The Political Implications of Epigenetics: Emerging Narratives and Ideologies

Robison, Shea K. “The political implications of epigenetics Emerging narratives and ideologies.” Politics & Life Sciences 35, no. 2 (2016): 30-53.

Copyright Cambridge University Press. Reprinted with permission.

Link to full text: The political implications of epigenetics

ABSTRACT

Background. Epigenetics, which is just beginning to attract public attention and policy discussion, challenges conventional understanding of gene-environment interaction and intergenerational inheritance and perhaps much more besides.

Question. Does epigenetics challenge modern political ideologies?

Methods. I analyzed the narratives of obesity and epigenetics recently published in the more liberal New York Times and the more conservative Wall Street Journal. For the years 2010 through 2014, 50 articles on obesity and 29 articles on epigenetics were identified, and elements in their causal narratives were quantitatively analyzed using a well-described narrative policy framework.

Findings. The narratives on obesity aligned with the two newspapers’ reputed ideologies. However, the narratives on epigenetics aligned with neither ideology but freely mixed liberal and conservative elements.

Discussion. This small study may serve as a starting point for broader studies of epigenetics as it comes to affect political ideologies and, in turn, public policies. The narrative mix reported here could yet prove vulnerable to ideological capture, or, more optimistically, could portend the emergence of a “third-way” narrative using epigenetics to question atomistic individualism and allowing for less divisiveness in public-health domains such as obesity.

Introduction

At present, the study of epigenetics is not yet on the radar of most policy makers. This article helps initiate the eventual policy discussion around epigenetics by identifying the emerging narratives of epigenetics–that is, the causal stories that are constructed from the science of epigenetics. In particular, this article assesses the reporting on epigenetics in two ideologically distinct news sources, the New York Times and the Wall Street Journal, to examine the effects of ideology on the emerging narratives of epigenetics and the potential effects of epigenetics on ideology.

More specifically, I determine whether reporting on epigenetics displays specific patterns or differences related to the ideological bent of the source of a particular narrative. In addition to providing a starting point for discussing the narratives of epigenetics, this analysis provides a first look at the potential ideological uses of epigenetics. Thus, this article establishes a useful baseline against which we can compare the policy narratives of epigenetics that will emerge as scientific debates about epigenetics cross over into public awareness and political discourse.

Epigenetics in politics and policy

If the scientific challenges of epigenetics are great, the political challenges are perhaps even greater. These political challenges come in a couple of different forms. First, the scientific identification of epigenetic causes of health effects has potential consequences for public health policies across many different domains. For this reason, policy analysts, policy makers, and others concerned with public policy should pay considerable attention to epigenetics.

Second, epigenetics-related public policy debates will involve profound aspects of political ideologies. As I will demonstrate, the identifications of novel causes and effects being realized in epigenetics research substantially complicates the foundational assumptions around which so much of our contemporary politics are organized, such as what defines an individual and how humans relate to their environment. In this way, the emergence of the science of epigenetics has the potential to force a fundamental reconfiguration of our politics to an extent not yet seen by the emergence of any other science, save perhaps the introduction of Darwinian evolution in the mid-19th century and the emergence of the modern science of genetics itself in the 1930s. As such, epigenetics could end up having more of an impact in politics than in science.

The true political implications of epigenetics

Although the main implications of epigenetics for policy stem from its complications of the conventional self-versus-environment dichotomies that characterize liberal-versus-conservative positions in contemporary policy domains such as obesity, epigenetics also has the potential to upend fundamental assumptions about human nature that have been the basis of prevailing conservative and liberal Western worldviews for at least the last 200 years. Specifically, the science of epigenetics introduces novel information about our relations with each other and with our environments that profoundly challenges the foundational modern Western concept of atomistic individualism, in which each person is regarded as a distinct and autonomous entity, ultimately separate from other people and from the environment.

This concept, which is espoused in Cartesianism, Lockeanism, Kantianism, and other philosophies, simply does not reflect the interconnectedness of humans with each other and with their environments, which may even span multiple generations, that is being revealed by the science of epigenetics. To the contrary, epigenetics shows the self, at least on a biological level, to be an inherently relational concept which is constituted through interaction with other people and the environment.

