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What's in the Autoclave? A Blog about Science

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A Guinea Pig's History of Biology [Feb. 27th, 2010|04:58 pm]
What's in the Autoclave? A Blog about Science
Today I finished reading Jim Endersby's A Guinea Pig's History of Biology (2007). As the title suggests, it is a history-of-science book, focusing on biology from the 19th century to the present. The book has an interesting organizational conceit: instead of a strict chronological progression, the author organizes his chapters around several of the most important "model organisms" that have been used in biology over the past 200 years, describing how those organisms (from the evening primrose to the fruit fly) came to prominence in scientific circles and some of the important and fundamental discoveries to which they led.

The author's style of writing is very clear, and the book should be accessible to any lay reader who has had a solid high school or college introductory biology education. The book focuses more on the process of the science than the discoveries themselves, so it doesn't get bogged down in the details that might turn off a nonprofessional (although the significance of some of the discoveries is therefore sometimes understated, and I suspect that I got more out of the book for already having known a little about many of the key scientists and discoveries mentioned. For instance, in the chapters on Mendel and de Vries, it would have been helpful had the author stated more clearly which of their hypotheses were wrong, and why.)

The biggest weakness of the book, unfortunately, is that the organizing principle (each chapter on a different organism) doesn't always work very well. There is no clear argument that the author is trying to put forward, no central theme. As work on different organisms often occurred contemporaneously, the author necessarily jumps back and forth chronologically in a way that can at times become confusing, but even within each chapter the author leaps quite a bit from topic to topic such that the work often feels more like a collection of anecdotes rather than a continuous story or progression.

That said, the anecdotes are at least interesting, and I did learn a great deal about how today's community of science came about. The transition from the solitary naturalists of Darwin's day to the hierarchical structures of a modern university or industrial laboratory did not happen overnight, of course. And the author does convincingly make the case that the emergence of these particular organisms as lynchpins of modern biology was often as much by chance as by intention on the part of the researchers.

One final quibble: although the last chapter of the book is ostensibly on the laboratory mouse, research in mice is barely mentioned before the author moves on to talk about some general concluding philosophical themes. I found this odd, considering that the mouse is arguably the most important model organism in modern medical biology. The author alludes to the ethical issues of performing research on a vertebrate mammal, and then beats a hasty retreat. Of course, the history of mouse research could no doubt fill a book all on its own.

So: on the whole, it was an interesting book, which included many stories that were new to me even about some of the organisms I've studied myself. Although the way the book was organized was as often a detriment as a strength, it filled in some of the gaps in my knowledge about how we as scientists got to where we are today, and the challenges that our predecessors faced in the pre-genomic era of not-so-very-long-ago. As a survey of two centuries of science, this book just barely scratches the surface, but it did hit many of the high points.

(Also, there is a very cute guinea pig on the cover.)

I'm not sure what I'll read next. At Christmas my dad gave me a general-audience book about the disease that I study (as I am a PhD, not an MD; but still, after four years of working on this disease, I doubt that I will get much out of the book that I don't already know.) I also have The World Without Us on my shelf, untouched; it was also a gift from the previous Christmas, but I've been avoiding it because I suspect it may be very depressing.

Has anyone else read A Guinea Pig's History...? Or do you have suggestions of similar history-of-science books that might be an interesting read?
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Happyhour [May. 29th, 2009|10:26 am]
What's in the Autoclave? A Blog about Science
The current issue of Cell includes a research article from those whacky Drosophila1 geneticists that describes a gene which, when mutated, increases "resistance to the sedative effects of ethanol." They have dubbed this gene mutant happyhour. (Article: here with commentary here.)

There is a long history of fly geneticists giving genes colorful and memorable names. I don't work on fruit flies, but I can name a few of their genes off the top of my head: frizzled, moth-eaten, lunatic fringe, hedgehog and (of course) sonic hedgehog. Let no one ever accuse scientists of lacking a sense of humor.

Recently some have argued that these whimsical names ought to be changed. The argument is that physicians shouldn't have to tell patients that they may have a mutation in their "lunatic fringe homologue." (For more, here at the website of the HUGO Gene Nomenclature Committee website.) The patient might take offense.

Precision is important in science, so it may make more sense to rename lunatic fringe to O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase -- the latter name tells you something about what the gene actually does -- but the former is certainly easier to pronounce and remember!

1Fruit flies, one of the most well-studied model organisms used in genetics and biology.
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Vaccine [Nov. 14th, 2008|01:15 pm]
What's in the Autoclave? A Blog about Science
It's been a while since I posted here; it's been a very busy summer and fall as I try to get the last experiments finished for a paper.

