sale.

Now "a clone" is defined as

"a cell, cell product, or organism that is genetically identical to the unit or individual from which it was derived. "

from http://dictionary.reference.com/browse/clone

what if clones may be affected by epigenetic inheritance as the article in the OP suggests and therefore have different traits between generations although they are genetically identical?

It is a bit like buying a music CD which plays different music on different CD players.

You still miss the point of additional toolbox

A DESIRABLE trait of say a plant is that it be able to adapt to a wide set of external conditions....

ie for a plant if a lot of nitrogen is available then the gene expression differs and that limited trait is heritable...there is no reason not to engineer that heritability into GM strains....

It's more like buying a CD that plays louder under certain conditions and only certain passages...

I really see NO conflict...just more complicated toolbox with more layers of tools available...

Predator stress in a pool will alter the tadpole's gene expression...is it much of leap to understand that continued stress includes a mechanism where the beneficial expression is carried on to the next generation epigenetically

To a degree gene expression also influences in womb development for the offspring - hell it even has sexual selection of male or female in some species..

Crocs I think

But it has limits to engender changes...in my view it is an enhancement of the mechanism of natural selection whereby a species tolerates and adapts to a wider set of conditions in a shorter period of time....

pretty solid advantage wouldn't you say?

[Earthborn]

Epigenetics doesn't mean Darwin was wrong about natural selection, it means he was not quite as wrong about the mechanism of inheritance as we used to think.

[casebro]

Hmmm, would epigenetics account for that old saw "It skips a generation"?

[Wowbagger]

Hmmm, would epigenetics account for that old saw "It skips a generation"?I think good 'ol Mendellian dominant/recessive gene theory covers most of that.

[Wowbagger]

Epigenetics doesn't mean Darwin was wrong about natural selection, it means he was not quite as wrong about the mechanism of inheritance as we used to think.

<reaction type="typical creationist">

Bah!! Epigenetics proves Darwin was wrong about everything! Therefore evolution is lie! And, totally falsified!!!!

</reaction>

[!Kaggen]

IK


You still miss the point of additional toolbox

A DESIRABLE trait of say a plant is that it be able to adapt to a wide set of external conditions....

ie for a plant if a lot of nitrogen is available then the gene expression differs and that limited trait is heritable...there is no reason not to engineer that heritability into GM strains....

It's more like buying a CD that plays louder under certain conditions and only certain passages...

I really see NO conflict...just more complicated toolbox with more layers of tools available...

Predator stress in a pool will alter the tadpole's gene expression...is it much of leap to understand that continued stress includes a mechanism where the beneficial expression is carried on to the next generation epigenetically

To a degree gene expression also influences in womb development for the offspring - hell it even has sexual selection of male or female in some species..

Crocs I think

But it has limits to engender changes...in my view it is an enhancement of the mechanism of natural selection whereby a species tolerates and adapts to a wider set of conditions in a shorter period of time....

pretty solid advantage wouldn't you say?

Your sentiments are noted, however the reality is that genetic engineers engineer not for possibilities, but for definite outcomes.

The problem with BT Cotton in India for instance is that it is an clonal F1 hybrid variety which only performs with well planed and sufficient irrigation and fertilizer. This was not made known to the farmers who purchased the seed using debt finance and who have worked in the past with open pollinated varieties which had much bigger genetic variation to tolerate erratic rainfall. The result being the now infamous Indian cotton farmer suicides of the last few years.

A similar story was the cause of the famous Ethiopian famines back in the '80's where hybrid wheat varieties were distributed to farmers with the promise of large yields. The caveat being -under the right conditions. One season of erratic rainfall resulted in complete crop failure since the hybrid variety all had the same phenology, whereas open pollinated varieties traditionally used had a large variation in phenology and late rains would still have made for some yield.

In fact if anything epigenetics is telling us is that our tool box does not need more tools, but the tool user needs to understand when to NOT use a hammer to fix a cellphone.

[Cuddles]

What if Darwin's theory of natural selection is inaccurate?

The only answer to this is that there is no "what if" Darwin's theory of natural selection was very much inaccurate. He was writing 200 years ago and was pretty much the first to to set it out as a formal narrative, what would you expect? And while we know much more now than we did back then, of course it's still inaccurate. If we knew our knowledge of evolution was perfect, we wouldn't need all these scientists around. So the article doesn't get off to a good start when the headline is pointless hyperbole rather than something sensible.

