Debunking myths on genetics and DNA

Monday, November 19, 2012

Proteins as gene carriers

By now you probably know everything about pluripotent stem cells, right? They are the hot topic in genetics right now, to the point that the fear of being scooped has pushed some people to lie about their results. Pluripotent stem cells are cells that have the ability to divide into a specialized cell and another undifferentiated cell. This of course is greatly useful in repairing damaged organs and/or regenerating tissue, and has great potential in medicine.

Lately there has been a lot of buzz on the notion that pluripotency could be re-induced in already differentiated cells. Studies have shown that four reprogramming factors can indeed reprogram fibroblast cells into pluripotent stem cells when over-expressed.

But how to over-express these factors?

The typical route is to transfect the genes into the cells by means of a viral vector. Basically, the genes are delivered into the cell using a retrovirus. Though effective, this poses the question of side effects: whenever you introduce foreign DNA into a cell you have the potential to silence secondary genes or disrupt the usual gene regulation. Unanticipated epigenetic changes in the cell can occur. A recent study [1] shows a safer alternative: cell-permeant proteins, or CPPs. These are small proteins that can cross the cell membrane and carry peptides inside the cell in a process called "protein transduction," thus offering a valid alternative to viral vectors.

By comparing the two methods (CPPs and viral delivery) on human fibroblast cells, Lee et al. noticed that gene expression was achieved much faster when using the viral vector. Puzzled by this difference, they wondered what was so special about the viral route that made the gene delivery so much more efficient. There had to be something in the viral vector that aided the delivery of the genes. Lee et al. hypothesized that this could be linked to the fact that the viral vector somehow activated an inflammatory pathway in the cells which in turn aided the delivery of the genes. So the next question was: can we enrich the CPPs so they too activate the inflammatory pathway?

Indeed they could! They used TLR3 agonists, molecules that activate the TLR3, or Toll-like receptor 3, a receptor that recognizes double-stranded RNA generated by retroviruses and thus activates inflammatory pathways. Once combined with the TLR3 antagonists, over-expression of the reprogramming factors was achieved faster through CPPs than it was with the viral vectors, validating the hypothesis that the gene delivery has to be achieved via the activation of the immune pathway. In fact, the contrary was also true: when TLR3 was knocked down (biology jargon to say that the gene was silenced), the viral vector was also inefficient in delivering the genes.
"TLR3 activation enables epigenetic alterations, including changes in methylation status of the Oct4 and Sox2 promoters as well as changes in the expression of epigenetic effectors, that promote an open chromatin configuration. The knowledge that the activation of innate immune response affects nuclear reprogramming permitted us to enhance the efficiency and yield of human induce pluripotent stem cells by using reprogramming factors in the form of CPPs."
Lee et al. conclude:
"Our observations highlight a previously unrecognized role for innate immunity activation in nuclear reprogramming. The viral vectors constructs used to induce pluripotency are more than mere vehicles for the reprogramming factors. Innate immune activation causes striking changes in epigenetic modifiers that favor an open chromatin configuration. These changes enable a fluidity of cell phenotype that contributes to successful nuclear reprogramming."

[1] Lee, J., Sayed, N., Hunter, A., Au, K., Wong, W., Mocarski, E., Pera, R., Yakubov, E., & Cooke, J. (2012). Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming Cell, 151 (3), 547-558 DOI: 10.1016/j.cell.2012.09.034

Thursday, November 15, 2012

Is creativity an illness? But then... what is an illness?

Are you creative? Do you ever feel that when your creativity strikes you become absolutely compulsive about your "inspiration," and totally depressed when, for some reason, your inspiration wanes? It always strikes me to read about how some of the most beautiful works of art were created: their creators were obsessed, compulsive, borderline dysfunctional. Gabriel Garcia Marquez sold his car and had his family live on credit for eighteen months so he could write One hundred years of solitude. Brunelleschi's obsession was the dome of Santa Maria del Fiore, Antoni Gaudi's obsession was La Sagrada Familia. It seems to me that obsessions may ruin your life (or most likely the life of your closest ones) when you have them, but they may also lead to the most wonderful things.

So, is creativity a good thing or is it an illness?

