Obesity and diabetes: Actual epigenetics or just IVF?

This press release that appeared in my newsfeed titled "You are what your parents ate!" caught my eye because I'm a new mom of a new human and also because I study and teach human evolution.

So I clicked on it.

And after that title primed me to think about me!, the photo further encouraged my assumption that this is really all about humans.

"You are what your parents ate!"

But it's about mice. Yes, evolution, I know, I know. We share common ancestry with mice which is why they can be good experimental models for understanding our own biology. But we have been evolving separately from mice for a combined total of over 100 million years. Evolution means we're similar, yes, but evolution also means we're different.

Bah. It's still fascinating, mice or men, womice or women! So I kept reading and learned how new mice made with IVF--that is, made of eggs and sperm from lab-induced obese and diabetic mouse parents, but born of healthy moms--inherited the metabolic troubles of their biological parents. And by inherited, we're not talking genetically, because these phenotypes are lab-induced. We're talking epigenetically. So the eggs and sperm did it, but not the genomes they carry!

This isn't so surprising if you've been following the burgeoning field of epigenetics, but it's hard to look away. This fits with how we see secular increases in human obesity and adult-onset diabetes--it can't be genomic evolution, it must be epigenetic evolution, whatever that means!

As the press release says...

"From the perspective of basic research, this study is so important because it proves for the first time that an acquired metabolic disorder can be passed on epigenetically to the offspring via oocytes and sperm- similar to the ideas of Lamarck and Darwin," said Professor ...

Whole new ways of thinking are so exciting.

Except when you remember a two-year-old piece by Bethany Brookshire (because you use it to teach a course on sex and reproduction) which explained something that suggests we may have a major experimental problem with the study above.

In IVF, the sperm gets isolated (or "washed") from the semen.

You know what happens, to mice in particular, when there's no semen? Obesity and other symptoms of metabolic syndrome! There are placental differences too. This was published in PNAS.

"Offspring of male mice without seminal fluid had bigger placentas (top right) and increased body fat (bottom right) compared with offspring of normal male mice (left images)" from The fluid part of semen plays a seminal role by Bethany Brookshire.

So I went back to look at the original paper that the press release with the donut lady was about. I wanted to see if they are aware of this potential problem with IVF and whether it explains their findings, rather than the trendy concept of epigenetics...

So even though they titled it "Epigenetic germline inheritance of diet-induced obesity and insulin resistance," I wanted to see if they at least accounted for this trouble with semen, like how it's probably important, how its absence may bring about the same phenotypes they're tracking, and how IVF doesn't use semen.

But I don't have access to Nature Genetics.

Who has access to Nature Genetics, can check out the paper, and wants to write the ending of this blog post?

Step right up! Post your work in the comments (or email me holly_dunsworth@uri.edu, and please include a pdf of the paper so I can see too) and I'll paste it right here.

Update 12:19 pm
Two very good comments below are helpful. Please read those.

I'll add that I now have the pdf of the paper (but not the Supplemental portion where all the methods live and other important information resides). This quote from the second paragraph implies they do not agree with the finding of (or have forgotten about) the phenotypic variation apparently caused by sperm washed of their seminal fluid:

"The use of IVF enabled us to ensure that any inherited phenotype was exclusively transmitted via gametes."

As the second commenter (Anonymous) pointed out below, there does not appear to be a comparison of development or behavior between any of the IVF mice and mice made by mouse sex. So there is no way to tell whether their IVF mice exhibit the same metabolic changes that the semen/semenless study found. Therefore, it is neither possible to work the semen issue into the explanation nor to rule out its effects. Seems like a missed opportunity.

Completely unrelated and inescapable... I'm a little curious about how the authors decided to visualize their data like this:

Remembrance of things past--in your genes? Part III: Was Lamarck so laughable?

A favorite sport of those holding to strict Darwinian views (to the extent they understand Darwin),  is to ridicule Jean Baptiste de Lamarck (1744-1829), he of the stretchy giraffe neck.

Lamarck

Lamarck has gotten a very bad name and at least partly undeservedly.  As are we all, he was a product of his time, his academic environment, and the knowledge then available.  He was apparently a quirky personality and got crosswise with other powerful French biologists, notably Georges Cuvier.  For various reasons it became important for Darwinians to distance themselves from Lamarck as an important intellectual ancestor, in particular, to avoid crediting him for his insight about evolution. Intentional PR-spinning to advance Darwinians (and British over French science)?

