Culturing Science – biology as relevant to us earthly beings

Archive for March 2010

Quote of the Day: Lamarck on Species

From Lamarck’s Zoological Philosophy (1809)

The farther we advance in our knowledge of the various organised bodies which cover almost every part of the earth’s surface, the greater becomes our difficulty in determining what should be regarded as a species, and still more in finding the boundaries and distinctions of genera.

According as the productions of nature are collected and our museums grow richer, we see nearly all gaps filled up and the lines of demarcation effaced.  We find ourselves reduced to an arbitrary decision which sometimes leads us to take the smallest differences of varieties and erect them into what we call species, and sometimes leads us to describe as a variety of some species slightly differing individuals which others regard as constituting a separate species.

Just as true now as then.

And for your information: Lamarck’s full name is Jean Baptiste Pierre Antoine de Monet Lamarck.

Written by Hanner

March 29, 2010 at 12:14 pm

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The Trajectory of Biology, Pt. 1: an introduction

Early in the month, Nick Merkelson, a cultural heritage studies graduate student writing at Culture in Peril, challenged me to think about whether humans have the capacity to fully understand a system on the large-scale, whether cultural or biological.  And while I, no philosopher, cannot address that question directly, have ever since had my mind set on the field of biology as a whole, and what “Biology” means exactly.

Sure, it means the study of biological systems.  But beyond that.. can we really generalize?  Can we even generalize based on purpose or intent of the study of biology?

The intents I will focus on are understanding and creation.  Studying biology for the sake of simply understanding how it all works, versus studying biology to create medicine, or reduce climate change, or benefit mankind in some way.

I will spend the next week or two exploring different ideas about where the purpose of science stands, how it got there, and predictions on where we are heading.  I’ll probably raise more questions than I answer, but, hey, isn’t that what science is like anyhow?

Written by Hanner

March 27, 2010 at 6:00 pm

Culturing Science: Best New Blog of 2009?!

Thanks so much to the Research Blogging community for voting Culturing Science best new blog of 2009!  I couldn’t be more excited and honored.  I’m going to work hard to post more frequently, always questioning why I am a scientist and what that means exactly.

Make sure to check out the other winners and finalists – there is some incredible writing and science out there.

In case you’re new to the place, here are some of my favorite posts you might want to check out.

Thanks everyone for reading and for the support.

Research Blogging Awards 2010 Winner!

— Hannah

Written by Hanner

March 23, 2010 at 11:06 am

Posted in Uncategorized

Why evolution is right, and your headline is wrong

On Friday, the Guardian published an article by Oliver Burkeman called “Why everything you ever learned about evolution is wrong.”  Pieces have been written against the article already so I won’t go into too much detail (well, a little maybe) – most notably by Jerry Coyne and the Guardian’s own response by Adam Rutherford.

The gist of the article?  Natural selection is more complicated than Darwin thought.  But put in more belligerent terms.

And it certainly is complicated.  As the article brings up, non-Darwinian forces have played a part in evolution in the past.  Microbiologist Carl Woese suggests that early microbial evolution was driven not by Darwinian evolution, but by horizontal gene transfer, where genes are traded between organisms and not passed down vertically through generations.  Burkeman also describes the phenomenon of linked genes, but does not explain the genetics.  Sometimes when two genes are next to one another on the genome, they will be passed along together as a package, even if only one is selected for.  Thus sometimes genes can be “selected” without being “selected for,” to put it in Burkeman’s terms.  But this effect can still be explained by Darwinian evolution.

The bulk of the article is about epigenetics – or how physical modifications to DNA, usually the binding of proteins, can turn a gene “on” or “off,” or change its expression level.  (See here for a primer.)  The article cites several incidents where changes in the epigenome (the full picture of an organism’s epigenetic character) caused by environmental factors affected the grandchildren of the organisms.  For example, a study where researchers confused the night/day internal clock of chickens by altering their lighting conditions found changes in their epigenetic profiles, and also found that their offspring had trouble locating food.  Thus – environmental changes are heritable?  Was Lamarck right about his giraffe necks?

Beyond the fact that most of these studies see their effects lost after a few generations – couldn’t one just argue that this is an issue of nurture?  That when you mess up a chicken’s internal clock, maybe it might have trouble raising its chicks, so that they have trouble surviving on their own?  Bottom line – I am not convinced.

What is most infuriating is the idea that because maybe there are exceptions to Darwinian evolution, it negates his theory.  I don’t think we know everything about evolution.  I don’t think that Darwin is right 100% of the time.  But I do think he is right 99% of the time.  And that’s what’s important.  As scientists, we’re seeking the patterns to life – patterns that can be applied large-scale to many organisms.  Study after study has shown that Darwinian evolution explains changes in organisms through generations most of the time.

We also should seek the abnormal – the horizontal gene transfers, the other forces at work that differ from our patterns.  But to take a field like epigenetics – which is still developing and which we barely understand, trust me, I study epigenetics for a living – and say that it somehow proves Darwin wrong?  That is absurd.  This isn’t a war.  Darwin is right.  Someone else may be right as well.  There are many forces at work here, people.