As for the detail, as others have mentioned there's really nothing much new here. The idea that genes don't account for absolutely everything is hardly a new idea, and I really don't understand why it keeps getting media attention as some amazing new idea that overturns everything we ever knew about biology. For a great example, look at sex determination. Humans, and most other mammals, have a genetic system of XX/XY. However, we know that can be overridden to a greater or lesser extent by altering the environmental conditions, both within the womb and later in life. So clearly something as fundamental as sex is not solely about genes.

It gets even more obvious when you look at the various animals that don't have a genetic sex determination system at all. With some reptiles, the temperature of the egg is the important factor. With some animals it depends on proximity of other individuals, or even just social dominance. Apparently in some arthropods sex is actually determined by bacterial infection.

So the idea that DNA isn't the be-all and end-all is really not some new, revolutionary idea. Wikipedia cites papers on sex determination from at least as far back as 1977, and I have no doubt that other aspects of epigenetics were known about well before then. There's certainly plenty more interesting stuff to learn about the hows and whys, and there may be some argument that there has been a disproportionate focus on the DNA itself since mapping genomes became a reality, but all the media hype is nothing more than the usual nonsensical media hype.

[ponderingturtle]

I don't know enough about epigenetics, yet, to fully comment on how much it renders natural selection inaccurate. But, I would have no problem with it, if it did. Much of the material I have read, so far, sounds reasonably plausible, at least.

Remember:
Epigenetics does not completely replace natural selection. It just adds some "corrections" to it, to render the evolutionary system more accurately. (This is similar, in some ways, as to how relativity added corrections to gravity, without completely replacing it.)

Does it replace evolution at all, or just add more complexities too it than just genetic changes?

[Wowbagger]

Does it replace evolution at all, or just add more complexities too it than just genetic changes?It would add some complexity to evolution and development. Why would it replace the whole thing?

[krazyKemist]

Hmm, does epigenetics have a place in lower life forms? Plants? Or strictly on the highest forms, mammals and/or primates? Possible difference between Man and____ ?

Difference between eukaryotes and prokaryotes - between those who have histones and those who don't. Between us animals and plants, and bacteria/archea.

If you think about it, it makes sense - we already have right in front of us the undeniable fact that eukaryote genes are expressed differentially : a muscle cell is different from a neuron. Since the genetic material is the same for both, the source of that difference can't just be genetic. There has to be some environmental control - thus epigenetics. Epigenetics has been a known entity in biology for quite some time, just not under that name.

It has become "revolutionary" when some people got results which suggest that epigenetic modifications also happen in germ cells, and therefore could be transmitted to offspring - therefore transmission of acquired trait - "Lamarckian" genetics as opposed to "Mendelian" genetics.

The thing is that both of these are broad models, and if you have more data, it becomes apparent that they are not as opposed as some people would have us think. Mendelian genetics doesn't preclude transmission of acquired traits, both can happen. Just as crossing-over doesn't disprove or make mendelian genetics useless, even if mendelian genetics doesn't make any provision for such a phenomenon. Mendel was really, really lucky in his experimentations - the genes he chose were segregating independently. That is not the case for all genes.

And the actual historical opposition was between the mendelian model and the so-called lamarckian model, not between Darwin's natural selection theory and the lamarckian model, so I really don't understand why it gets creationists all excited. It's about the mecanism of transmission of hereditary traits, not about evolution.

Well, I guess it's for the same reason as usual - willfull incomprehension and ignorance.

[Foster Zygote]

What epigenetics seems to do is add a mechanism for teleology.

Care to explain how?

[dakotajudo]

The problem with BT Cotton in India for instance is that it is an clonal F1 hybrid variety which only performs with well planed and sufficient irrigation and fertilizer. This was not made known to the farmers who purchased the seed using debt finance and who have worked in the past with open pollinated varieties which had much bigger genetic variation to tolerate erratic rainfall. The result being the now infamous Indian cotton farmer suicides of the last few years.
macdoc, if you're confused as to what this has to do with epigenetics, don't feel bad; !Kaggen has pretty well mucked this up.

Where to start?

First, a clonal variety is typically one that is propagated asexually - bananas, for example - no seeds.