Lamarck did his best to clarify very explicitly that he was seeking material explanations not being mystical as he is essentially accused of being.  His basic idea of the inheritance of acquired characteristics was not even that new. It was the obvious thing to infer from the data available at the time, and the idea was commonly held as far back as Hippocrates (probably classics scholars can find it elsewhere as well).

In fact, Lamarck was very clear that he wanted a strictly materialistic explanation for species evolution and diversity. This is interesting, and if it weren't for the rather smug glee with which Lamarck is so universally ridiculed by biologists (whether or not they've read his actual work or even much of Darwin's), we might not want to make the following points.  But under the circumstances, we think it's merited, especially in light of the interpretations being given to widespread reports of various sorts of epigenetic inheritance, that is, of DNA marking rather than sequence change during life.

In our two prior posts in this series (here and here), we took the usual view and stated that any suggestion that epigenetic inheritance is Lamarckian inheritance is trying too hard to be revolutionary, because epigenetic inheritance is imposed by the environment, not by some mystic inner drive on the part of the organism as Lamarck is supposed to have suggested as the cause of adaptive evolutionary change. So, as the usual view has it, even if genome marking is inherited, it is not Lamarckian.  But is that actually so?

"Laws of Nature": who was right?

As we use the term, a Law of Nature is a concept that grew out of the so-called Enlightenment period in European culture history beginning around the mid-1600s.  Darwin's view of natural selection was that it was a Law of Nature that Isaac Newton might have been proud to recognize.  In the amended introduction to the 6th edition of the Origin of Species, Darwin added a review of the history of evolutionary thinking, and there he couldn't have expressed his views better: Darwin said that Lamarck "...did the eminent service of arousing attention to the probability of all change in the organic, as well as in the inorganic world, being the result of law, and not of miraculous interposition."  (italics mine).  

But in fact Darwin was quite wrong, reflecting his own ideological commitment, not Lamarck's. This is because Lamarck said something far more important in my view than the way Darwin thought, and in fact the exact opposite. Here's a fundamental point that Newton himself made very clear, about the central characteristic of a Law of Nature: Principia in 1687: 

"Those qualities of bodies that . . . belong to all bodies on which experiments can be made should be taken as qualities of all bodies universally."

That is, if you find something to be true in a local, restricted setting or 'sample', such as dropping an apple or the orbit of the moon around the earth, the same would be true everywhere else that you didn't or couldn't study.  That was the very essence of what it meant for some phenomenon to be a 'law'.   In his books and other writings it is repeatedly crystal clear that Darwin accepted this Newtonian view: natural selection is a law of nature the way the law of gravity is.  Indeed, in the autobiography he penned for his children near the end of his life, he couldn't have been more clear, writing "...now that the law of natural selection has been discovered..." and "Everything in nature is the result of fixed laws.”

Lamarck was closer to Newton in time than Darwin, but what were his views about laws of nature?  I know not, but Georges Cuvier gave a scathing 'eulogy' upon Lamarck's death, a bitter attack that poisoned posterity about Lamarck's reputation, and Cuvier notes of Lamarck "He had meditated on the general laws of physics and chemistry, on the phenomena of the atmosphere, on those of living bodies, and on the origin of the globe and its revolutions."  If accurate, Lamarck shared the prevailing idea of laws of Nature with Darwin.  Yet, when it came to life, Lamarck in his book said something very cogent, that Darwin and his intellectual descendants seem not fully to realize, even to this day: 

"In dealing with nature, nothing is more dangerous than generalizations, which are nearly always founded on isolated cases: nature varies her methods so greatly that it is difficult to set bounds to them."

Lamarck wrote this basically before the widespread development of statistical thinking, but it is a fact that has still not yet been absorbed by most biologists in evolutionary or biomedical genetics. Lamarck said that when the environment changes, that change in turn induces responses in behavior of organisms. His theory was about the consequent importance of (1) habit, (2) the use and disuse of traits, (3) the inheritance of acquired characters, and (4) the very slow process of adaptive evolution. 

As Lamarck described things, organisms have ways of life that depend on their circumstances.  They seek out resources, like food, that they are able to find, and the resulting 'habits' are essentially their ways of life.  Traits that are used seem to become more important over time but traits that are not used seem to wither or disappear.  Traits acquired during life are passed down to descendants.  The process is very slow, almost unimaginably so.

None of this seems to be at all forced, invented, or strange, and in fact, Darwin adopted all of these ideas in his own way.  As noted above, the idea that one's characteristics were controlled by some sort of transmitted substance is ancient, and the idea of evolution of species was hypothesized in classical times and here and there after that.

