Epigenetics as a Bridge Between the Natural and the Social Sciences?

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by Shea Robison (@EpigeneticsGuy)

As I say in the introductory page of this blog, my interest in epigenetics is both in the science but also in the historical, political and philosophical aspects of epigenetics. However, while the science is already extensively discussed and debated in academic journals and the blogosphere, these other more political and philosophical implications of epigenetics are not yet being addressed to the extent they warrant given the scope of epigenetics. As discussed below, epigenetics provides a unique bridge between the natural and the social sciences for unprecedented levels of interdisciplinary cooperation. As I say in the tagline to this blog, I am setting up this blog as a place to conduct these next-level discussions.

Luckily, I am not alone in recognizing the need for such discussions. Randy Jirtle, one of the most prominent epigeneticists working today, also recognizes this bridging capacity of epigenetics.

In this video Q&A, Jirtle notes the expansive reach of epigenetics and its ability to unify the natural and life sciences, observing that “the umbrella of epigenetics basically covers in effect every biological field we have – every one of them,” and that “epigenetics isn’t simply influencing the way we study biology—it is in fact becoming biology. That is the beauty of epigenetics. It is inseparable from the study of life.” Jirtle concludes the video with his prediction that “at some point, we will not even really have a field of epigenetics because you will not be able to do biological research without doing this, so it might not even have a name any more; its just biological research.”

In this Q&A with Jirtle posted by Nancy Barrand of the Robert Wood Johnson Foundation, Jirtle also remarks upon the explosion of interest in epigenetics in the sciences (a topic I have also addressed in this post and this post), observing that “the field of epigenetics is growing exponentially with the number of papers published in this field doubling about every three years—a rate that is three times that for science in general.” Jirtle locates the impetus for this exponential growth of interest in epigenetics in its inclusive nature as “increasing numbers of scientists from other disciplines, such as epidemiology, neurobiology, psychiatry, psychology, and the social sciences, are realizing the critical importance of environmental epigenomics in human health and disease,” and that as a result “over 12,000 papers were published this past year in epigenetics, many of which described the social and behavioral aspects of epigenetic programming.”

What do you think: Is epigenetics capable of unifying the biological sciences and the social sciences? If so, what would it take? If not, why not? In this post, I compare the publication rate of articles on epigenetics in the sciences and academia with the rate of exposure in the mass media and observe a significant lag. What will it take for awareness of epigenetics to crossover from the sciences to the general public? Finally, to paraphrase Karl Marx, does epigenetics contain the seeds of its own destruction in that eventually the field of epigenetics itself will disappear and become the backbone of the biological sciences?

I am curious to hear what you think. Leave your comments below and I will respond.

Also, if you find these thoughts I’ve shared interesting and worthwhile, Like this post, Reblog it, or Tweet about it using the buttons below.

Epigenetics Before Epigenetics was Cool?

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by Shea Robison (@EpigeneticsGuy)

I recently came across this blog post about this recent article on the discovery of epigenetic alterations in infants delivered through C-sections, and it reminded me of an anthropology class I took as an undergrad. One of the books for the course was Molded in the Image of Changing Woman: Navajo Views on the Human Body and Personhood. This book mentioned that the Navajo believe what both mothers and fathers experience before conception and what the mother experiences during gestation has a physical impact on the development of the baby, especially during critical moments in development.

For example, “the Navajo cultural system dictates that particular parts of the human body…are more susceptible to effect than others, and that the human body is more open to effect at critical times in the life cycle – for example, at birth, at puberty and during pregnancy. Knowledge is evoked by such occasions, as well as by illness or accident, at which times knowledge is transferred” (32).

“Precautions must be taken by all Navajo of childbearing age to prevent exposure to death or events of a traumatic nature. Such exposure can negatively affect the mother during delivery or the child before or after birth, or even prior to conception” (125).