Even within the Western tradition, there are alternative philosophical frameworks that are not built upon an ontological commitment to atomistic individualism. For example, the ethics and political theory developed by the 17th-century Dutch philosopher Benedict Spinoza are premised upon a concept of the self as ultimately relational. At the same time, Spinoza’s system is also a product of the same intellectual and cultural history that produced other modern Western political theories. As such, the philosophy of Spinoza provides a potential bridge between atomistic individualism and the relationality of many non-Western traditions.

The concluding paragraph of this article is not the place to begin to formulate this new politics. Although this article is meant to initiate a discussion about what such a politics could or should look like via its descriptions of the science and the narratives of epigenetics, and their implications for policy, I recognize that whether such an alternate perspective will or could ever emerge in the West is an open question. However, this article does suggest that the ideological bases of our conventional policies and politics as currently conceived are ill-equipped to deal with the descriptions of our biological relationships with each other and with our environments now emerging from the science of epigenetics.

Link to full text: The political implications of epigenetics

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The Trans-ideological Potential of Epigenetics

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by Shea Robison (@EpigeneticsGuy)

As discussed repeatedly on this blog, epigenetics is a rapidly emerging field of research akin to genetics but with some substantial differences. In addition to the differences in the sciences of genetics and epigenetics—which differences are more a function of the ontological assumptions of each than the actual science—there are significant differences in the narratives of both. In the contexts of policy and politics, these differences in narratives are perhaps more salient than are the scientific differences.

In this context the “narratives” of epigenetics refers to the politically relevant interpretations of epigenetics which, while related to the science of epigenetics, are not the science itself but the political use of that science. As such, there are a number of aspects of the science of epigenetics which complicate the conventional ideological dichotomizations of conservativism versus liberalism around which are organized so much of our historical and contemporary politics[1]. For example, most of the policy solutions prescribed for obesity have their roots in either a conservative narrative of obesity which emphasizes personal responsibility, or a liberal narrative of obesity which emphasizes the overriding causal influence of the environment [2]. The opposition of these ideologies in obesity policy narratives is reflected across a wide swath of policy domains. These ideological orientations are generally assumed to be diametrically if not fundamentally opposed.

The science of epigenetics, though, contains elements of both dispositional and environmental influences at once. Thus, both conservative and liberal narratives can both be constructed simultaneously from the science of epigenetics. At this early stage in the emergence of both the science and the narratives of epigenetics there are two potential routes for the policy narrative use of the science of epigenetics: Either those aspects of epigenetics which are conducive to the different ideologies will be emphasized, resulting in mutually exclusive conservative and a liberal narrative of epigenetics, or that by complicating or combining these longstanding ideological orientations epigenetics will actually provide a ‘third-way’ for the ascription of causes for highly politicized issues such as obesity. In the former case, policy contests will be more or less business as usual with epigenetics as just one more arrow in the ideological quivers of opposing sides. The latter case, though, would open the way for unanticipated policies which are not beholden to either one of these currently predominant ideological poles. This complication of conventional ideologies resulting in unprecedented combinations of policy orientations would be just one indication of the true political impact of epigenetics.

Revealing the narratives

I conducted searches for articles on epigenetics in two major newspapers: the Wall Street Journal (WSJ) and the New York Times (NYT) to see how epigenetics is talked about, and whether there were these ideological differences in the narratives of epigenetics. These newspapers were selected for the level of circulation of both their print and digital editions, the scope of their readership, and their differences in ideological biases. These two posts are the number one and number two newspapers in the United States in terms of weekday circulation, and are also two of only three newspapers with a national instead of a local or regional readership[3].  As discussed by Lawrence (2004)[4], while these two posts are perhaps not as direct an indicator of the general public perception of an issue as a national survey, they are still excellent sources for tracking how an issue is framed by and for elites, and how an issue is presented to the general public.