The current issue of Nature Immunology has an editorial about the declining use of vaccines in the West and the corresponding rise in measles and mumps outbreaks.

I've been reading a pop-science book about the history of vaccines lately, and I have grown to understand where some of the anti-vaccine arguments are coming from. There were serious missteps in the early days of vaccine development, when (frankly) doctors didn't really know what they were doing. The original smallpox vaccine in the 1800s was nearly as bad as the disease itself, for instance. But it is unfair to compare pre-1960s medicine to the medicine of today, and enough safety studies have been done on today's vaccines to establish that they work and work well, with minimal side effects -- side effects certainly less severe than those associated with actual measles and mumps infections.

Vaccines have gotten a lot of attention recently for their supposed connection to autism. What I was not aware of until reading this editorial is that the scientist who originally suggested the autism link had a major conflict of interest -- his work was funded in part by personal injury lawyers involved in a lawsuit against the MMR vaccine manufacturers. This kind of thing is the reason why researchers are increasingly being asked by journals and the institutions at which they work to file annual declarations of their conflicts of interest... but that's a separate topic entirely.
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Miles per gallon, versus gallons per mile [Jul. 24th, 2008|12:50 pm]
What's in the Autoclave? A Blog about Science
There's a very cool article in the June 20 issue of Science (I'm a bit behind in my reading) that talks about a better way of thinking of fuel efficiency in vehicles. (The article is here for those with access to Science online.)

One of the few things I remember from my undergraduate statistics class is the importance of choosing the right thing to measure. You can make a statistic out of any measurement(s) you like, but it is important to step back and think about whether you are really measuring what you want to, whether the comparisons you make are actually the most appropriate for a given problem. The Science article argues that the standard United States measurement of a vehicle's fuel efficiency -- the number of miles it can travel per gallon of gasoline -- may not be the most appropriate measure when thinking about that vehicle's environmental impact.

Miles per gallon (mpg), as the authors point out, is a great measure of a vehicle's useful range -- how far can you travel without refueling? And so for a consumer purchasing a car, it is a useful metric. However, an environmentally-conscious consumer -- or a policymaker setting fuel efficiency standards -- might be more interested in the reciprocal of this number, the number of gallons of fuel that it takes to travel one mile. (Or, since this is likely to be a decimal number with one or more zeroes in front of it, the number of gallons it takes to travel 100 miles, or 1000, or any other arbitrary distance.)

Why does this reshape the way we think about fuel economy? Well, most drivers (apart from vacation travel) use their vehicles to travel a set distance every day -- their commute to work. In most cases, the distance part of miles per gallon (distance divided by amount of fuel consumed) is effectively a constant. The variable is the number of gallons which the car consumes to travel that fixed distance. So consider a hypothetical driver whose vehicle gets 20 mpg (or, reciprocally, uses 0.05 gallons to travel one mile.) He or she is thinking of buying a new car, and his choices are one that gets 25 mpg versus one that gets 15 mpg. The 25 mpg car uses 0.04 gallons per mile (an improvement of 0.01 gallons per mile), while the 15 mpg car uses 0.0667 gallons for the same distance (a loss of 0.0167 gallons per mile.) A difference of 5 mpg in fuel economy is not the same at the lower end of the scale as it is at the higher end.

The authors point out, then, that an improvement in fuel efficiency from 16 mpg to 20 mpg actually has more of an effect on gas consumption than a change from 34 mpg to 50 mpg -- a savings of 125 gallons per 10,000 miles in the first case, compared to only 94.1 gallons per 10,000 miles in the second. They argue that stating a vehicle's fuel efficiency in terms of gallons per mile (or similar) would help consumers make more environmentally-conscious (and economically-conscious) decisions. People, including policymakers and environmental advocates, may undervalue the importance of small improvements at the lower end of the mpg scale, focusing instead on the high end of the mpg scale, because it seems counterintuitive that a small improvement in a low mpg vehicle should have more of an effect on fuel consumption than the same absolute mpg difference at the higher end of the scale.

Will this stop me from being disdainful of "hybrid" SUVs? No. The more environmentally friendly choice remains a high mpg subcompact. But averaged over the useful life of the vehicle, every little drop of fuel counts.
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Vaccines (again) [Jun. 19th, 2008|12:26 pm]
What's in the Autoclave? A Blog about Science
CNN.com, as usual, is doing a very bad job at reporting on the current vaccine debate that is playing out in the mainstream media.

Today their website includes an article headlined "Should I vaccinate my baby?" The "story highlights" at the top of the page includes the bulletpoint "Parents have concerns about possible vaccine and autism link," but nowhere in the article itself is it mentioned that the current consensus in the scientific community is that autism is not vaccine-induced. The article seems to do little more than fan the flames of anti-vaccine hysteria.

