Discussions and reflections on science and life


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So, I’m alive. When the dust settles, I’m still here, still kicking, and am now (apparently) a master of something.

Which brings me to the point of what to do with this blog. This was always a student’s exercise, and now that I am no longer a student, I am not sure if I will keep it going. I DO want to continue blogging, but maybe not with such a hard-science focus. So right now the toss-up is in between keeping this place, splitting my time between blogging here and elsewhere, or just starting another blog without a specific focus.

We’ll just have to see where it goes.


Written by Caudoviral

05/30/2011 at 22:17

Posted in Personal

Mini-Review: Monkey Girl

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So this is going to be brief, and not just because I am reviewing a book that is four years old.


Monkey Girl is Edward Humes narrative coverage of the landmark Kitzmiller v. Dover Area School District. In addition to the highlights of the court proceedings, Humes delves into the events leading up to the case and often takes time to cover the background of the key players.


I never intended to pick this one up, I really have much more important things I should be doing. But Kitzmiller v. Dover remains a fascinating legal battle and my copy was a cheap buy at a Borders that was going out of business.

I was put off by the narrative style. Apparently this is a hallmark of Humes’ reporting (he has even won a Pulitzer for it), but I never warmed up to it. Maybe it is the soulless biologist in me, but I prefer details to narrative flourishes. I felt like I was constantly being distracted from the actual matter at hand by being told how “fiery” and “soulful” people were; nor is he often satisfied with letting the chief players simply “say” things. I kind of feel like this was written with a thesaurus in one hand as though simple language would bore his readers. It had the opposite effect on me and several times I found myself scanning large passages for the kernel of actual detail. In favor of this style, it did make for a quick read.

The narrative style also lent itself to the chronological nature of the narrative and facilitated his introduction of characters in a memorable way, I am just not sure it was the only or best way to accomplish this. The text is also plagued with a great many diversions: details of peoples ancestry, local history, and similar conflicts elsewhere that feel a little like padding. Some of them seem valid, such as the tangent on the history of the Discovery Institute and excerpts from Creationism’s Trojan Horse. Which are bound to be useful if this book is your introduction to this controversy. Others, not so much. In this latter group I would count the several sentence tangent that the title comes from. A brief interlude whose only purpose seems to be to justify an eye-catching title, and does absolutely nothing to further the account. It would have been nice if this book about Dover and the Kitzmiller v. Dover court case hadn’t spent approximately a quarter to a third of its narrative elsewhere.

As far as the analysis and fact gathering go, the book does a great job. If you can stomach the style there is actually quite a bit of information within the narrative and the helpful (if a bit sparse) notes section. He seems to have a talent for succinctly and clearly presenting the arguments and motivations of the fairly large group of people involved. I also appreciate that he tracks the conflict back to its origin in the school board meetings rather than just picking up once the suit was filed. This is especially important in this particular case since the perjury committed by several board members about what had happened played a key role in the decision.


Overall, I enjoyed reading this book. I found it to be an informative look at the events leading up to trial and an interesting overview of the case itself. I do think that the style hurts rather than helps. Humes seems to try to walk the line between informing and entertaining, and it just didn’t work in my opinion. Humes has an excellent eye for noting and including a wealth of detail, yet he seem to have trouble differentiating between relevant and irrelevant details. It is something that probably won’t have a permanent place in my library, but it was definitely worth reading once.

Available via Amazon

Written by Caudoviral

04/15/2011 at 17:14

Posted in Review

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Life goes on…

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So as you may or may not be able to tell from the long silence, things have been kind of busy and crazy on this end. Our semester effectively ends on the 3rd of May, and well, there is a ton to get done before then. Of note, I am doing some very involved research for a literature review on HIV latency, so I might wind up posting about some of the interesting things I have been finding. HIV does some really odd things, even when the virus is supposedly ‘controlled’ by HAART.

Written by Caudoviral

04/14/2011 at 18:11

Posted in Personal

Here Be Dragons

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One of the more common misnomers flying around the pop-sci publications is this idea of “Junk DNA”. Now to be fair, this label originated with the scientific community. Even Francis Crick was dismissive of its utility, but that was thirty years ago. As it turns out, junk DNA (more accurately called non-coding DNA) contains both a variety of sequences with biological utility and large portions of our genomic history. It is the later that I wanted to bring up today.

One of the major forms of transcriptional control involves histone deacetylase. You can think of histones as essentially spools of DNA. If DNA is wrapped tightly around histones it is unavailable to be transcribed to RNA and then translated to protein. Modification of histones determines the precise manner in which the DNA interacts with them, and acetylation of histones loosens the wrapping of the DNA, making it available. So your cells employ histone deacetylase to make sure that regions of the genome stay nice and silent. Which is good, cause there is some scary stuff hiding in the sea of non-coding DNA.