An hybrid variety is most commonly the first generation of seed produced from the mating of two inbred lines. This should be distinguished from hybrid as used in taxonomy, to denote an organism result from a cross between two species. It also should be noted that in some production systems, dihybrids are used - the seed planted in the field is the product of two hybridization steps involving four inbred parental lines.

The F notation is used to denote the number of selfing (self-pollinated or inbred) generations since a crossing event; it's generally assumed that a hybrid variety is F1, and it's not clonal, so !Kaggen is simply talking about a hybrid cotton variety, as opposed to a purebred line.

Almost all commercial crop varieties are referred to as adapted lines - they have been selected for their performance in, their adaptation to, target environments. Grow these lines outside their zones of adaptation, they might not do as well. For this reason, most breeders, commercial or public, develop a wide selection of lines, to ensure profitable years for their many varied clients, in spite of changing conditions.

Typically, varieties are continually tested, year to year, at various locations throughout the target production environment. The results of these test are released to producers shortly after harvest, so the producers can make informed decisions about which varieties to select. In the US, we count on county extension agents and independent agricultural consultants to disseminate this information and help producers make choices based on these trials. Breeders select a range of promising lines, but growers must also make selections.

That system may have failed in India; sometimes county agents and consultants simply don't understand the technology.

Notice I haven't said anything about Bt yet. That's because it's not particularly important at this point.

Bt cotton was introduced to India when Maharashtra Hybrid Seed Co. (Mahyco) obtained a transformed line from Monstano and introgressed (inbred) into MECH-12, MECH-162 and MECH-184, these being the adapted lines I described above. In testing prior to release, the Bt lines outperformed their non-Bt counterparts; if the counterparts did poorly (due to drought, for example), the Bt lines also tended to do poorly.

Therefore, the issue with Bt hybrid cotton versus what !Kaggen is calling open-pollinated lines has little to due with the Bt part; it's an issue of adapted lines vs what we call "landraces".

Before the advent of modern breeding methods, say, about 100 years ago, most farmers planted and harvested landraces - locally adapted, mixed populations, genetically heterogenous. It is true that these populations tend to be more stable over many seasons, but what !Kaggen is not telling you is that these populations tend to do relatively poorly, even in the best years, when compared adapted lines.

That is, if you plant a landrace, you might get, over 5 years, get 5 mediocre harvests. Plant an adapted line, it's true you might get a crop failure over one season, but you can expect at least 3 good harvest, and probably 1 great harvest. Over the course of several seasons, adapted lines greatly outperform landraces.

What !Kaggen is also failing to mention is that the diversity of landraces makes it virtually impossible to get a harvest without some seed loss. As he noted, individual plants in a landrace population don't mature at the same rate; this allows for some individual to survive to harvest during bad conditions. However, this also means that some individual plants are mature and starting to drop seed while other plants in the field as still green. Either you lose harvest due to immature seeds, or to seed lost to shatter. This is one of the reasons landraces have been almost entirely replaced by adapted lines.

So what does this have to do with epigenetics?

Nothing, really.

When a genetic modification is introgressed into adapted lines, the resulting offspring are tested for their phenotypes, not genotypes. Any factors that affect gene expression - heterosis, epistasis, pleiotropy, additive dominance, cytoplasmic inheritance, on and on and including epistasis, are testing under these conditions. The results of these tests - performance under field conditions - are generally available to growers and their advisors.

Sure, there's advertising on the part of companies that might influence buyers. Just as there's advertising for various drugs. Would you buy an over-the-counter drug without consulting your pharmacist? Of request an advertised prescription without a discussion with your doctor?

Well, people do just that, so of course producers in India bought seed they didn't need or didn't know how to use. That does not negate the simple observation that, for the majority of producers, Bt cotton has improved yields.

As for the claim about increased suicide rates, you should be skeptical. Most farmers expect a bad year once in a while, it's part of the job. There is no evidence that the introduction of Bt cotton had any affect on suicide rates:
http://www.nature.com/nbt/journal/v27/n1/full/nbt0109-9.html




Sorry for the FRAT, everyone, but some kinds of ignorance must be addressed.

Well, not entirely off-topic, I guess.

The link in the OP suggested What if Darwin's theory of natural selection is inaccurate?

Several people have pointed out that epigenetics is simply a mode of inheritance, and as such is not Darwin's theory of natural selection. The development of Bt cotton is primarily an artificial selection process; independent of how that genetic material to be selected from, is created, GM or otherwise.