“Illness can also result from a parent’s unavoidable exposure to a dangerous situation, as is illustrated [in the following account]. In this case, harmful effect was transferred to a child through her father’s sperm.” In the account, a contemporary Navajo woman describes a conversation with her mother in which she is explaining fetal alcohol syndrome and other effects of drug use on fetal development, and the mother said “Well, of course! That is the reason you had to have a Squaw Dance, was because when your father was away in Kansas on the railroad, you know, he saw an accident…where a white man was killed right in front of his face. And he came back and made love and created you, and so that particular traumatic experience affected every part of him, even his sperm” (126).

At the time I thought this was just an interesting anthropological observation, but an example of some of the far-fetched things ‘primitive’ people believe (boy, they clearly don’t understand how cause and effect works, huh?). However, later I encountered these same kinds of references to critical developmental windows,the effects on fetal development of the environmental conditions and stressors of both mothers and fathers and even grandparents, the transgenerational transmission of these effects, and so on, as prominent features in the emerging research in epigenetics.

I also recently encountered a blog post by epigenetics researcher Ben Laufer appropriately titled The Haunting of Fearful Memories Across Generations that discusses just these kinds of issues, including links to other articles on the transgenerational transmission of the effects from environmental conditions, including stress. I also appreciate how other researchers in recent papers on epigenetics can say things like “when food is scarce, children may be born ‘pre-programmed’ to cope with undernourishment,” and how “from an evolutionary point of view [transient transgenerational inheritance] makes sense. Our environment changes and we can move from famine to feast, so our bodies need to be able to adapt,” as if these are surprising and novel insights – which they are in the dogmatic context provided by modern genetics – but that traditional Navajo would say “Well,  of course!”  In other words, I could cite any number of articles of cutting edge research in epigenetics published in prominent scientific journals, which when rephrased in the appropriate vernacular would be accepted as common knowledge by traditional Navajo. Fascinating.

This juxtaposition of the cutting edge of research in contemporary genetics and the life sciences with ancient indigenous beliefs is extraordinarily compelling to me, and fuels my enduring interest in not only the science of epigenetics, but also the history and the philosophy behind it.

So what do you think? I try and steer away from the ‘New Age’ interpretations of epigenetics as much as I can, but do you know of any other similar examples of ancient indigenous knowledge coinciding with ‘new’ scientific results from epigenetics? What do you think of these coincidences? What do they say about contemporary science?

I am curious to hear what you think. Leave your comments below and I will respond.

Also, if you find these thoughts I’ve shared interesting and worthwhile, Like this post, Reblog it, or Tweet about it using the buttons below.

Epigenetics in the Media versus Academia

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by Shea Robison (@EpigeneticsGuy)

In a previous post I looked at the publication rates of articles on epigenetics in Science magazine. I picked Science as a measure of the exposure of the science-informed public to epigenetics. The take-home point from that post is that attention to epigenetics by this segment of the population is increasing at an increasing rate.

However, there are other sources to consider as well in gauging the attention to and acceptance of epigenetics.

In terms of assessing the spread of epigenetics within the scientific, medical and academic literatures, I searched two major databases: PubMed and Academic Search Complete.

The PubMed database, sponsored by the National Center for Biotechnology Information, contains references to over 24 million citations from the biomedical literature, including life sciences journals. When it is searched for the term “epigenetic” the following results are returned:

PubMedEpi
Figure 1

As can be seen, for the first thirty of the last fifty years the presence of articles referring to epigenetics was practically nonexistent in this literature. Through the mid-1990s and into the 2000s the number of epigenetics-based articles began to grow gradually and then precipitously, exceeding 1,000 for the first time in 2005, then doubling by 2008, doubling again by 2010 and then topping over 5,000 by 2013. This is by any measure a significant increase, especially in the rate at which it has occurred.

While PubMed focuses on the medical and life sciences, the Academic Search Complete database is “the World’s Most Comprehensive, Scholarly Full-Text Database for Multidisciplinary Research.” Thus, the number of epigenetics-based publications returned from a search of this database is indicative of the broader level of attention of the topic of epigenetics in academia, likely including most of the articles from the PubMed search.

