caudoviral

Discussions and reflections on science and life

Posts Tagged ‘Evolution

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.

Abstract

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.

Discussion

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.

Conclusions

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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Mitochondria are Weird

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Let’s get one thing straight: I like my mitochondria. They are a necessity for eukaryotic life (although there have been some theories about alternate high yield ATP production pathways or schemata of power management). But for all that…dang are they weird.

The situation is basically a symbiosis event. At some point the ancestor of eukaryotic cells engulfed a prokaryote (most likely Rickettsiales). However, instead of being broken down into constituent molecules, this prokaryote persisted, reproduced, and evolved within the cell. One of the most fascinating things about this arrangement is that, as time went by, the mitochondria actually began to outsource their genome to their host. This is debatably the point at which they completely lost their independence and became organelles as opposed to organisms.

The human mitochondrial genome is 16,568 bases and contains no introns. It codes for about 37 genes, a fraction of what the organelle actually requires. The rest of the proteins are made from your nuclear DNA and imported through an annoyingly complex transport system. As we look across species, we can see that the mitochondria in different organisms have retained more or less of their original genome (e.g. plasmodium have 5 genes in their mtDNA and reclinomonas have 98 genes), but no organism retains completely independent mitochondria. And there are a lot of extra tricks that the genome picks up across species: sometimes linear, sometimes circular, sometimes with introns, sometimes not, multiple copies of the genome per mitochondria, etc. As an added bonus you can wind up with multiple mitochondria per cell with multiple different genomes in that mitochondrial population.

The practical side of this is that inheritance of mitochondrial disorders is emphatically not Mendelian, and tracking such disorders can be all sorts of a headache. A headache we are going to have to work through if we want to effectively study and prevent these diseases.

Sources & Further Reading

  • I highly encourage anyone with a background in genetics and some time to kill to go take a look at MitoMap. It’s the human mitochondrial genome database and includes some great references.
  • One of my commenters has recommended Nic Lane’s Power, Sex, Suicide: Mitochondria and the Meaning of Life, although I personally can’t speak as to whether it is good or not. Am looking for a copy but even if I find one it will have to wait its turn in a long line of reading material.
  • And because spec-fic is fun I find myself compelled to recommend Parasite Eve both the novel by Hideaki Sena and the PS1 game put out by Square. Nothing approaching scientific accuracy, just plenty of “What if mitochondria were an evil hive mind?” lovelyness and body horror. There is also a movie, but I hear that it wasn’t that great.

Written by Caudoviral

03/07/2011 at 14:09

Posted in Biology

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Blurring the Lines

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It is largely a Victorian myth that male gorillas would take a sexual interest in human females. Largely. No human has ever had to fear the sexual predation of (non-human) apes in the wild (dolphins, however, are a different story entirely). It is apparently rather a different story in captivity.

Reading Carl Sagan & Ann Druyan’s Shadow of Forgotten Ancestors, I ran across the following interesting passage:

“When raised among humans, they [Chimps] have been known to masturbate to pictures of naked people. (This is probably true only for those who, through prolonged contact, have come to consider themselves human. Wild chimps would no more masturbate to erotic images of humans than vice versa.)”

Now, if Sagan & Druyan have their information correct, this serves as a striking example of the dangers of observing animal behaviour in captivity.

Major pressure for behavioural change occur at boundary regions. This is one of the things that makes ecotones such a fascinating field of study. However, not all of these boundaries are terrain based. When two species are placed in close proximity, they tend to each adapt towards the presence of one another. The boundary between the species selects for adaptation. An excellent example of this is the Endler guppy experiments. Guppies placed in tanks with no risk of predation become brighter and more flamboyant to attract mates. Guppies placed in tanks with risk of predation become duller and more easily camouflage themselves in the substrate. In no way is either of these populations no longer a guppy, but the differences are striking. No animal exists in a vacuum. There is no eidos of any species. Take two populations of the same creature and put them in radically different circumstances, (if they don’t die) their behaviour and biology will begin to diverge (if this divergence continues long enough, speciation might occur). And the presence or absence of an entirely new species (a.k.a. the presence or absence of human observers) is one hell of a change in circumstance.

People like to draw a nice firm line between ourselves and the rest of Animalia, and it is just not merely wrong to do so, but actively misleading. It is fairly clear that people who interact with other animals in their daily lives are affected by the experience and they change their behaviour to match (entire myth structures have been built upon a human tribe’s native flora and fauna). So what does all this mean? Well…the practice of working with animals in any kind of setting where there is direct interaction between humans and animals is not of necessity accurate to the behaviour and condition of those animals in the wild. Your presence is going to cause an observer effect in them, and in all likelihood prolonged exposure will cause certain adaptive behaviours in you.

Of course, given that there is no eidos of a species is this such a bad thing? Not if you realise it. If you don’t, it can cause problems. We will look at a case study of this on Wednesday.

Sources & Further Reading

  • Shadows of Forgotten Ancestors by Sagan & Druyan, 1992
  • Finding a free full text of John A. Endler’s articles doesn’t look like it is going to work. Although it may be possible to get access to his work, and especially his 1980 Natural selection on color patterns in Poecilia reticulata through your libraries.