My friend and collaborator Tanmoy Bhattacharya brought to my attention an interesting BBC post that discussed the issue. The article came up in a Facebook discussion because it raised the question: "How do you define illness? When, exactly, does a behavior trespass the normality threshold and becomes an illness?" I really liked Tanmoy's take on the issue, and I asked him permission to repost it here on the blog. It's the best thing I could get since he won't do a guest blog for me. :-)

I think he raises excellent points on the complexity of the brain, its stimuli as well as its constraints. I enjoyed reading it, I hope you will too. And if after reading this you have questions for Tanmoy, go ahead and post them in the comments and I will forward them to him.

TB: In a system as complex as the brain, which interacts with such diverse environments, it is difficult to define health and disease. There has been a long standing hypothesis that certain brain functions like deductive logic and creativity are kept in check evolutionarily because the same "structure" that can give rise to very highly creative adaptations in one environment would give rise to maladaptive behavior in a different environment. The interest in the research is, therefore, understanding the architectural limits on the brain, not to stigmatize writers or expect every bipolar to pen out a story about an old man and the sea.

EEG: That's a very interesting theory. All greatest masterpieces required such great energy and dedication from their creators that these individuals had to, at some level, become unsociable, as focused as they were on their creation. I can see how, at a species level, "being socially fit" puts a constraint on the amount of time and "obsession" the brain can dedicate to a certain task.

TB: I do not believe that we yet have a definition of illness which is "biologically" meaningful. Sure, there is a diagnostic manual that tells a doctor today when to diagnose a particular mental illness, but it is more an expression of "social" reality than a "biological" reality. So, for example, the discussion of whether homosexuality is a disease is not argued on any grounds about what it does or does not do to the person, but rather whether the majority of doctors consider it within the "normal" spectrum of behavior. No wonder its classification changed from a disease to a non-disease as the social acceptability of homosexuality grew: not because such acceptance lessened the mental load on the person with the trait (it is now not considered a disease even when the person with the trait lives in a non-accepting community), but because it became "socially" acceptable as a "normal" behavior. Currently, there is a similar debate about whether bereavement distress should be considered normal even when it leads to behavior sufficiently aberrant to otherwise merit a diagnosis of clinical depression. In other words, the question is not whether the person is depressed after a loss: the question is whether it is a disease (possibly temporary like say getting the 'flu is a disease) or whether it is not a disease because it is "normal". The classification is not done based on any kind of biological reality, except whether it is considered normal; which is determined by methods of social science, not biology.

Does this concept of normality depend on a biological reality? In other words, is there a way, other than surveying doctors (the social science method), to figure out whether some one is abnormal? Remember that we know pretty much that all of us are different in many ways, if you defined me abnormal simply because I am unique (which I certainly am), then everyone would be abnormal. One could always say that one should not look at the totality (which made everyone unique), but trait by trait, and ask whether I have traits that very few other people have? Defining abnormality this way would, of course, make Picasso abnormal; but during a mass hysteria, it would classify everyone as normal. We again see that this definition fails to capture the abnormality that is relevant to defining disease.

I claim that the only way people have found to capture the relevant abnormality is by taking the design stance: human brains (and bodies) are supposed to be "for" something. When the organ (or the totality) is carrying out this function, it is normal; when it fails to carry out this function, it is abnormal. Note that this does not solve the underlying problem: someone still has to define the function, but that turns out to be an easier problem.

We could define a disease objectively as a malfunction if we could define function objectively. And, here, biology can bring an insight: the function of brains (and bodies) is to survive and use the environment, physical, biological, and social, to further the fundamental goals of long term survival of the traits. This is usually called reproduction, but it is far more subtle: for example, one can help raise grandchildren and contribute to the long term survival; under appropriate conditions, one can help other helpful members of one's community to help survival of the helpfulness trait. The mathematics is not simple, but recent work has made much of this clearer, and it is far more than pure reproduction. The part relevant to this discussion is that for a social animal this survival depends a lot on social calculations as well as other considerations.