Hmm, does epigenetics have a place in lower life forms? Plants? Or strictly on the highest forms, mammals and/or primates? Possible difference between Man and____ ?
Uh, what? Highest forms?

You mean more recently evolved forms? Mammals are no higher, or no lower, than "plants".

However, to answer your question, epigenetic phenomena can be found across nearly all kingdoms. Bacteria, for example, have DNA methylation patterns that change gene expression from generation to generation, without altering the underlying DNA sequences. The life cycle of Caulobacter crescentus ( http://en.wikipedia.org/wiki/Caulobacter_crescentus ) , for example, is controlled in part by such methylations.

[AlBell]

What epigenetics seems to do is add a mechanism for teleology.

Care to explain how?
I was considering in essence Lamarckism, the idea that transformation of species occurred as the result of individuals adapting to environmental stimuli in a way carried forward to progeny.

This implies to me directed rather than random change. ymmv.

[Toke]

I read of something similar in a book on obesity. (Fat wars)
It appears that a mothers level of body fat effects the adult body fat percentage of the children.
That is only one generation and could be foetus organs effected, but I don't see why it could not carry over by the same mechanism for several generations.

Rolfe's example with heights increasing is better for showing an effect over generations that I do not understand.
It does not bother me too much, I am not a biologist or specialised in genetics, so I just conclude that things are more complicated that we could cover in high school biology.
We did do genetic engineering, on E-coli moving resistance to antibiotics from one culture to another.

[Foster Zygote]

I was considering in essence Lamarckism, the idea that transformation of species occurred as the result of individuals adapting to environmental stimuli in a way carried forward to progeny.
You don't seem to have a very good understanding of what epigenetics is.

This implies to me directed rather than random change. ymmv.
How, specifically, does it imply this?

[krazyKemist]

I was considering in essence Lamarckism, the idea that transformation of species occurred as the result of individuals adapting to environmental stimuli in a way carried forward to progeny.

This implies to me directed rather than random change. ymmv.

Genetic change is also directed by selection pressure - broadly, the environment; random mutations lead to non-random results. That's also what is directing epigenetic changes. I fail to see the difference beyond mere mechanism - except maybe speed of adaptation. There are many other instances in biological systems of responses that occur with different speeds, and each have their limits. Epigenetic change transmitted to offspring is a fast adapative response, but there are severe limits as to what it can actually do.

Saying that epigenetics makes everything we know in genetics "wrong" is like saying that crossing-over makes mendelian genetics "wrong", or that quantum mechanics makes classical physics "wrong". When someone say such things, it is safe to assume that this person does not even understand what science is.

[AlBell]

Saying that epigenetics makes everything we know in genetics "wrong" is like saying that crossing-over makes mendelian genetics "wrong", or that quantum mechanics makes classical physics "wrong". When someone say such things, it is safe to assume that this person does not even understand what science is.
You should be happy I didn't say that then.

Are you? Be sure to let me know. I can hardly wait for your response!

[krazyKemist]

You should be happy I didn't say that then.

Are you? Be sure to let me know. I can hardly wait for your response!

:o

I'm sorry if you thought I thought you were saying that. That was a comment on the OP saying that Darwin was wrong because of epigenetics. I admit it might have interpreted as such.

But I am curious about what you perceive as a major difference between epigenetic adaptation and adaptation via natural selection.

[!Kaggen]

The problem with BT Cotton in India for instance is that it is an clonal F1 hybrid variety which only performs with well planed and sufficient irrigation and fertilizer. This was not made known to the farmers who purchased the seed using debt finance and who have worked in the past with open pollinated varieties which had much bigger genetic variation to tolerate erratic rainfall. The result being the now infamous Indian cotton farmer suicides of the last few years.
There is no evidence that the introduction of Bt cotton had any affect on suicide rates:
http://www.nature.com/nbt/journal/v27/n1/full/nbt0109-9.html

Dishonesty appears to be an epidemic amongst agricultural academics.

Support for my conclusion above:

From your nature article

Where such failures did occur, the IFPRI report blames the conditions in which the technology "was introduced, sold, and used" rather than the technology itself.
and
~snip~ "Nothing in that paper is addressing the issue of debt, which is the prime cause of suicide," she says.

Separating the technology from the context in which it is used IS the problem with GMO's and underlines the dishonesty of the academics who support it for technology's sake only.