Written by Caudoviral

02/07/2011 at 18:40

Posted in Behavior & Cognition, Biology

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“Is there a doctor in the fish?”

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Mental disorders are a hobby of mine, not a field of study (and we evil reductionist biologists generally look askance at the actual field devoted to studying them). But some of them are a little too odd not to pay attention to. I include in this the entire spectrum of factitious disorders.

Factitious disorder, sometimes and sometimes not synonymous with Münchausen syndrome, is characterised by exaggerating, faking, and sometimes even producing symptoms of a disease for the perceived emotional and social benefits of being sick. That last bit is important, someone who employs chicanery for an external benefit: money, draft-dodging, etc. is a malingerer and deemed not mentally ill. The genuine factitious disorder is considered difficult to treat and recovery is low (although notably some people do suffer from intermittent episodes of the disorder rather than being chronic sufferers).

There are several variants on the basic theme of the syndrome: Münchausen by proxy, in which the sufferer induces disease symptoms in another (usually a child). And the modern variant of Münchausen by Internet, in which the sufferer pretends to have a disease in interactions with individuals or communities over the Internet. It seems likely, given the relative lack of risk, that this latter expression has become the most common in recent years. Indeed there may even be several undocumented subtypes of Münchausen’s by Internet, consider the modern wave of so called “Internet Asperger’s” sufferers.

But why does this occur? It’s an interesting object of speculation. Dishonesty has been suggested as an individually beneficial, albeit ultimately self-limiting social behaviour (more details on this can be found in the works of Robert Trivers, and to a lesser extent Richard Dawkins). And it is easy to see the simplistic explanation of why: Organisms work for the benefit of their genes, meaning that we are skewed towards A) breeding, and B) survival. If we deceive others we are more likely to outcompete them, which is good on the gene scale. However, the genome (not the individual gene, sorry Dawkins) is the unit of evolution, and so we serve the propagation of those with similar genomes as well, thus kin-selecting behaviour arises. Kin selecting behaviour leads to the formation of society and society provides a certain base-line benefit to us all. So a little deception goes a long way to individual success, but a lot of deception leads to destabilising society, screwing over ones kin, and generally being more self-detrimental than it is beneficial.

That said, the urges for deception should naturally be towards staying alive and comfortable and getting laid. Münchausen’s sufferers fail at this. There deception is, evolutionarily speaking, faulty. Sickness is not sexy (to most people). A great deal of cosmetics and beauty involve providing the appearance of health (making eyes look wide and alert, lips fuller, hiding blemishes, etc). What we as creatures generally like to see in mate selection is evidence of health. So excluding a subset fringe, Münchausen’s sufferers seem to be lowering their chances of propagation for temporary creature comforts. Yet another manifestation of the fascinating way that individual consciousness can subvert evolutionary drive. Albeit a disturbing example.

Sources & Further Reading

  • Seriously, pretty much everything Robert Trivers has written. Even if I don’t 100% agree with him the guy is a genius with fascinating theories.
  • By the same token, most Dawkins (although the guy is an ass, and has a gene, as opposed to genome, focused view of evolution).
  • A solid review of Münchausen’s by proxy.
  • A 2010 review of Münchausen’s by Internet.

Written by Caudoviral

02/06/2011 at 17:13

Posted in Behavior & Cognition, Health

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The Cautious 60%

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So I am sure that some of my readers will have heard about this already, but there is yet another survey floating around showing that (surprise, surprise) evolution is not being well taught in the nation’s highschool classrooms. Given the general level of scientific literacy on the subject, it is no surprise that we find a flaw in primary education on it. It is very difficult to grow up in modern society without being exposed to the idea, and while it is an elegant idea, it is not necessarily a simple one. So the first exposure any given person receives to it is most likely going to be wrong or only partially true. It falls to the humble science teacher to correct and complete these mis and partial understandings.

But the truth of the matter appears to be that they do not. Why? Well, an article in the current issue of Science (“Defeating Creationism in the Courtroom, But Not in the Classroom“) goes into that. We recently all had cause to celebrate the Dover decision, yet the article’s authors state: “We suggest that the cheering was premature and the victory incomplete.”

And they make a pretty good, if depressing, point. Others have focused on the explicit creationists in the school system, and while they are a problem, I have to side with the article’s authors: the so called “cautious 60%” are much more of an immediate concern. Maybe I am biased in thinking that even a 15 year old child should be able to see through the arguments of a dogmatic creationist, or maybe I am just more concerned about a silent majority than I am about a vocal minority (since the latter tends to only thrive in the tacit approval of the former).

So the findings of the study show that vocal evolutionists and vocal creationists make up only a 40% of America’s highschool science teachers. What about the 60% left over? They just want to keep their heads down and teach in such a way as no one gives them trouble, regardless of the consequences to their student’s understanding. The tactics most commonly used to do so are three: (1) Teach evolution solely on the micro scale; (2) teach evolution to the test while giving vocal caveats that the test is structured as if evolution were true and that they are certainly not making any kind of statement on the matter or asserting it as really true (the tactic my particular highschool biology teacher used); and (3) teaching the “controversy”.

