Wednesday, January 18, 2012

Teaching Science: Ur doin' it wrong

So a few weeks back, a couple of people I know sent me the same video called "More on Genes" by premed2 to review. After watching it I was pretty surprised by how sloppy the work was (varying anywhere from being misleading to flat out wrong). Urged on by a morbid curiousity, I decided to look at the prequel of said video with my friend Chris over at In Vivo. Both videos were apparently inspired by an article in Scientific American that was published last month. We both agreed that it was pretty bad so we left some critical comments. This is where the situation got interesting....

Now, premed2 claims to be a tutor in "premedical sciences". I honestly thought that meant he just tutored intro biology. In reality it seems he is actually a fairly decent ogranic chemistry tutor who is fumbling with genetics. I was under the impression that someone who helps students learn scientific concepts would, at the very least, be a little embarrassed by the errors and perhaps would take steps to rectify the mistakes. Boy, was I wrong. Apparently, having some sort of respect for accuracy while teaching a subject is purely optional and only employed by neurotic people. The sad part is that he has some how managed to convince a decent chunk of his audience that they're learning something. The main purpose of this post is to correct his errors so that if anyone sincerely wants to understand these topics they will have a starting point.

I have a feeling that addressing both videos in one post is going to bring the total length perilously close to tl;dr so I'll deal with his second video More on Genes later.

Video 1: Epigenetics: Addiction/Bullying/Depression

Now, there are some minor issues with this video. One of the little nitpicks I have is premed2 never actually specifies that he's talking about humans when he mentions that chromosomes are linear and that there are 23 pairs. That's not that big of a deal.

What really got me with this video was the incorrect definition of "epigenetics". Every time I have encountered the term in an academic setting there was always an emphasis on the heritable component. The term itself still seems to be debated when it comes to the precise definition but all of them include some form of heritability. An article in Science called "What is Epigenetics?" states pretty clearly that an epigenetic system:
...should be heritable, self-perpetuating, and reversible.
Another article that discussed the conclusions of  a meeting held with the express purpose of defining epigenetics had this to say:
An epigenetic trait is a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence.
Now why does any of this matter? The generally accepted definitions are pretty specific which means that what our friend premed2 here is teaching is not eipgenetics, he's teaching gene regulation. Some histone modifications** can definitely be epigenetic if they are heritable. In this case, heritability can either mean one of two things. It could mean from cell to cell (think about when a skin cell divides - it becomes another skin cell - one of the reasons for this is epigenetics). Alternatively, it can mean from parent to offspring. The histone modifications discussed in premed2's video seem to be simple gene regulation. He points out that mice that are bullied undergo "epigenetic" changes as if it's something shocking and unpredicted. I find this confusing because any time you introduce an organism to a stressful environment one would expect to see regulatory changes (including histone modifications) to its genes.

Looking back at the Scientific American article premed2 used as a "primary" source when learning about epigenetics, I can see why he was confused. It seems that Dr. Nestler (the author of the article) is using a relatively obscure definition. Dr. Nestler isn't some backwater scientist on the fringe of academia. He's a medical researcher with a pretty impressive library of publications. I could go on a rant about medical research and how it relates to science in general but suffice to say I have a feeling that Dr. Nestler's unusually broad usage of epigenetics might have something to do with the current popularity of epigenetics as a field and securing funding.

Either way, this still doesn't excuse premed2's attempts to teach a subject which he only understands from a single Scientific American article.

I'd also like to take a second to suggest people be wary of Scientific American. While it was once a fairly respectable publication, in recent years it has taken a pretty serious dive. For example, notorious HIV/AIDS denialist Peter Duesberg was given a glossy 8 page full colour spread devoted to his latest nonsense rallying against cancer being primarily caused by mutation.  Just sayin'.

**I've already had some people ask me what histones are so I'll describe them briefly here. Histones are proteins which DNA is wrapped around. This helps maintain chromosomal structure etc. The modifications of histone proteins include methylation (which causes DNA to be wrapped more tightly) and acetylation (causes DNA to be more loosely wrapped). Methylation of histone proteins essentially causes the DNA to become so tightly wrapped that the transcription machinery cannot access it so any genes in that area will not be expressed. Acetylation has the opposite affect. 

The reason this works is because DNA has a net negative charge while histone proteins have a net positive charge. By adding chemical groups with different charges to the histones (or to the DNA)  the charge is changed and as a result there are changes to how tighly or loosely the DNA is bound to the histones. These modifications can (but not always) be inherited from cell to cell. During gametogenesis (production of sperm and eggs), a lot of histone modifications become reset so regulatory changes are not always inherited by the offspring.

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