[If you are skeptical of our take on this, given Lamarck's clown-like image (due in large part to Darwin and his pals and Cuvier), that would not be surprising.  But that image is wrong, as you can see if you check his book itself and the Introductions by two highly respected evolutionary scholars (the 1984 U of Chicago Press English translation of Lamarck's Zoological Philosophy itself with very informative introductions by Hull and Burkhardt.), or Stephen Jay Gould's The Structure of Evolutionary Theory, or Ernst Mayr's The Growth of Biological Thought.]

So, what was so laughable about Lamarck?

Lamarck is routinely sneered at because, among other things, Darwin and his colleagues were motivated essentially to claim more credit for evolutionary ideas (I'm not the first to suggest this). Lamarck was a human with all the associated failings, but his work is derided because he suggested that the very striving or habits of life caused the associated heritable changes.  By contrast, the Darwinian idea is that new variation arises randomly relative to any need it might or might not have (one can debate how clearly Darwin understood or held such a view).  

However, Lamarck was trying to explain the same phenomena as Darwin, and to do so in terms of natural, historical evolutionary processes, rather than individual events of divine creation.

In our two previous posts in this series we basically took the Darwinian view, that Lamarck was laughable and any attempt to say that epigenetic inheritance was Lamarckian was equally wrong, trying too hard to challenge standard evolutionary theory. In fact, one can argue that epigenetic inheritance really is Lamarckian, based on what he actually said rather than what Darwin said about him, and adjusting for what was known in Lamarck's time.

(1) Habit: How do epigenetic changes arise?  
They arise because of the conditions and behavior of the organism: where they live, what they eat, stresses they are exposed, etc., and how their bodies respond to those exposures.  That is, they are the effects of the habits, as one could say, of the organisms.

And such changes are obviously adaptive if they allow the organism to persist and reproduce! If epigenetic changes are important and persist, over time they will be built into the characteristics of the species. Indeed, there are means by which such traits can eventually be built into the genome in the usual DNA-sequence way (one term for this is 'genetic assimilation').  Over time, nothing strange need be involved for epigenetic changes to be wholly compatible with our understanding of evolution.

(2) What about use and disuse?
In modern theory, 'disuse' means that eventually mutational or gene-expression changes (even if due to epigenetic mechanisms) lead a function or a gene to become more degenerate--as Darwinians would say, because there's no selection pressure to maintain it or even because it's costly if not useful and selection will favor its disappearance. And 'use', of course, would mean of adaptive value.  All perfectly compatible with Darwin (and part of his own theory).

(3) What is epigenetic inheritance?  
When and/or if it occurs, it is the modification of DNA (or the contents of cells) that arises in gametes (sperm or egg) during a parent's life and is transmitted to offspring.  The modifications of interest affect gene usage and hence the traits of the organism.  That is, this is the inheritance of acquired characteristics.

(4) What about the pace of evolution?
As to time, Lamarck was every bit as clear about the slow, gradual nature of evolution.  Both stressed this, recognizing the need to avoid creationist explanations.

So many of Lamarck's basic  ideas were similar to Darwin's (again, historians, not just I, have pointed this out).  What matters is not what someone said 200 years ago.  Instead, the bottom line is that if transgenerational inheritance by way of epigenetic changes acquired during life occurs and is functionally relevant, it is basically Lamarckian, but is also just a different form of 'mutation'.  And the differential proliferation of successful inherited traits, however acquired, will be a natural form of selection.

In that sense, it is Lamarck who is being misrepresented, and whose work in this context, given his context, is not risible.  It doesn't make Lamarckism entirely 'true'; there are wildly wrong things in Lamarck (but also in Darwin).  Cuvier, himself grossly wrong about life in many ways, cruelly portrayed Lamarck as a real nut case.  Despite Lamarck's sometimes free-wheeling ideas, that is not the judgment of history, and in any case, based on what Lamarck wrote in regard to the issues here, if epigenetic inheritance does turn out to have long-term relevance, which is not yet the case in terms of current evidence, it does not in any serious way undermine Darwin. What it does do, is to undermine ideological Darwinism.  And that is a very good thing for science.

The anti-Lamarckian gut reaction: keep the bar high--but your minds open

Biologists tend to ridicule Jean-Baptiste Lamarck for his version of evolution, expressed in his 1809 Philosophie Zoologique.  Laughing at him is one of our favorite sports.  Of course most of those who do the laughing never bothered to do any actual reading of Lamarck's famous book, but who's gonna sweat the details?