The article then goes on to list a few options that parents who are concerned about over-vaccination of their children might take. Most of these probably won't make any difference one way or another. The only one of these that I actually find seriously objectionable is #2, "Not doing some shots at all." The examples given are chicken pox and rotavirus vaccines, which some would consider unnecessary. However, the chickenpox virus (varicella zoster virus), despite often being dismissed as a harmless and expected part of childhood, can actually be quite serious in some cases -- most importantly, it can cause birth defects if a pregnant mother is infected. But also, the virus is never completely cleared from the body -- it persists in a latent (inactive) form in nerve cells and can reactivate later in life (generally in the elderly) to cause "shingles," an extremely painful (and symptomatically distinct) condition.

More information about the Varicella zoster vaccine can be found here, at the World Health Organization website. Interestingly, VZV is thought to be specific to humans (i.e. there is no insect or animal reservoir) so the virus could, in principle, eventually be eradicated in the same way that smallpox was, although this would be somewhat more challenging due to the virus' ability to reactivate from a latent infection.

As for rotavirus, if you want to deal with your child's digestive "difficulties" that is entirely up to you!

The hysteria over vaccines is a huge pet peeve of mine. I will say, though, that I'm currently reading a popular-science book on the history of vaccines, and I am beginning to appreciate why so many people still are afraid of them. The first vaccine, against smallpox, was developed even before Pasteur's demonstration of germ theory. Early smallpox vaccines were nonsterile, and often contained the tetanus bacteria, making the cure seem worse than the disease. So I can understand that vaccines historically may have a bad reputation -- but modern medicine is very different than the "medicine" of the 19th and early 20th centuries. Vaccination has saved millions of lives and unquantifiable morbidity, but like most preventative medicine, it can be a tough sell to the general public.
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Mergers and Acquisitions [Jun. 12th, 2008|04:12 pm]
What's in the Autoclave? A Blog about Science
Today's New York Times business section reports on the just-announced purchase of Applied Biosystems by Invitrogen. These two companies are big names in the American scientific supplies and tools world. Applied Biosystems is probably best-known for making equipment including machines that perform "real time PCR," a sensitive and quantitative method of measuring gene expression that has become widely used in many subfields of biology over the last decade. Invitrogen is one of the largest suppliers of biomedical research supplies in a wide array of areas, particularly relating to genetics and in vitro cell culture. Their purchase in 2000 of rival Gibco (a major supplier of in vitro tissue culture reagents) ensured that pretty much every US cellular or molecular biology research lab is using at least some of their products.

Mergers are always a little bit worrysome; competition among vendors for our research dollars helps keep costs down across the board. But I'm not an economist, so I probably shouldn't speculate too much on the impact of this merger. Invitrogen, as far as I know, doesn't currently produce instrumentation for real-time PCR, although both companies sell the consumables required to use the machines. There are other providers of all of these products, including Stratagene, so there won't be an absolute monopoly.

A press release on the acquisition is found on the ABI website, here.
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Bacteria everywhere! [May. 23rd, 2008|12:04 am]
What's in the Autoclave? A Blog about Science
The New York Times reports today on early findings from the "human microbiome project," a survey of all the microorganisms that live on and in our bodies. (The original research paper is not yet available on the website of the journal Genome Research, where it apparently will be published tomorrow.) In particular, this study looks at the bacteria that live on the skin of our inner elbows -- interesting if only because it isn't the first place most people would think about being loaded up with bacteria. Apparently, these bacteria help keep our skin nicely lubricated -- they metabolize fats in our skin.

This is the first I've heard of this microbiome project, but it seems like a sensible thing to survey. After all, it's been known for a long time that bacterial cells outnumber the actual-human cells in our bodies in terms at least of absolute numbers. Almost all of these bacteria are harmless passengers, and many are thought to be helpful -- the best known example being the intestinal bacteria that help digest food. However, until recently microbiologists were limited in their ability to study these bacteria because most won't grow in a lab -- they're well adapted to growing in their real-world niches, but not in a test tube or petri dish. So the bacteria that have been best-studied are the ones where growth conditions have been determined by trial and error, essentially; ones where you can easily simulate their real-world niche in a lab. More recently, though, more sensitive techniques have been developed that allow a scientist to analyze very small amounts of DNA without actually having to grow up a large test-tube-full of bacteria first. So now we can get an idea of how much genetic diversity there is directly at the site of interest. As for the microbiome project, it would be useful to know what the "normal" bacterial composition of our bodies are so that we have a reference for comparison to situations in which the bacterial composition has been changed (for instance, we know that treatment with broad-spectrum antibiotics can affect the bacteria in your gut, at least temporarily, causing digestive problems. Similarly, an imbalance or overgrowth of one species at the expense of others can cause problems, as in a staph infection.)