Also, according to the analysis of Gentzkow and Shapiro (2010)[5], on a scale of user-based ratings of conservativeness—from 1 (liberal) to 5 (conservative)—the NYT (owned by the NYT Company) scores a 2 and the WSJ (owned by Rupert Murdoch’s News Corp) scores a 4. Each post is also located on opposite ends of the liberal-conservative slant index constructed by Gentzkow and Shapiro (2010). These differences in ideology are important for identifying possible differences in the composition of the epigenetic narratives from these sources.

When the epigenetics narratives—or the words used to describe epigenetics—in articles from both sources are compared with each other, a number of interesting patterns emerge (full results to be published in forthcoming paper). Again, a reasonable expectation is that the reporting on epigenetics in the NYT would emphasize those aspects of epigenetics which are congruent with a liberal emphasis on the causal influence of the environment, while the reporting on epigenetics in the WSJ would emphasize the personal and dispositional aspects of epigenetics. Instead, there are many instances in which the narratives from both sources share narrative elements, even to the point that the epigenetics narrative in the NYT demonstrates both liberal and prototypically conservative elements, just as the narrative of epigenetics from the WSJ also shows both conservative and liberal elements

The Trans-ideological potential of epigenetics

At the beginning of this post, two possibilities were offered for the emerging narratives of epigenetics. Because of the causal mechanisms revealed by the science of epigenetics which blur the conventional boundaries of our insides and our outsides and between the individual and their environment, epigenetics is capable of producing both conservative and liberal narratives. One possibility of this potential dualism is that each ideological orientation would just co-opt those aspects of epigenetics which fit its preconceptions. The other possibility is that epigenetics would compel a unique third way narrative which, while containing elements of both ideological narratives, is actually beholden to neither conventional ideology.

The preceding suggests the latter much more than the former. As discussed before, science-based policies are the result both science and narrative development. Science-based narratives do not reflect just the science but also an ideological interpretation of the science, just as science itself is a process of narrative formation often informed by ideology[6]. A valid question at this early stage is therefore which factor will have more influence on the other. Indications are that at this early stage the narratives of epigenetics are molding the existing ideological narratives and not vice versa.

Given the high level of attention devoted to epigenetics in the sciences, the incorporation of epigenetics into policies is only a matter of time. Although there are as yet no epigenetics-informed policies per se, this vector of influence suggests that when there are such policies they will be composed of both individual and environmental aspects and not isolated to either ideological orientation, regardless of the source. What these new policy prescriptions will be which result from this unique combination of the previously juxtaposed environmental and personal narratives remains to be seen, but the results just discussed suggest that the science and narratives of epigenetics promise potentially transformative possibilities for politics and policies which transcend the conventional ideological dichotomizations.

What do you think? Do the narratives of epigenetics provide a potential ‘third way’ for policy? Or is this just a result of the early formative stages of the narratives of epigenetics?  I am curious to hear your thoughts. 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] Conover, P. J., & Feldman, S. (1981). The origins and meaning of liberal/conservative self-identifications. American Journal of Political Science, 617-645; Huntington, S. P. (1957). Conservatism as an Ideology. American Political Science Review, 51(02), 454-473.

[2] Kersh R. 2009. “The politics of obesity: a current assessment and look ahead.” Millbank Quarterly 87(1):295–316; McBeth, M. K., Clemons, R. S., Husmann, M. A., Kusko, E., & Gaarden, A. (2013). The Social Construction of a Crisis: Policy Narratives and Contemporary US Obesity Policy. Risk, Hazards & Crisis in Public Policy, 4(3), 135-163; Niederdeppe, J., Robert, S. A., & Kindig, D. A. 2011. “Peer Reviewed: Qualitative Research About Attributions, Narratives, and Support for Obesity Policy, 2008.” Preventing chronic disease, 8(2).

[3] Alliance for Audited Media. 2015. “Research and Data.” http://www.auditedmedia.com/news/research-and-data/top-25-us-newspapers-for-march-2013.aspx (April 6, 2015).

[4] 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.

[5] Gentzkow, M., & Shapiro, J. M. (2010). What drives media slant? Evidence from US daily newspapers. Econometrica, 78(1), 35-71.