Recently there has been a push to use histone deacetylace inhibitors to cause expression of genes of interest (e.g. it is suggested they could be used to flush latent virus out of memory T-Cells to destroy latent reservoirs of HIV). Now, these ideas seem really sound on the surface. If we could destroy that reservoir of latency, we could see long-term drug free remission in HIV infection. But what else might you wake up? As far as I know there is no reliable method (if there is indeed a method at all) to target histone deacetylase inhibitors to specific regions of the genome, so this would be a general approach inhibiting all of a cells histone deacetylase, which I can’t but think would lead to A) steps towards tumor transformation as cell cycle controls  were disabled, and B) the activation of unfriendly endogenous elements in the genome. Fishing out integrated HIV provirus is an excellent idea, but what else might we pull in with it?

Written by Caudoviral

04/07/2011 at 11:29

Posted in Biology, HIV/AIDS

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Contextualizing Radiation

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So I wrote about ionizing radiation dose a couple of weeks ago. But it wasn’t until today that I found a good, visual rendering of the equivalences between radiation doses from different activities. Randall Munroe, the delightful mind behind XKCD, has made a chart of common radiation doses, standards, and equivalences. It’s definitely worth a look.

Written by Caudoviral

04/04/2011 at 11:51

Posted in Physics

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Activists targetting students with violence

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I tend to be wary of activists. To me, an activist is someone who has taken it upon themselves to support a particular opinion, regardless of that opinion’s status as right or wrong opinion (which is to say its truth value). This leads to a turbulent relationship with fact that may involve everything from cherry picking ideas to outright denialism, and generally makes for a very “fair-weather friend” relationship between opinion and (my personal tool of the trade) reason. Now, many activists can and do behave responsibly and rationally and they have my greatest respect (another tip of my hat to the intelligent and thoughtful feminists over at Fishnet Bluestockings, they are on my blogroll for a reason), but I find that it pays to be on my guard against those that don’t. Which is why I employ the following guidelines with activists:

  • You are entitled to your opinion and the expression of that opinion in the appropriate forums and manner. To give you any less than that would be a violation of your rights and my moral code.
  • Do not confuse an opinion with an argument. Don’t expect to persuade without evidence or reason, it will get you ignored.
  • Attempts to persuade through lies & half-truths, the propagation of misinformation, shame or peer pressure, or any other end-run around mutual respect and properly formulated argumentation will get you ridiculed.
  • Resorts to threats and violence will get you watched, reported, arrested, and (in the most regrettable cases) hurt.

I feel the need to bring this up today, since there is a group out to threaten, harass, and possibly attempt to kill me and my fellow students (as if a bisexual, transgendered person doesn’t have enough animosity directed towards her/him already). Negotiation is Over is a hate group directed at researchers in the life sciences. They call themselves animal rights activists, but they seem much more interested in attacking researchers than saving animals. And now they have specifically turned their gaze on students as they announced yesterday:

Every time a vivisector’s car or home — and, eventually, the abuser him/herself — blows up, flames of liberation light up the sky.


When we attack professors, we can only expect limited gains. They are deeply entrenched in the holocaust, have vested financial interests, and enjoy a network of support and protection. Students, however, have no round-the-clock police protection, no access to the FBI, and no access to legislators. The weakest link in the chain is the student body. Vivisectors-in-training can be shut down with relative ease.


Students also need to understand that making the wrong choice will result in a lifetime of grief. Aspiring scientists envision curing cancer at the Mayo Clinic. We need to impart a new vision: car bombs, 24/7 security cameras, embarrassing home demonstrations, threats, injuries, and fear. And, of course, these students need to realize that any personal risk they are willing to assume will also be visited upon their parents, children, and nearest & dearest loved ones. The time to reconsider is now.

It goes on like that for quite some time, with a lovely picture of a firebombed car just to make sure there can be no ambiguity about what they are advocating. As an added bonus their site has links to state by state directories of research universities they consider offenders via their “Animal Abuse Crime Database”. Guess whose uni is on their list?

But I’m not afraid of these creeps, and I urge you not to be either. Stay safe, don’t let them get to you, and promptly report any threats. These people are terrorists, and terrorists like to cause terror. So don’t give them the satisfaction. And if you have a forum for it, I hope you will speak out and let them know that their tactics are impotent. In time they will try to do something stupid and get arrested/shut down, or they will tire of their game. Either way, the wanna-be scary monsters will be stuffed back under the bed and we can get on with the business of saving lives.

Now, my opinions on the morality of animal research are complex, and I will talk about them in a later post and hopefully be able to present a rational basis for them. But my opinions on this issue are stark: this is unacceptable. Even if you personally find animal research reprehensible and feel that making transgenic mice is on par with Tuskegee, realize that this sort of behavior is not the way to go about effecting a change.

Violence remains the last refuge of the deluded and incompetent.

Written by Caudoviral

03/31/2011 at 09:00

New Resources

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This is just a heads up that a new site has been added to the ‘Resources’ links down there on the bottom right. I was trying to look up something about mitochondrial fusion proteins and kind of stumbled across a site that hosts a number of very interesting science videos. Despite the name, DNAtube appears be a multidisciplinary site hosting videos on all aspects of science and math. Probably worth checking out, I know I would be if I had time to take a study break.

Written by Caudoviral

03/27/2011 at 14:55

Posted in Science