So what was it that he said, and why was it so risible?

Larmarckian Inheritance

Jean Baptiste de Lamarck

About 50 years before Darwin's famous theory was published, Lamarck explained the diversity of complex organisms by what we term the inheritance of acquired characteristics.  In his theory, traits that were used by an organism were transmitted to its offspring, and traits that were not used were not transmitted.  Very gradually, organisms would develop, refine, and elaborate useful traits.  Lamarck may have been wrong but not entirely so, given the data and attitudes of the time, and he was seeking a material explanation for biological complexity and its origins.  Good overviews can be found in the prefatory material to the 1984 English translation of Philosophie Zoologique published by the University of Chicago, and by SJ Gould's 2002 The Structure of Evolutionary Theory.  Other authors seem typically more derogatory and pejorative and less clearly acknowledging what Lamarck actually said.

The point is not to defend Lamarck, but to see why his views evoke such gut negative reactions.  The modern purely materialist theory of evolution (largely of Anglo-American origin) stresses randomness of inherited change due to external forces of mutation, and the brutal screening by natural selection to favor those genotypes that confer advantageous traits on their bearers.  Self-satisfied in what really is somewhat our own arrogant dogma (see our series on the mythology of natural selection, which begins on Monday of next week), we brook not even the slightest breach in our own dogma.  Still, in the way he tried to explain things, Lamarck does seem to have been mistaken, and his ideas (which were in the air at the time) in a way set the table for a better kind of material explanation for evolution and the traits of organisms, due to Darwin, Wallace, and a few others who ventured correct partial statements of things.

Lamarck's idea was that what organisms do during their lives, in response to the challenges of their environment, is somehow materially transmitted to their offspring.  This is an inner rather than outer source for the variation: systematic habit-induced physical change rather than externally screened random variation.  It didn't help Lamarck that the Soviet era genetics tried to appropriate Lamarckian rather than Darwinian evolution for various ideological and sociopolitical reasons, nor that some of Lamarck's contemporary rivals denigrated him, nor that Darwin found basic holes in the idea (despite holding a very similar theory of inheritance). 

Our point here is that there are some very good reasons based on 19th and 20th century biology, to hold the view that Lamarck's mechanisms don't hold much water, and this is why when one argues for anything that might seem even the slightest bit Lamarckian, the ridicule begins and the burden of proof is raised to a much higher level than when biologists venture their routine Just-So stories about how the elephant got his baggy skin.

What we do know
One thing we know very well is that gene usage does involve experience-based feedback onto cells' genomes. Cells use a subset of their genomes, and which subset is dictated by their context--by aspects of the cell's local environment.  Indeed, cells are loaded with environment-sensor (like receptor molecules) that monitor the world outside the cell and adjust gene expression accordingly.  This is clear, experience-based modification of the genome.  Of course, the modification is epigenetic:  it is not a change of the code book (the DNA sequence) itself and that is the key.  It is a change in the DNA molecule that affects how it's used, but not the sequence-based code.  To oversimplify, it is the binding of a molecule to a specific sequence-based bit of DNA near a gene that affects whether that gene is used by the cell at that time. When circumstances change, the molecule may leave the DNA, changing whether the gene is used or not.  Because the molecule binds to specific DNA sequence, epigenetic change does involve DNA sequence, but doesn't change it.

Second, in many if not most multicellular organisms the experiences of life affect its body tissues.  If a vertebrate does hard work, its muscles and joints may gain improved strength--something all of us know very well.    But if cell structures are produced by genetically coded molecules, the code itself isn't changed by the experience.  More importantly, an entirely separate line of cells, the germ line (sperm, eggs, pollen, etc.) is separated from the rest of the body's cells early in development.  Pumping iron may pump up your pecs, but it doesn't alter the relevant genes in your germ cells.  Even if it would be a good thing, the basic idea for over a century, supported by lots of evidence, has been that there is no way for a (say) muscle-specific genetic change to be built into the genome of a muscle cell, much less into a germ cell.

Instead, if pumping iron is good for your reproductive success, then those who by good mutational luck carry muscle-related genetic variants will reproduce better, passing the screen of natural selection and proliferating their good genes into the future.

Arnold Schwarzenegger in Pumping Iron; Wikimedia

The problem with a Lamarckian genetic alternative would be that pumping iron selectively mutates the muscle-related gene and when it turns out to be useful then engineers that same mutation in his germ cells. There is no known mechanism by which a specific mutation in a specific useful gene can be engineered into a germ cell, just because it happened to be useful in a muscle cell.  If it exists it will have transformative effect on biology, and that is why the standard of proof is so high, and skepticism so great against anything that seems like such a claim.