[6] Fuchs, H. U. (2015). From Stories to Scientific Models and Back: Narrative framing in modern macroscopic physics. International Journal of Science Education, (ahead-of-print), 1-24; Sheehan, R. J., & Rode, S. (1999). On Scientific Narrative Stories of Light by Newton and Einstein. Journal of Business and Technical Communication, 13(3), 336-358; Wise, M. N. (2011). Science as (historical) narrative. Erkenntnis, 75(3), 349-376.

“Understanding the Impact of Epigenetics” podcast

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by Shea Robison (@EpigeneticsGuy)

Understanding the Impact of Epigenetics podcast

Below are links to posts and papers I mention in this podcast about epigenetics and health that I participated in as a panel member hosted by the health and fitness website BreakingMuscle.com:

When it Comes to Epigenetics, How Much Fun is Too Much? Comment and Reply

Epigenetics By Any Other Name? What Epigenetics Should and Should Not Be

Epigenetics and Drug Discovery: The Missing Link?

Gene Sequence but not Structure? The Costs of Excluding Epigenetics from Genomics

Ben Laufer Comments on “Gene Sequence but not Structure”

Epigenetics Minority Report Part I: Epigenetics, blame, precrime and politics

All of these posts have many links to other posts on this blog and to external materials about epigenetics so click on these links for supplemental information. You can also navigate through the posts about the different topics I discuss on this blog using the pages in the header above or the Categories list located on the righthand margin of this blog.

Below is a link to a PowerPoint presentation in which I discuss the Agouti mice experiments and the longitudinal studies in humans that I mention in the podcast:

Agout Mice 2

Epigenetics PowerPoint

The link below is to the paper on the emerging narratives of epigenetics in regards to obesity that I reference in the podcast, which I presented at the 2014 annual conference of the Association of Politics and the Life Sciences:

The Emerging Obesity Policy Narratives of Epigenetics

I have also summarized a number of research papers on epigenetics. You can find these research summaries here:

Reasearch Summaries

Additional Information:

For a visual of how epigenetics work, you can watch this video from the University of Utah Genetic Science Learning Center.

Also, in this video:

a world class epigeneticist explains some of the mechanisms of epigenetics, as well as discusses some of the intriguing possibilities (video from the RWJF).

You’ve come this far, so I am curious about what brought you here. Read the posts that interest you, leave a comment or question, and let’s see what we can do.

Feel free to contact me at epigenetics.guy@gmail.com with any questions or comments.

Follow my epigenetics and policy themed Twitter feed @EpigeneticsGuy

When it Comes to Epigenetics, How Much Fun is Too Much? Comment and Reply

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by Shea Robison (@EpigeneticsGuy)

This post began as a simple reply to a comment from Alison M to this post about epigenetics and drug discovery, but suddenly bloomed into a full-fledged post of its own. Below is Alison M’s original comment in italics for purely aesthetic purposes, followed by my reply (and I think Alison is actually responding to more than one post here, including this one about epigenetics as a possible bridge between the sciences):

TBH, I don’t think that combining the fields [genomics and epigenetics], at least at this point, would be beneficial to either. Both are still in discovery, and the known mechanisms of action of genetics and epigenetics are different enough that they might not ever be appropriately combined. Epigenetics needs to be better presented, especially to the public, so that it doesn’t fall prey so much to magical thinkers – not only for the sake of understanding, but also so that its legitimacy can be embraced by other scientific fields.

In this, some researchers do themselves no favors. Even Dr. Jirtle has some articles on his site that present ideas that look more like speculation than hypotheses. These are good for getting attention, but what I see among laypeople as a result is the wrong kind of attention. Bruce-Lipton-level wrong kind of attention.

Thanks to Alison M for taking the time to post her comments.

First, I definitely appreciate her point about both fields still being in discovery mode, and how the known mechanisms of both genetics and epigenetics are possibly different enough to defy unification even in the future when they have both ‘matured’ so to speak. However, one of the questions I still have about this integration of epigenetics and genetics is ‘But why not?’ (How is that for an emotional/unscientific reply? Having said that, I think I have more than merely emotional responses to support this question)

In this post and this post I discuss the first divergence of epigenetics and genetics in the 1920s, which had both scientific and less-than-scientific components to it, and in this post and this post I discuss some of the political (i.e., non-scientific) reasons for the subsequent…stigmatization (for lack of a better word) of epigenetics until fairly recently. My question through all of these posts is what if these circumstances were different during these  pivotal times?