In all these areas, there is a noticeable absence of irrigation and sustainable harnessing of
water resources. As a result, agriculture is mostly rain dependent (more so in the context
of the crisis in groundwater availability for farming). The over dependence of the farmer
on the HYV seeds, pesticides and fertiliser-based cropping demands water. It was noticed
that there was a noticeable scarcity of water, including groundwater.
7
The tendency towards commercial (cash) crops increased in the late eighties, and this
tendency is not limited to big and medium sized landholders alone. Even the landless and
small landholders have been acquiring land on lease for cash crop cultivation. In the
absence of credit and other inputs like facilitation and support price, dependence on cash
crops may have contributed to the agrarian crisis in the areas. Thus, the life of farmers is
governed by loans taken mostly to support farming.
Life histories and case studies conducted for this study reveal that there has been sharp
increase in the dependence on loans to enable cultivation. The tendency to take loans
increased in the nineties. The farmers took their first loan from banks (banks gave loan
only once, with a further loan possible only after repayment of the outstanding loan). The
later loans were from private parties to repay the bank loan (default of which would result
in attachment of the land or mortgaged house). Even for those with an ability to get loan
from the formal sector, access to informal sector loans was indispensable. Thus, over
75% of the farmers had loan commitments to non-formal sources.

from http://www.tiss.edu/Causes%20of%20Farmer%20Suicides%20in%20Maharashtra .pdf

Debt is the reason for Indian farmer suicide
from http://blog.monsantoblog.com/2009/03/26/indian-farmer-suicide-the-bottom-line/


For the whole story from people on the ground who work with Indian farmers daily to alleviate their poverty
http://www.grain.org/research_files/Story_of_Bt_Cotton.pdf


And then there is this pearl of academic morality

Sure, there's advertising on the part of companies that might influence buyers. Just as there's advertising for various drugs. Would you buy an over-the-counter drug without consulting your pharmacist? Of request an advertised prescription without a discussion with your doctor?
Well, people do just that, so of course producers in India bought seed they didn't need or didn't know how to use.

Ironically you summarized the failure of genetic engineering pretty well in your own words

That system may have failed in India; sometimes county agents and consultants simply don't understand the technology.

I put this in the context of epigenetics

In fact if anything epigenetics is telling us is that our tool box does not need more tools, but the tool user needs to understand when to NOT use a hammer to fix a cellphone.

specifically transgenerational epigenetic inheritance which is the topic of the OP article link.

Something you appear to ignore by harping on about DNA-methylation, which is only one known biochemical mechanism of epigenetic inheritance. The important bit is the influence that the macro environment has in affecting not only gene expression, but the inheritance through the male germ line of this gene expression.



That is, if you plant a landrace, you might get, over 5 years, get 5 mediocre harvests. Plant an adapted line, it's true you might get a crop failure over one season, but you can expect at least 3 good harvest, and probably 1 great harvest. Over the course of several seasons, adapted lines greatly outperform landraces. What dakotajudo fails to mention is the context in which success is required for "adapted lines" (another dishonest semantic twisting) which are hardly adapted to local conditions. They may be adapted to the support infrastructure of debt, fertilizer, irrigation, machinery, herbicide and pesticide yes but without this support they are useless.

What !Kaggen is also failing to mention is that the diversity of landraces makes it virtually impossible to get a harvest without some seed loss. As he noted, individual plants in a landrace population don't mature at the same rate; this allows for some individual to survive to harvest during bad conditions. However, this also means that some individual plants are mature and starting to drop seed while other plants in the field as still green. Either you lose harvest due to immature seeds, or to seed lost to shatter. This is one of the reasons landraces have been almost entirely replaced by adapted lines. What dakotajudo fails to mention is that this is only important when harvesting by machine. The traditional harvest methods from landraces is done selectively by hand when individual plants are ripe. All that this argument once again indicates is the dependence on machinery implied in hybrid seeds.

[little grey rabbit]

Epigenetics does, hypothetically, allow a Larmarckian element to enter the equation.
Although I am not aware of anyone actually demonstrating a mechanism.

I will create a purely fictional example. Suppose a key skin pigment gene was upregulated by methylating it's promoter region. And this methylation was increased by exposure to UV by (ahem) a feedback mechanism of some kind. This methylation state could be passed on by as an example of epigenetic inheritance to offspring so they would be expressing high levels of skin pigment from birth.