In fact, there are many examples in the literature of trans-generational transmission of epigenetic states. Each has been blasted and for essentially this reason:  biologists are generally not willing to open a breach in their Darwinian selectionist firewall.  Since anything truly Lamarckian could threaten the most solid bits of biological-evolutionary theory, it is entirely appropriate that a high bar and burden of proof be maintained.  But if it's true, it really is no threat to the state of the world; it's just knowledge of a new mechanism for at least short-term adaptability of complex species. In fact, it was anticipated way back into the late 19th century.

Current contentious examples

We write this because a report has just appeared in Science that claims something that seems like Lamarckian inheritance.  In this example, a starvation induced in laboratory mice when they were pregnant led to an epigenetic change in various genes that, the authors say, led to risk of diabetes, and that risk also was characteristic of the next generation, the grandchildren, even though their mothers were not subject to starvation. As described in a commentary in 10 July Nature, the experiment is in effect a test of the aftermath of a winter of starvation in Denmark in 1944-45.  Children conceived during this time were born underweight, and experienced health problems which their children, too, seemed to go on to experience.  

This report was just the most recent of several related to claimed epigenetic transmission of chronic disease-related traits that have appeared.  An even eerier recent report claimed that male mice exposed to fear-stimulus in the presence of a specific odor, were conditioned to hyper-express an odor-receptor gene that detected that order, but then this same gene was marked for over-expression in their offspring, and their grand-offspring, even though there was no further fear-conditioning.  (We blogged about this here.)  Gene expression induced by experience in the nose and then the same gene primed in sperm cells to be expressed in the males' offspring--and maintained in the sperm-line for a third, grandchild, generations?  Are you kidding?  

And there are other reports of similar multigenerational epigenetic transmission, some of them in controlled experimental settings like these examples.

The key reason for the strong skepticism at reports like these is that a specific gene in a germ cell line, a cell not directly affected by the environmental factor, is modified by that experience and the modification is then transmitted.  This might not seem like a problem, except that, genome-wide, the epigenetic state is generally highly programed for embryonic development, with sperm and egg genomes are subjected to heavy genome-wide epigenetic reprogramming before conception.

The idea that an experience-based epigenetic responsive state can get into the germ line and be transmitted for several generations is a threat to a Darwinian dogmatist--emotionally, it's like trying to get a biblical literalist to accept that Genesis might be at least a bit metaphoric.

Science is about learning new things
But we shouldn’t just defend dogma by being dogmatic!  There really shouldn't be any problem at all with this kind of multi-generational transmission--if it's true.  If it is, then we just have learned of a new mechanism of adaptability by organisms by which they change their biological state to reflect their circumstances (like shivering when it's cold, or an adrenalin rush when frightened).  Somehow, the body would know which gene was modified epigenetically by experience, and finds that same spot in the genome of a sperm or egg cell and makes the same modification.  That this could be transmitted to future generations could be a fine adaptive mechanism because circumstances might not change, and organisms would be epigenetically prepared from birth to meet them.  If true or shown somehow to be general, we'll all say that this is a marvelous aspect of evolutionary adaptation, and how could we have missed it!  

One can conjure up various ways this might happen….except for the minor detail that we don’t actually know of any such mechanism!  That doesn’t mean it can’t exist but it’s proper that one must find it before the results will be accepted.  Still, the more results of this sort that are reported, the harder should be the search for something that a century of work suggested didn’t exist.  Can all these reports be wrong?  If not…..what can make them true?  If so, are they wrong for some murky methodological artifact?  At some point, sneering should stop and hard work to find the mechanism should start.

We've tried to outline what the controversy is and why it is reasonable to be very skeptical of these reports, that seem so 'Lamarckian' even if we take into account that he was writing, or guessing, based on the state of knowledge 200 years ago.  If indefinite proliferation of an epigenetic change is ever proven, then it will show that this sort of inheritance, even if not affecting DNA sequence directly, is a part of evolution. It won't be exactly Lamarckian, but it won't be exactly Darwinian either.  It will be a remarkable revelation whose discovery we'll celebrate.

But if it's warranted that we give these reports a very hard look, that should not require that we cling to a cartoonesque oversimplification of the current dogma, that everything about everything is the result of Darwinian style competitive natural selection.  And with this comment, we'll return to writing our series about selection and the origin and genetic basis of complex traits.