Figure 2
Figure 2

The rate of publication of epigenetics articles in academics more generally mirrors that for epigenetics articles in the life sciences in particular. Again, by any measure these are significant increases in the rate of publication, indicative of a commensurate increase in the attention being devoted to epigenetics.

An interesting comparison, though, is comparing the rates of publication in scientific and academic journals with publication rates in other more popular-focused sources: The increasing rate of publication of epigenetics articles in Science magazine is similar to the exponential rates of publications in PubMed and the ASC databases, though not as dramatic or extreme. This difference in publication rates suggests that the high level of interest in epigenetics in academia is just now crossing over into the awareness of the informed public.

Figure 3
Figure 3

An additional and even more revealing point of comparison is with the rate of publication of epigenetics articles in the mass media. The source for this comparison will be the New York Times (NYT).

While the NYT not as good an indicator of the general public perception of an issue as a national survey, it is at least an excellent source for tracking how an issue is framed by and for elites, and how an issue is presented to the general public.[1]  Also, the NYT is the number two newspaper in the United States in terms of weekday circulation and is also one of only three newspapers with a national instead of a local or regional readership, therefore it is a reasonable proxy measure for public attention at the national level.

Figure 4
Figure 4

Contrary to the academic and scientific sources, there was no mention of epigenetics in the NYT, before 1983. Still, per the pattern established by searches in these other sources, epigenetics received practically no mainstream public attention until the 1990s, and then suddenly took off in the 2000s. One major difference is that while there is a significant increase in the late 2000s, there is not the precipitous climb to a peak; another major difference is in the magnitude of the numbers of articles – instead of thousands or even hundreds of articles, the number of articles on epigenetics per year in the NYT has just barely hit double digits.

Thus, while there is evidence of an increasing awareness of epigenetics by the general public, it is nowhere near the level of attention given to epigenetics in the sciences and academia. There is an extensive literature on the lag between scientific research, public awareness, and the eventual incorporation of that research into policy.[2] This literature suggests that given the vector of attention given to epigenetics in the sciences and academia, the pressure will build and eventually at some point epigenetics will spillover into public awareness and become a significant factor in policy discussions. How long this will take is difficult to predict, as is to what use the causal narratives of epigenetics will be utilized. The analysis of these emerging narratives of epigenetics is the core of my dissertation, and will be a significant focus of this blog.

For now, though, the main question is how long will it take for the significant attention given to epigenetics in the sciences and academia to spillover into the popular awareness? What do you think it will take for epigenetics to become general knowledge? Is such a thing even possible?

I am curious to hear what you think. Leave your comments below and I will respond.

Also, if you find these thoughts I’ve shared interesting and worthwhile, Like this post, Reblog it, or Tweet about it using the buttons below.

[1] Lawrence, R. G. (2004). Framing Obesity The Evolution of News Discourse on a Public Health Issue. The Harvard International Journal of Press/Politics, 9(3), 56-75.

[2] Guthrie, S., Pollitt, A., Hanney, S., & Grant, J. (2014). “Investigating time lags and attribution in the translation of cancer research: A case study approach.” Retrieved June 27, 2014, from http://www.rand.org/pubs/research_reports/RR627.html; Bradshaw, G. A. and J. G. Borchers. (2000) “Uncertainty as information: narrowing the science-policy gap.” Conservation Ecology 4(1): 7. [online] URL: http://www.consecol.org/vol4/iss1/art7/; Abbasi, D. R. (2006). Americans and climate change: closing the gap between science and education : a synthesis of insights and recommendations from the 2005 Yale F & ES Conference on Climate Change. New Haven, CT: Yale School of Forestry & Environmental Studies; Leshner, A. I. (1997). Addiction is a brain disease, and it matters. Science,278(5335), 45-47; Wynne, B. (1992). Misunderstood misunderstanding: Social identities and public uptake of science. Public understanding of science, 1(3), 281-304; Locke, S. (1999). Golem science and the public understanding of science: from deficit to dilemma. Public Understanding of Science, 8(2), 75-92; Yearley, S. (1999). Computer Models and the Public’s Understanding of Science: A Case-Study Analysis. Social Studies of Science 29(6), 845-866; Locke, S. (2002). The public understanding of science—A rhetorical invention. Science, Technology & Human Values 27(1), 87-111.