Just as biological evolution can take many different trajectories depending upon initial conditions and random events (e.g., killer asteroids, etc.), so can the evolution of science. Given the influence of these non-scientific influences just mentioned, it is easy to imagine alternative circumstances in which epigenetics and genetics evolved together at this relatively early stage of both their developments such that today there are no disciplinary boundaries between what we call genetics and epigenetics as Dr. Jirtle proposes. Forgive my philosophyspeak for a moment, but there are no “ontologically objective”[1] reasons that genetics and epigenetics are mutually distinct fields; in fact, there would seem to be more reasons for them being unified than being distinct fields. However, given the path dependent nature of both biological and scientific evolution as discussed here, because these fields diverged when and how they did, epigenetics now represents some pretty fundamental challenges to genetics in both methods and conclusions (e.g., transgenerational inheritance). Again, though, there is no objective reason this should be—all we know is that this is the case now.

Finally, I wholeheartedly support the suggestion that epigenetics needs to be presented better than it currently is. The core of my dissertation—soon to be made Flesh, so stay tuned—is discussion and analysis of the different narratives of epigenetics that are emerging in major media outlets. I have posted elsewhere about the impact of epigenetics in the sciences and academia relative to the mass media for public consumption, as well as about some of the current misconstruals and misinterpretations of epigenetics amongst the general public, precisely because such misconstruals bring the wrong kind of attention and distract from what epigenetics actually is and does. In my professional career—and personally, because I am just fascinated by this stuff—I am concerned with the political implications of epigenetics both in terms of policies based on epigenetics as well as the internal and external dynamics of the science of epigenetics. This is why I also think more rigorous and sound presentation of epigenetics within the scientific community and to the general public is critically important—though by no means does the careful use of terms and definitions guarantee anything, as we can all think of instances of the misappropriation of genetics despite the best efforts of geneticists, from the insipid use of genetics, such as “DNA Love Connection?”[2] to the truly scary uses, such as the eugenics movements of the early 20th century.

To this end, @EpiExperts and @EpgntxEinstein recently recommended a very cogent commentary in the form of a review of an incredibly interesting-looking book[3] on this issue of the recent popularization of epigenetics (not to mention the blog post which kicked this whole thing off). While the author of the article proposes a definition of epigenetics that is perhaps too restrictive for my tastes, I still appreciate the effort to rein in the ‘Bruce-Liptonizing’ of epigenetics as Alison M wrote in her comment (and no offense intended to Bruce Lipton, whom I do not know and who I assume is a wonderful and well-intentioned and sincere person).

In the end, although I appreciate the almost intoxicating excitement that comes from witnessing the emergence of a field of research like epigenetics, at this point more caution in the description, interpretation and popularization of epigenetics is probably better than less…but hopefully not so much caution that it takes all the fun out of it.

[1] By which is meant phenomena which are ‘observer-independent’ (from Searle, John R. The construction of social reality. Simon and Schuster, 1995: 9-10)

[2] Special thanks to @AlexisCarere for bringing this gold mine of an example of genetics gone awry to my attention

[3] Weissmann G. (2012) Epigenetics in the Age of Twitter. Bellevue Literery, New York, NY.

Gene Sequence but not Structure? The Costs of Excluding Epigenetics from Genomics

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by Shea Robison (@EpigeneticsGuy)

(Thanks for stopping by and reading this post. I’ve linked to a number of other resources in this post, so check those out as well. When you’re done, leave a comment and let me—and the others who read this post—know what you think. This post is attracting a lot of attention from around the world the past couple of days, so this post is a good opportunity to interact with others interested in genomic and epigenetics. Check out more of my posts on epigenetics through the menu at the top of this page and the lists on the righthand margin.)

by Shea Robison

A recent tweet from @dgmacarthur recommended an article from The Telegraph (UK) newspaper about “an investment of almost £300 million in Genomics England, a new initiative to read and decipher the genetic codes of 100,000 NHS patients.”

