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Monthly Archives: January 2015

Quora activity for June – December 2014

Quora is a question-and-answer site. You can view all my contributions here; selected highlights are listed below. I encourage you to check out the other answers submitted for each question, too!

I haven’t been as active as usual over the last few months; I took a break over the summer, and then entered the busiest few months of my professional life (as well as doing my usual full-time job I also helped organise and run the 2014 Joint Annual Meeting of the International Human Epigenome Consortium and the Canadian Epigenetics, Environment, and Health Research Consortium, then studied intensively for my Project Management Professional exam, which I passed just before Christmas). I still managed to write a few answers though!

Cancer

Which cancer strains are contagious among humans and how can they be contracted?

Do you think the government knows the cure for many illnesses like cancer but hides the information to make more money off the unsuspecting general public?

What types of cancer are affected by epigenetics?

Epigenetics

How difficult is epigenome sequencing, as compared to genome sequencing?

What are all the elements of an epigenome?

What are some great resources to teach epigenetics to a class?

Does DNA methylation and histone acetylation add to the amino acids of the histone or nucleotide?

Other Scientific Subjects

Why isn’t there a cure for Ebola yet? Is it as mysterious as HIV?

What does it mean to have a genetic predisposition to a disease?

Why are longer DNA sequencing read lengths preferred over shorter read lengths?

What are the most amusing figures or images from academic journals and articles?

Do siblings who share the same set of parents each have the same distribution of parental DNA? Can one sibling have more of one parent’s DNA or would the parental DNA distribution be equal?

Does a chromosome contain a thousand genes, or is it gene pairs (i.e. 2000 genes in all)?

About Scientific Research and Careers

Why are biologists so secretive of their data?

What happens to old scientific grant applications?

What’s competitive research funding?

Miscellaneous

What has been the toughest decision of your life? Did it turn out to be the right one?

What is the wittiest thing a child has ever said to you?

Is the term “agnostic atheist” a double negative?

What are the best examples of people “gaming the system”?

What’s the worst logo failure you have ever seen?

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Posted by on 2015/01/03 in Quora

 

The epigenetics of The X-Files

(Originally published on Occam’s Corner at Guardian Science, in December 2014)

Epigenetics is helping us to solve DNA mysteries that cannot be explained by genetics alone. It might even help explain some of the spooky phenomena described in the 1990s science documentary series The X-Files

Epigenetics has the power to open up possibilities beyond those offered by genetics alone – including the occasional triple word score Photograph: Cath Ennis

Dana Scully was a scientist, always looking for a perfectly rational explanation for the strange phenomena encountered each week. Many of these explanations were based on genetics, especially in the “monster-of-the-week” episodes featuring assorted freaks and other abominations not part of the main alien conspiracy storyline. Memorable monsters included such delights as a sewer-dwelling fluke man, and a charming creature possessing the lethal combination of an ability to squeeze through any gap and a taste for human liver.

It was easy enough to explain some of these freaks as genetic mutants – the man with a tail and an unusual muscle structure allowing him to mimic facial features surely had some kind of mutation in a muscle fibre gene – but the scientific basis of many other cases remained unknown. This shouldn’t be surprising: science moves quickly, and we’ve learned a lot about genetics since the ‘90s. One of the major advances made since then is in the field of epigenetics – a field that I believe has the power to resolve some X-Files cold cases.

X chromosome inactivation can definitely be explained by epigenetics. X-Files? Less certain. Image from Reinius et al., BMC Genomics 2010, 11, 614.

Epigenetic modifications include the addition of a methyl molecule to the DNA itself (could this be the mysterious fifth letter that Scully found in a segment of alien DNA?), and changes to the histone proteins around which the double helix coils itself. This molecular highlighting affects how the DNA text is read in that region, helping to determine which genes are switched on or off in each cell.

Many unresolved X-Files cases that might be accounted for by a genetic mutation could just as easily be explained by an epigenetic modification of the same gene.

For example, in cancer (where the cell’s epigenetic patterns go just as awry as everything else), the same tumour suppressor genes that are often lost by mutation or deletion can also be eliminated by abnormal methylation patterns in that part of the DNA. If there’s also a “psychic abilities suppressor gene” lurking in our genome, then we can provide a perfectly rational explanation for multiple cold cases in one fell swoop.

But let’s move on to something a little more challenging.

An important feature of epigenetics is that the pattern of molecular highlighting isn’t fixed. The DNA sequence itself is essentially the same in every cell of the body and through all stages of life; in contrast, epigenetic modifications are different in different cells, change during processes such as metamorphosis (definitely in frogs, so probably also in shape-shifting extraterrestrial species), and can change in response to the environment.

Even identical twins (or, say, genetically engineered clones), who have identical DNA sequences, have different epigenetic patterns – and these differences increase as the twins get older. This helps to explain why identical twins aren’t actually identical, and also why some clones are evil and others are able to overcome their genetic programming to become productive members of society.

Experiences as diverse as chemical exposures, traumatic experiences, and exercise have been shown to cause epigenetic changes. I haven’t yet seen any published scientific papers documenting the epigenetic effects of exposure to alien abduction, alien virusesparasitic ice wormshallucinogenic fungal spores, or questionable tattoos, but I’m sure they would be spectacularly interesting and could account for the strange behaviour of some of the unfortunate people involved. They probably also explain Scully’s cancer; if carcinogens such as bisphenol A can operate at least partially via epigenetic mechanisms, I don’t see why alien experimentation techniques can’t do the same.

There’s even evidence that the epigenetic changes caused by some experiences, such as periods of starvation or drug use, can be passed on to future generations. Could epigenetic inheritance account for the supernatural abilities of Mulder and Scully’s son William? (Yes, William’s abilities were demonstrated in seasons eight and nine. Yes, I just said that I refuse to admit that these seasons ever happened. If Chris Carter doesn’t have to be internally consistent, then I don’t have to either). Some might even argue that epigenetic inheritance can also explain memories of past lives, but hey – that’s just silly.

In summary, the hypothesis that we can use epigenetics to finally close several X-Files cold cases seems to have some merit. (We can ascribe anything we can’t explain via epigenetics, such as invisibility and possibly the conception of baby William, to epic genie tricks instead). I hope the FBI are paying attention…

Add your own cold case explanations in the comments!

Cath Ennis is, like all the best X-Files episodes, based in Vancouver, Canada. She doesn’t really believe The X-Files was a documentary.

This article most definitely does not represent the official position of the International Human Epigenome Consortium. However, Cath and other consortium members did discuss some of the cold case explanations included in the article (on their own time and their own dime) during the 2014 Annual IHEC Meeting in Vancouver. Thank you Dena Procaccini and other participants for your contributions!

Cath is on Twitter as @enniscath, and on Words With Friends as Wonderbrit. The Truth is out there, and it’s worth at least eight points.