The EPA and Epigenetics: Baby Steps or Going Nowhere?

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by Shea Robison (@EpigeneticsGuy)

Epigenetics research in both animal and human studies has identified a number of environmental factors – from maternal behavior to levels of physical exercise to food types and availability to the presence of certain endocrine disrupting chemicals – which can alter epigenetic patterns, sometimes in ways which can be effectively transmitted to subsequent generations without these future generations being physically exposed to the original trigger of the epigenetic change.

That there are specific environmental and behavioral factors which can produce such significant changes in gene expression in the present, and which can now be linked to such far-reaching transgenerational effects in the future,[1] presents a significant collective action problem similar to problems such as air and water pollution, or global climate change.  As resolving or mediating collective action problems is perceived as one of the primary functions of government, the collective action problem of transgenerational epigenetic inheritance recommends a significant role for government in the regulation of such factors.

There are a number of existing regulatory structures and statutes already in place that could be used to address these epigenetic effects.  At the federal level, the Environmental Protection Agency (EPA) and the Food and Drug Administration (FDA) are two of the more prominent entities that would have significant oversight of regulation for epigenetic purposes, but so also could the Department of Agriculture, the Department of the Interior – and really any agencies dealing with the food supply or the environment.  A very short list of federal regulatory vehicles which could be modified to account for these epigenetic effects would be the Clean Air Act (CAA), the Clean Water Act (CWA), the Toxic Substances Control Act (TCSA), and the Federal Insecticide, Fungicide and Rodenticide Act (FIFRA). However, these existing acts of legislation as currently constituted require significant reworking to properly address these epigenetic effects.  The discussion of what are some of these issues with existing legislation, and what are potential ways to incorporate epigenetics into existing policy or for drafting all-new epigenetic-centered legislation is one of the main purposes of this blog.

In particular, in an extensive legal and ethical analysis of the implications of epigenetics, Rothestein et al. have identified the FIFRA as amended by the 1996 Food Quality Protection Act (FQPA) as the federal statute most likely to first incorporate epigenetic data into risk assessments and regulatory decisions.[2]  This is because the amended FIFRA is the only federal environmental statute that requires pre-market safety testing and approval of chemical products which must pass through a battery of approximately 100 toxicological assays conducted by the EPA (although it bears mentioning at this point, though, that none of these assays currently evaluates for epigenetic effects).  In addition, the FQPA amendments also require the EPA to develop a program for testing for endocrine disruptors in pesticides.  Given the importance of epigenetics in the functioning of the endocrine system, this aspect of the FIFRA is particularly a propos in the context of the policy emphasis of this blog.  Finally, the FQPA also requires the EPA to apply an extra ten-fold safety factor in regards to children which, given the importance of the critical epigenetic developmental windows, is also an especially applicable provision.

However, the EPA has yet to implement any of these provisions or to produce any formal recommendations for epigenetics-based policies.  A 2010 article in the New York Times discusses EPA efforts to address the growing evidence of the epigenetic effects of exposure to chemical pollutants common in contemporary society.[3] In this article, the senior research fellow in drug safety research and development at Pfizer Inc. observes that “the mix of chemicals a fetus is exposed to has exploded in the past 200 years, heralded by the Industrial Revolution,” and that “technology has outstripped evolution.” As a result of the growing body of research in epigenetics which demonstrates both immediate and transgenerational epigenetic effects of this modern cocktail of chemicals on humans, EPA regulators met with scientists to discuss how to design regulations based on these findings, but again no formal recommendations of policies have been produced.