The author of this article supports this investment in genomics, but paradoxically opens the article with a personal account of the wildly disparate results of three different genetic tests he submitted a few years ago. He writes that “though each service examined the same DNA, and evaluated the same diseases, each set of results was dramatically different. My lifetime risk of glaucoma, an eye condition, was as low as 2 per cent or as high as 36 per cent, depending on which service I chose to believe. One company thought my chances of a heart attack were twice as high as another,” and that his experience was the sort of experience that “has fed a growing sense that the sequencing of the human genome…as the future of medicine, has failed to deliver on its promise.”

However, despite these disappointments, the balance of the article is about the practical benefits of genomics which justify such a significant investment. The author concedes that while genomics has not been successful in unlocking the genetic factors for most common diseases, “quite staggering progress” has been made for cancers, rare congenital diseases and infections. In particular, the author notes, genomics is benefiting those already sick – those who have certain kinds of tumor,families with congenital disorders, and the tracking of infectious diseases. According to the author, genomics does not yet allow for much prediction of illness or disease which could benefit the “worried well,” but its benefits in these other areas already justify further investment.

I don’t have any issue with anything the author has written; I assume he is correct about the shortcomings and benefits of genomics. My question, and how this relates to epigenetics, is ‘the dog that doesn’t bark’ – or what the author doesn’t mention.

As discussed in significant detail in this article, genomics relies on genome-wide association studies (GWASs) and genome-wide complex trait analyses (GCTAs) to identify the genetic components of traits and diseases. One of the primary problems with these efforts to locate the cause of diseases and really almost any traits in the genes is the complex nature of interactions between genes and between genes and the environment – encapsulated by what is called the “missing heritability problem” (e.g., traits like intelligence have been found to be highly heritable, but why have no genes for intelligence been identified? If there is such a strong hereditary component to such traits, it seems reasonable to assume identifying the genetic basis for these traits would be relatively straightforward).

GWASs and GCTAs may be able to identify specific genes and sequences of genes which are correlated with specific outcomes, but this seems like only one part of the equation. The problem with such approaches, the author observes is that “the simplistic model of additive genetic variance upon which GCTA relies (and which assumes no epistasis and no gene x environment interactions) is out of touch with current understanding of the complex, multifactorial nature of most human traits that have a genetic component.” This is where epigenetics obviously enters the picture.

In this article, though, the author refers to an aspect of genetics that is new to me as a confounding factor for GWASs and GCTAs, writing that “there is now overwhelming scientific evidence…that persons do not possess a single NUCLEAR genome [and] that the normal human condition is one of SOMATIC MOSAICISM.” Somatic mosaicism is when different cells and tissues contain different DNA sequences (or ‘genomes’), and appears to be particularly prevalent in the human brain. To the degree somatic mosaicism is legitimate, the results of a GWAS or GCTA from one part of the body will be different from a GWAS or GCTA from another part, and may not be generalizable even from within the same person. This is the first I have heard of such a thing, and I would have to investigate it much further, but the implications for genomics and for the assumptions of orthodox genetics of this somatic mosaicism are quite obvious.

Even so, this is not what initially prompted my interest about the implications for epigenetics from the article in the Telegraph: GWASs and GCTAs can identify sequences of genes, but this sequence is only one part of how genes function; another critical aspect of gene function pertains to its structure, and the role of chromatin and histones.

Chromatin are the end product of DNA being tightly wrapped around proteins called histones.  These chromatin are then also tightly wrapped together which bundling allows the meters of DNA to be packed into cell nuclei only 5 to 10um in diameter.  This tight bundling gives DNA its unique three-dimensional structure which also has a significant effect on genetic expression.

According to conventional genetics, what is determined by natural selection is the sequence of genes in DNA and their expression, both of which are for all practical purposes immutable; in other words, the sequences of genes in a tightly-packed segment of DNA are fixed, and then switched on or off in specific patterns to produce ostensibly more adaptive patterns of gene expression.