Apparently most of the bacteria in our inner elbows fall into one of six groups (the article in the NY Times calls them "tribes," which is not a part of any classification system with which I'm familiar. Depending how the study was carried out, and given that the definition of "species" starts to get a little fuzzy with microorganisms, I'm guessing that they're talking about six different genera (one step up from a species.) I'll have to read the article.) Anyway, the point seems to be that it's actually a pretty limited number of different "things" living there... but what they lack in diversity they make up for in sheer numbers.

The Times article does include a pretty good description of the importance of commensal bacteria, and the idea that each of us is essentially a "superorganism" made up of us + our commensals.
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Book review: Simon LeVay's "When Science Goes Wrong" [May. 4th, 2008|05:04 pm]
What's in the Autoclave? A Blog about Science
Recently I bought When Science Goes Wrong: Twelve Tales from the Dark Side of Discovery by Simon LeVay. The author appeared on The Daily Show, and it sounded like it might be an interesting read. I thought that an every-now-and-again book review might be interesting for this blog -- I don't read a ton of nonfiction, but there's a lot of underappreciated pop-science writing out there.

So, obviously the following is subjective; your mileage may vary.


Accessibility / readability: A-
Scientific merit: B-
Overall: B

When Science Goes WrongCollapse )
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Genetic testing and the law [Apr. 23rd, 2008|08:20 am]
What's in the Autoclave? A Blog about Science
I've been crazy busy for the last week and a half, but here's a brief topic of interest.

Congress is nearly ready to pass the Genetic Information Nondiscrimination Act. The law, which has widespread support in both political parties, would make it illegal for health insurers to deny coverage to someone based on the results of genetic tests, including currently-available tests for known breast cancer susceptibility genes, for instance. The bill had been held up in the Senate by Oklahoma Republican Tom Coburn, a medical doctor, who wanted some changes apparently in insurer's liability -- the NY Times article doesn't specify what exactly those changes are, but presumably it will be a part of the Congressional Record after the bill goes to the floor if people are interested.

In any case, this law should help alleviate one of the biggest fears about genetic testing: namely, that if a risk factor for some disease is discovered in a particular patient, that patient might be left uninsurable.

A few weeks ago, National Public Radio's "Science Friday" had a great discussion about genetic testing (available in podcast form here) discussing the current state of the field. Many companies are offering genetic testing kits, which are not currently regulated by the FDA and which, in some cases, may not even have very strong science behind them. Some gene variants (BRCA2 for breast cancer) have been well-characterized, but in many cases these "risk factors" still aren't strongly predictive for a particular disease. Very few diseases or physical traits are controled by single genes anyway, so it may be a bit early to be applying this kind of technology. It's technically very simple these days to test your DNA for "polymorphisms" (the small changes that make individuals different from one another) but it is often less clear what functional effect those variations have. Of course, ten years from now the story will likely be very different as we learn more; the Genetic Information Nondescrimination Act is an important example of anticipating an ethical/legal problem rather than reacting to one too late.
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Open access to scientific papers [Apr. 7th, 2008|04:22 pm]
What's in the Autoclave? A Blog about Science
As of today, all newly-accepted-for-publication peer-reviewed scientific manuscripts describing work funded (in whole or in part) by that National Institutes of Health must be submitted to an open-access online database called PubMed Central within one year of their publication in a print journal.

That was a complicated sentence. Sorry.

Anyway, the policy statement is here.

The issue of open access has been a contentious one. It is, of course, expensive for a publisher to run a scientific journal -- they generally have relatively small audiences. A large part of their revenue comes from access fees charged to Universities that allow investigators to access the journals' content over the Internet (rather than charging individual investigators, the University or its library are charged a blanket fee instead.) On the other hand, the content of the journal is not generated by the journal itself -- it is generated by the investigators who have received public funding. Open access advocates argue that if the public paid for the studies, it shouldn't have to pay again to read them. The new compromise is to allow journals this one-year window of exclusivity, after which time the information must go into the central PubMed database. There's still a bit of confusion, I think, as to whether the journals should automatically submit this material to PubMed Central themselves or if it is up to the individual investigator to be compliant -- at this point, I think it's up the individuals -- but I suspect that open access is here to stay. How this will affect the economics of scientific publishing remains to be seen. (Note also that there are some major loopholes as well: this doesn't cover privately funded research, such as that performed at a pharmaceutical/biotechnology company.)
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