Thats how it could work (for that particular example there is absolutely no indication that it does)

I see a lot of very muddied thinking when biologists try to prove evolution (I am a Dembski follower myself).

This following from a Steve Jones review is an excellent example

I was fascinated to learn that, in 1971, Belgian scientists transferred a group of lizards from one small island off the Yugoslav coast to another, free of native members of that species, nearby. During that same summer, a few miles inland in the wild backwoods of Croatia, I myself was hard at work moving thousands of snails between habitats in the hope of picking up differences in survival. Thirty-seven years later, the descendants of the transferred lizards had changed – evolved – to gain stronger jaws and a modified gut to deal with their new and more vegetarian diet; but, alas, just a year after moving the molluscs I could find almost none of them (which proves not that evolution is wrong but that experiments in the wild usually do not work).

First kudos for Prof. Jones for not finding his molluscs and not publishing some bollocks finding, but the Belgian scientists finding are impossible to take seriously.

Most likely the stronger jaws and modified gut involved no genotypic changes at all - simply a phenotypic alteration to environmental conditions exposed to from birth (like pasty Englishman will raise fit, tanned, healthy Australian offspring if they emigrate - despite the enormous phenotypic changes, no genetic change has taken place at all).

It is just possible that some pre-existing genes already in the population may have been selected for, it is even just possible that there might be some epigenetic inheritance (if indeed this occurs) which has resulted in rapid change in response to the new environment.

But realistically after only 37 years you shouldnt expect to see anything different in quality from the miracle wrought on pale-faced Englishmen when they move to God's own

[little grey rabbit]

Oh and I should add Darwin himself included larmarckism as one element in his evolution theory. So epigenetic inheritance would not alter that.

[casebro]

It is just possible that some pre-existing genes already in the population may have been selected for,...

Isn't this the very definition of "Evolution"?

But realistically after only 37 years you shouldnt expect to see anything different in quality from the miracle wrought on pale-faced Englishmen when they move to God's own

37 years ought to be ple ty of generations for "some pre-existing genes already in the population to be selected for", since lizards would have time for many generations. They don't live as long as tortoises.

[Rolfe]

Isn't this the very definition of "Evolution"?


Well, no, not really. It explains a lot of population shifts, such as the black moths, but on its own it's not sufficient. In order for evolution to go anywhere in the long term you also require random mutations, some of which produce beneficial characteristics and will thus be favoured by selection pressure. What little grey rabbit is saying is that the changes in the lizards might not have involved any actual new (mutated) genes.

Rolfe.

[zeusbheld]

wow, a discussion of epigenetics without resorting to bloated new agey claims like, "epigenetics disproves the very idea of human nature!"

i don't post on this forum much but i do read it fairly often. i love you guys. (snif)

[Astrodude]

I'm just going to throw this out:

correlation =/= causation


There are so many variables that cannot be controlled for in this study...I don't see how we can reasonably draw any worthwhile conclusions.

But, that's probably just my own $0.02
Don't throw this out at all! Darwinism is not a religion; it's perfectly okay to question it. It's just a matter of how and why it is questioned. In this case, it is questioned because of many studies. Also, it doesn't contradict the idea of evolution by natural selection. Rather, it supports that theory but simply argues about the mechanism. Darwin's own mechanism of natural selection was called pangenesis and was discredited by Mendel's experiments.

The idea that epigenetic traits are sometimes inherited appears to be legitimate and has been observed in several repeated studies. If you run mice through a maze over and over again, their progeny appear to have greater natural ability than other mice. RNA replication has been cited as a factor. Immunology also provides evidence like the Swedish chicken study.

I see evidence of epigenetic transmission as a harmonizer of Lamarckian evolution under the umbrella of Darwinian evolution.

[TubbaBlubba]

Difference between eukaryotes and prokaryotes - between those who have histones and those who don't. Between us animals and plants, and bacteria/archea.

Some archaea do have histones. It's a very good reason to believe that most of the eukaryotic cell is descended from a symbiosis between archaea and bacteria (mitochondria), by the way.

[ThunderChunky]

Some archaea do have histones. It's a very good reason to believe that most of the eukaryotic cell is descended from a symbiosis between archaea and bacteria (mitochondria), by the way.

Yup. Steven Henikoff has some nice papers on the evolution of histones. For example:

http://www.ncbi.nlm.nih.gov/pubmed/14583738