However, according to the research in epigenetics, sections of DNA can be acetylated causing the chromatin to relax and open up, exposing different gene sequences to methylation which can then change the pattern of on/off switches and the nature of the gene expression; this chromatin relaxation also changes the relative proximity of different genes and gene sequences which can also affect the pattern of expression – all without changing the actual DNA sequence in any way.[1]  Chromatin remodeling is an important step in cell growth and differentiation, and thus modifications of chromatin remodeling functions are associated with a number of cell-based diseases such as cancer,[2] and are also now associated with obesity.[3]

Those genes which are located on the outside of a bundle are the most accessible to processes like methylation, and thus are most susceptible to changes in suppression or expression; vice versa, those genes located inside a bundle are likewise shielded from changes in expression.  Also, the three-dimensional structure produced by the wrapping of chromatin places some genes adjacent to each other which are actually quite distant sequentially, which proximity also impacts the expression of these gene loci in ways which are not detectable using conventional gene sequencing.

A specific example of the effects of gene structure on expression is discussed in this paper[4], which establishes “the existence of a regulatory network between the INS [human insulin] gene and other distant genes through long-range physical interactions, and suggest that such networks may have general importance for insulin biology and diabetes.” As the authors of this study observe, “of necessity, chromatin is not linear in the nucleus, but compacted to fit into the small nuclear volume. However, packing is not random; rather, it is dynamically arranged into functional loops,” and that “these chromatin loops are usually established in a cell type-specific manner, through the formation of long-range chromatin interactions mediated by proteins bound at specific DNA regulatory elements (e.g. enhancers, promoters, insulators).” As shown in the figure below, depending on the structure of a loop these enhancers and promoters can either be in positions to interact or insulated from each other:

Chromatin

In other words, genes can be distant from each other in sequence, which distance seems to logically preclude any significant interaction; however, owing to the physical structure of DNA, genes which are sequentially distant can actually be close to each other in three-dimensional space, which then allows them to interact in ways which are not detectable using conventional sequencing. And this structure is determined and manipulable through epigenetic mechanisms.

This conclusion returns me to the original Telegraph article and the significant investment in genomics and its standard gene-sequencing methods: If both sequence and structure play such important roles in gene expression, it seems only reasonable that considerations of both be included in any attempts to diagnose or predict genetic effects; therefore, funding for epigenetics should likewise be included on a par with funding for genomics – otherwise, we are only getting at most half of the story (though more likely genomics gives at best a third of the story, as it excludes gene structure and environmental interactions via the epigenome).

It may be that genomics already accounts for these considerations of three-dimensional structure and chromatin remodeling and so on. I don’t know; I am a political scientist with a professional interest in genetics and an enthusiastic dilettante’s understanding. If these considerations are already accounted for within genomics, and accounted for properly, I would welcome some well-intentioned enlightenment from those who know better than I.

However, what I have observed from my outsider’s perspective is that many genomicists seem remarkably antagonistic towards epigenetics. Apart from legitimate questions about the scientific validity of many of the results from epigenetics, this unwarranted antagonism often seems a function of the competition for scarce funding, or overzealous turf defending, or any number of other non-science-related factors (some of which are discussed here and here). A better approach, as discussed here by Randy Jirtle, is to promote the integration of epigenetics and genomics. This way as little as possible is left out of the equation. Otherwise, I’m not sure what we end up with.

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] Thurman, R., Rynes, E. and Humbert, R. (2012).  The accessible chromatin landscape of the human genome. Nature 489(7414), 75-82.

[2] Crews, D., & McLachlan, J. (2006). Epigenetics, Evolution, Endocrine Disruption, Health, and Disease. Endocrinology 147(6), s4-s10; Lehner, B.(2012). Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature 488, 504-507.

[3] Wang, F., Liu, H., Blanton, W., Belkina, A., Lebrasseur, N., & Denis, G. (2010). Brd2 disruption in mice causes severe obesity without Type 2 diabetes. Biochem. J, 425, 71-83.

[4] Xu, Z., Lefevere, G., & Felsenfeld, G. (2012). Chromatin structure, epigenetic mechanisms and long-range interactions in the human insulin locus. Diabetes, Obesity and Metabolism 14(s3), 1-11.

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 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.