In 2009 the EPA did begin an Epigenetics Project with the objective to closely study DNA methylation, which the official EPA documentation refers to as “the most common type of epigenetic modification [which] plays an important role in cancer, aging, neurodevelopment, and fertility.”[4]  As of 2014, this project has produced six journal articles and twelve publications on the impacts of DNA methylation, but as of yet no concrete policies based on epigenetics have resulted from this research. This project is also set to expire in October of 2014.

However, there are some very good logisitical reasons for this seeming lack of action. For one, the process for assessing the toxicity of chemicals and for recommending policies for legislation is a long and multi-faceted one which already faces a significant backlog of conventional analyses even before epigenetic concerns are taken into account. According to the article in the New York Times mentioned before, in 2010 the EPA already had a backlog of 478 chemicals in need of an environmental health assessment. The process for conducting such assessments involves the careful review both within and outside of EPA of the impact of the chemical, as well as assessments of the legal and political feasibility of any new restrictions that the agency might impose on industry as a result of this assessment, generating a thousand-page risk assessment document called IRIS which can take years to complete

Given all the administrative and scientific and legal and political strictures the agency is faced with, progress of these assessments is slow. During the George W. Bush administration, the EPA was able to assess two chemicals a year; this number increased to nine per year under the Obama administration, which still leaves a significant backlog of chemicals yet to be assessed – and these are just assessments of the environmental effects of chemicals according to conventional standards. These number do not include the requests for assessment of the epigenetic effects, of which the science is compelling but still in many cases far from providing enough justification for policy.

As observes the author of the New York Times article, “given such a backlog for toxins that are harmful as demonstrated using traditional science, regulating based on epigenetic research is perhaps many years away.”

Even so, given the rapid increase in the weight of the evidence from epigenetics as to the toxic effects of these chemicals, especially when so many of these effects are transgenerational, what is the appropriate balance between caution and action? Is the fact that the current assessment processes are so mired in bureaucratic procedures a valid justification for not taking action? What can be changed in the EPA processes to facilitate epigenetics-based assessments? Should the current backlog be dealt with before epigenetics are considered?  Finally, what about the state of the science of epigenetics? What is the appropriate threshold of scientific proof before political action is deemed necessary?

I am curious to hear what you think. Leave your comments below and I will respond.

Also, if you find these thoughts I’ve shared interesting and worthwhile, Like this post, Reblog it, or Tweet about it using the buttons below.

[1] Jirtle, R. and Skinner, M. 2007. Environmental epigenomics and Disease Sucsceptibility. Nature Reviews Genetics 8; 253-262; Watson, R. and Goodman, J. 2002. Epigenetics and DNA Methylation Come of Age in Toxicology. Toxicological Science 67(1): 11-16.

[2] Rothstein, M. A., Cai, Y., & Marchant, G. E. 2009. The ghost in our genes: legal and ethical implications of epigenetics. Health matrix 19(1):1-62.

[3] Epigenetics Project | Research Project Database | NCER | ORD | US EPA. 2009.Epigenetics Project | Research Project Database | NCER | ORD | US EPA. Retrieved July 29, 2014, from http://cfpub.epa.gov/ncer_abstracts/index.

[4] Vaidyanathan, G. (2010, November 15). Prenatal Exposures Prompt EPA to Re-examine Chemical Regulations. New York Times.

Michael Skinner, Transgenerational Inheritance, and the Smithsonian

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by Shea Robison (@EpigeneticsGuy)

Short video clip of Michael Skinner from the Center for Reproductive Biology  at Washington State University and the Smithsonian Ingenuity Award for his work in transgenerational epigenetic inheritance.

Michael Skinner Smithsonian Ingenuity Award

Sums up the ‘threat’ to genetics posed by epigenetics.

Michael Skinner is also a co-author of the first Research Paper of the Week.

From @laufer_ben

Epigenetics in Science magazine

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by Shea Robison (@EpigeneticsGuy)

Consider the number of articles on genetics published by Science over the past fifty years:

ScienceGen
Figure 1

The number of articles per year was relatively steady through the 1960s and 1970s, climbed steadily through the 1980s, and appears to have peaked in the mid ’90s.