Now all three of these are very problematic: (1) Ignores the very sizeable amount of evidence and very important role of macro-evolution. It leaves their students ill-informed and ill-equipped, and undermines the entire theory as a whole. (2) & (3) are even worse. They introduce into the classroom this air of intellectual relativism, to whit an idea that demonstrated scientific fact should have only as much credence as opinion. And moreover that the individual students opinion is more important than the proceedings of the entire scientific community. A very odd and obviously misguided notion. While encouraging free thought is a noble endeavour, encouraging a disregard and disrespect of rational thought and evidence is quite the opposite.

The cautious 60% may play a far more important role in hindering scientific literacy in the United States than the smaller number of explicit creationists. The strategies of emphasizing microevolution, justifying the curriculum on the basis of state-wide tests, or “teaching the controversy” all undermine the legitimacy of findings that are well established by the combination of peer review and replication. These teachers fail to explain the nature of scientific inquiry, undermine the authority of established experts, and legitimize creationist arguments, even if unintentionally.

I think that this silent majority should come under as harsh (or potentially even harsher criticism) than the misguided minority. I have no more respect for the craven than I do for the deluded (and indeed the deluded have a certain air of genuine good-intention behind them, misguided as it is, while the craven only care about their own asses). And after all, I believe someone once said something quite eloquent about planks v. splinters.

Sources & Further Reading

  • Defeating Creationism in the Courtroom, But Not in the Classroom
  • While not directly related, I keep finding myself recommending Dawkin’s new text The Greatest Show on Earth as an excellent primer on evolution, written in accessible language. Although I do generally detest the man’s rhetorical style and patronising attitude.

Written by Caudoviral

02/01/2011 at 21:51

Posted in Education

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This isn’t the antibiotic crisis you’re looking for…

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So there is a lot of talk going around right now about the antibiotic crisis. And a good bit of it is on HuffPo. No, I won’t link you. You will never find a more wretched hive of anti-vaxers and homeopaths. Suffice to say, Dan Rather, writing on the antibiotic crisis, made the following comment about a week ago:

[…] there isn’t a single known antibiotic to which bacteria have not become resistant.

I think that everyone who is taking the time to read this probably already has a good idea of my attitude towards scientific misinformation. And the above quote is a particularly good one because it manages to pack two mistakes in only thirteen words. What a value! Now, lets be clear about one thing, there is an antibiotic crisis, but the nature of it is subtly and importantly different than the picture many people are trying to paint.

Okay, the first mistake is a high school biology one. And its pedantic of me to even point it out, yet still important to know. Bacteria do not “become” resistant to antibiotics. That’s not how evolution works. A certain small percentage of bacteria already are resistant. In the absence of antibiotics this percentage remains small because antibiotic resistance (like every trait) has a cost, and it is not efficient to have it when there are no antibiotics. When we start using antibiotics, that small percentage grows and while the rest of the bacteria die off. Thus the already pre-existing resistant bacteria replace the vulnerable ones. This was once and for all conclusively demonstrated when we isolated penicillin resistant bacteria from among the gut flora of polar explorers who died and were frozen in permafrost in 1845 (Medical Tribune, December 29, 1988, p. 1, 23.) This one just bugs me.

The second mistake is the big one: “there isn’t a single known antibiotic”. Do you have any idea how many antibiotics we know? Dan Rather certainly doesn’t. I don’t either, so I guess I shouldn’t throw stones. But Mr. Rather seems to think that the number of antibiotics known is somehow equivalent to the number of antibiotics in use. I can guarantee you that he is at least an order of magnitude off. And if he wants to talk about the antibiotics that exist, then he is multiple orders of magnitude off. See, we tend to be anthropocentric, another pet peeve of mine. This means that we naturally want to view the battle against microbes as us vs. them. And that’s not true. We do not make antibiotic agents de novo to wage our war against tiny invaders. Rather, we subvert their own mechanisms (or the mechanisms of other types of life) and use those. As far as I know, there is no wholly synthetic antibiotic compound. No one is going to waste the money making one when they can be plucked from anywhere. These things are literally more numerous than if they grew on trees.

So why the crisis? Why, if there are so many antibiotic compounds known are we running out of ones that are effective to use? Because it is just not profitable. Because there are other, higher profit yield things that the pharmaceutical industry could be doing, and it doesn’t want to waste the time and resources on deriving, testing, and going through all the governmental red tape to get approval for a new antibiotic. Not to mention they have no pressure. In terms of the numbers game, the number of people who are dying from resistant strains is too small to raise a great public outcry. And because of people like Mr. Rather, everyone is going to be too busy pointing the finger at doctors and ag business to ask why the hell the pharmaceutical industry wasn’t prepared.

Should we stop being so careless with our antibiotics? Certainly. But are we going to run out? Well, no. Not unless we sit around twiddling our thumbs and playing the blame game when we could be isolating and testing more.

[featured image source: By Janice Haney Carr, Centers for Disease Control and Prevention (Public domain)]

Written by Caudoviral

01/21/2011 at 17:45

Posted in Biology, Health

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