So, then, we can define function as being able to properly calculate and take appropriate action; but that depends on the environment one faces. The same trait of fast decisive action to take the life of an unexpected person is wonderful in times of violent combat but completely malfunctional in a peaceful society. Similarly, it is easy to show that a mental make up that helps everyone, whether or not they are helpful to others, is malfunctional in the sense that it does not help its own survival except in societies that pays a high moral premium on that. Now, since most traits will find themselves in various environments, the malfunctional has to be defined as an intermediate: it should not be "fatal" in any of the environments that an individual is likely to face. But, this depends on the environments one is "likely" to face.

Given this situation, therefore, most traits tune themselves to intermediate values, because extreme values are typically extremely ill suited in some environments one is likely to face. And, all this is further constrained by the possible organization of the brain: for example, it is completely possible that the brain is composed of two parts, one that can analyze and model its environment in terms of an "open-loop" system controlled by impersonal physical laws which constrain and guide change, and a social system that can alternately assign agency (or "will") to parts of the environment. If this simple separation of thought patterns is an useful approximation, the division of resources between the two will affect a lot of behavior: a lot of resources devoted to the physical system will make one unable to understand complicated social dynamics; whereas too high a reliance on the social system might make one unable to understand that physical phenomenon often do not have wills and desires. Both of these taken to an extreme are obviously malfunctional, and, therefore, diseased: one can think of autism or schizophrenia as examples illustrating such symptoms. But, where exactly one stops being analytical and starts being high-functional autistic will depend on what environment one is defining with respect to: when the norm is highly complex social environments, one will probably classify some highly analytic people as diseased because they cannot function in society (i.e., the "mad scientist" or "computer geeks" will get classified as "mad" or "autistic"), whereas when complex physical systems but with little social structure are the norm, some people who see willful patterns in the universe will find themselves considered ill (e.g., a "religious fanatic" will be considered "mad").

So, what have we done through all this argument? We started by arguing that DSM (diagnostic manual) definitions depend on a certain standard of normal and are not objective. Through the chain of arguments, I have tried to establish that the former (i.e. dependence on the standard of normal) is inherent part of the problem, and cannot be removed except in the trivial sense that some things have never been normal. I have also argued, however, that this dependence does not need to be subjective: what is important is not what the "doctors" have experienced as normal, but rather the environments that the *person* being diagnosed has experienced and is likely to experience.

The interesting question is that supposing we take a bunch of brains and tune up their creativity (by changing whatever neurotransmitter chemistry or electrochemical connections that we need to). Now, in some environments and depending on the rest of the circuits in the brain, this will work perfectly fine and be very useful in understanding and modeling otherwise-hard-to-model systems (somewhat similar to a physical effect called "annealing"). If the same tuning is done to a different brain which does not have the same set of controls, this tuning could lead to a bipolar disorder. Basically this hypothesis would say that creativity needs to be balanced by other control systems, so any means of independent inheritance will quite often lead to getting the creativity structures without the control structures, leading to madness. Under this hypothesis, creative people are not insane, but biology would dictate that they are at a higher risk of having insane relatives (children/siblings/etc.) than less creative people.

But, there is a different possibility as well: the "control" unit hypothesized in the previous post may not be inherited much, but developed based on experiences; or its need may be dependent on the environment. In this case, the only difference between creative people and people with some forms of insanity would be the environments they have faced or will face. Creative people can then look at bipolars and paraphrase Bradford "But for the grace of environment, there go I". We do not know if either of these hypotheses are correct, but I hope I have explained why I find it interesting to ask these questions, and why the data presented in the article is consequently interesting.

Monday, November 12, 2012

I haven't abandoned the blog!

Sorry for the absence, I've been, and still am, extremely busy. Unfortunately I have to slow down the frequency of posts. But I'm still here!

We've had our first snow and I found a new photographic challenge: snowflakes. They're harder than water refractions, with the added difficulty that after a few clicks my fingers are frozen.

For those of you who know how I spend my nights... yes, you've guessed it, my muse struck again.

I'll leave you with a question to muse: What do you think the future of the Internet will be, say twenty years from now?

Tuesday, November 6, 2012

Don't forget to vote today (US)

It is not titles that honour men, but men that honour titles.
Niccolò Machiavelli

Don't vote based on ideal principles. Be pragmatic. Vote for our children, vote for the best of the Country.

When you vote, remember the past and look up to the future.