Although comparing genetics and epigenetics is kind of like apples and oranges (or is it more like comparing oranges and tangelos?), consider the number of articles referring to epigenetics published by Science over this same period:

ScienceEpi
Figure 2

This graph is one indicator of the sudden increase of interest in epigenetics at least among the science-informed public. For almost forty years, the number of articles on epigenetics hardly ever exceeded 10 articles a year. Beginning in the 2000s this number doubles and then doubles again by 2010. Although the raw number of epigenetics articles is not that of genetics articles, that the publication of epigenetics articles in Science is increasing at an increasing rate is a good indicator of the increasing attention being given to epigenetics.

Another way to gauge the rise of interest in epigenetics  is to compare the attention given to epigenetics with that given to genetics. Again, comparing epigenetics with genetics is not a straightforward comparison: Epigenetics – while an addition to and often a correction of conventional genetics – is not in direct competition with genetics and is not a replacement for genetics; in many ways, epigenetics could be considered a subset of genetics. Still, epigenetics articles as a proportion of genetics articles is one good way to gauge the relative attention being given to epigenetics in the literature.

ScienceEpiPct
Figure 2

When the numbers of epigenetics articles are divided by the numbers of genetics articles, a distinct trend emerges. For forty years, the number of articles about epigenetics published by Science were hardly ever 5% of the number of articles published on genetics. From 2000, though, the percentage of epigenetics-themed articles relative to genetics articles has risen to over 15%, reaching over 20% in 2012.

Again, this is not conclusive evidence, but it is an illustrative demonstration of the vector of interest in epigenetics, which is rising at what appears to be an exponential rate.

At this point, i was curious about the history of the coverage of genetics in Science and how that compared to the trajectory of interest in epigenetics. Going back through the archives of Science, I looked to see if there was a thirty year period in which the publication rate of genetics matched the current publication rate of epigenetics. I found that the thirty years from 1923 to 1953 were the closest fit of the publication rate of articles on genetics compared to the publication rate of epigenetics articles during the period from 1983 to 2013:

ScienceGenEpi
Figure 4

The fit is not perfect (although the correlation between the two series is .63). From 1923 through the 1940s the number of articles on genetics were more or less steady at between 40 and 60 articles per year before shooting up to 80 articles in 1950, then over 90 in 1953, and hitting over 200 articles by 1960, at which point as Figure 1 shows the number of genetics articles begins its steady increase until its peak of 774 in 1996. In contrast, until the 2000s the numbers of epigenetics articles did not exceed 20, and then doubled within the next decade and then doubled again.

In the history of genetics, this thirty year period begins a few years after Morgan proposed his theory of sex-linked inheritance and just before the discovery that x-rays cause genetic mutations, and ends just as DNA is proved to be the molecule of heredity and Crick and Watson (and Franklin and Wilkins) establish the double helix shape of DNA. Identifying what are the corollary historical watershed discoveries for epigenetics – if there are any – is not the purview of this post; the purpose, rather, is to suggest a possible coincidence in the patterns of attention given to first genetics and now epigenetics in a respected source for popular science.

Whether the numbers of articles on epigenetics published in Science  after 2013 continues to increase as occurred with genetics after 1953 remains to be seen, but to the extent this pattern holds it is suggestive evidence that epigenetics may be at the same point in 2013 as was genetics in 1953, at the cusp of its flowering into what is known today as the contemporary discourse of genetics.

In this post, the publication rates of articles on epigenetics in additional sources—from academic and scientific sources to mass media—are charted and analyzed. Putting it all together, is epigenetics at the point now that genetics was in 1953, just after the discovery of the double helix and on the cusp of its explosion as a focus of academic and scientific research and its emergence into the public consciousness?

I am curious to hear what you think. Leave your comments below and I will respond.

Also, if you find these thoughts I’ve shared interesting and worthwhile, Like this post, Reblog it, or Tweet about it using the buttons below.

Stay tuned for similar posts about the coverage of epigenetics in both  the mass media and in academic journals.