Which brings me to my final point: how could you ever publish an article called “Why everything you ever learned about evolution is wrong???”  This drives me insane.  If scientists are going to stand up and say, “we are objective, we are empirical, you can believe whatever we say because we are skeptical of ourselves and only seek truth,” we need to hold our science journalists up to the same standards.  I don’t know the credentials of the Guardian piece’s writer, but he clearly is not a trained biologist. As science becomes increasingly important in the daily lives of ever person on this planet, why is the field of science journalism and science writing shrinking?

Science writing should not be using grabber-headlines to gain readership.  I know, everyone wants their attention, every university press release wants the world to believe that they have discovered the cure to cancer or climate change or whatever else.  But, let’s face it: you haven’t.  Those problems will not be solved unless the scientific universe can form some semblance of a community.

Stop using headlines that are lies just to get attention.  Impatient internet users don’t even read the first paragraph of articles anymore, so even if your first line negates your headline, that is not good enough.  Just don’t do it.  Everything you ever learned about evolution is not wrong.  But as we learn more about how biology makes each of us who we are, our view of evolution may change.  And there’s nothing wrong with that.

[Edit: Thanks for the write-up, Genomeweb Daily Scan!)

Written by Hanner

March 21, 2010 at 11:49 am

How Genetics Works [Photo]

[via Flowing Data]

Written by Hanner

March 12, 2010 at 7:40 am

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Quote of the Day, Pt. II

From Carl Woese’s 2004 piece, “A New Biology for a New Century:”

A heavy price was paid for molecular biology’s obsession with metaphysical reductionism. It stripped the organism from its environment; separated it from its history, from the evolutionary flow; and shredded it into parts to the extent that a sense of the whole—the whole cell, the whole multicellular organism, the biosphere—was effectively gone. Darwin saw biology as a “tangled bank,” with all its aspects interconnected. Our task now is to resynthesize biology; put the organism back into its environment; connect it again to its evolutionary past; and let us feel that complex flow that is organism, evolution, and environment united. The time has come for biology to enter the nonlinear world.

More on this article to come in the next week.

This is essentially the reason I feared molecular biology for most of my life.  I felt like it removed organisms from their place in the web and analyzed their parts separately, with no connection to how they all worked together except on a very small scale.  The purpose of this mechanistic reduction seemed to be a way to apply nature to help ourselves, instead of getting the big picture of things, an understanding of the world, the patterns that make up life.  The former I saw as selfish, and the latter dignified and learned (or something like that).

Working in molecular biology, I’m learning that things aren’t so black and white.  Most molecular biologists are interested in these larger-picture, nearly philosophical questions, but are searching for their answers on the small-scale (looking for miniature models of larger truths).  Or, on the other hand, they are interested in curing cancer or other diseases.  As a Jewish cynic, I clearly hate my own species so see this as a waste of time — but I really shouldn’t blame scientists for wanting to help other people.

Or they are just looking for a way to spend their time, and there are a lot of jobs in science.

I would recommend reading the whole piece if you have an interest in reflecting upon the development of science in the 20th century.  Or if you’re a human living in the 21st century.  For real real.

Written by Hanner

March 6, 2010 at 1:20 pm

Posted in Reflection

Quote of the Day

“In an honest search for knowledge you quite often have to abide by ignorance for an indefinite period… The steadfastness in standing up to [this requirement], nay in appreciating it as a stimulus and a signpost to further quest, is a natural and indispensable disposition in the mind of a scientist.”

–Erwin Schrodinger, Nature and the Greeks

Written by Hanner

March 6, 2010 at 1:09 pm

Posted in Uncategorized

Invasive species corrupt DNA, not just ecosystems (Fitzpatrick et al., PNAS 2010)

I rarely think about how invasive species affect genetics.  It’s always in terms of ecosystems or species: invasive brown tree snakes gobbling up birds and lizards in Guam, or zebra mussels overwhelming and altering the environment of the Great Lakes.  How one species outcompetes and replaces another, changing the natural system.  This is partly because many of the common examples are of predator-prey relationships, where the two species are very distantly related and could never breed, thus keeping genetics out of the picture.  But what about situations where the introduced animal and native animal are similar?

This gets us into the muddy waters of what defines a species.  For sexually reproducing organisms, a species is the group of animals with whom one can exchange genetic material via reproduction, or, in other words, can produce fertile offspring.  To distinguish one species from another under this definition, a scientist would need a pretty wide worldview.  How else could he know that a squirrel from England could not mate with a US squirrel if it tried?  And the honest answer is: he can’t.  (Unless he collected squirrels from around the world and tried to mate them all with one another… but that’s a lot of work.)  Thus, species are often also defined based on location or geography, despite the fact that maybe they could mate if they had access to one another.  But what are the chances that a squirrel will swim across the Atlantic for a new girlfriend?

And there’s where invasive species fit in.  In a paper published this week in PNAS out of Knoxville, TN, Lexington, KY, and UC Davis, scientists studied the Salinas Valley in central California, where salamanders from Texas and New Mexico had been introduced in the 1950s for use as bait by fisherman.  These salamanders, the Barred Tiger Salamanders (Ambystoma tigrinum mavortium) had been defined as a separate species from the threatened native California Tiger Salamanders (Ambystoma californiense), as their populations had been living apart for 3-10 million years, and thus it was unlikely that they were still genetically similar enough to mate.  But – alas – this assumption was wrong.  The invasive salamanders have been mating with the native species for the last 50 years, producing hybrids which are able to mate with either species and one another.  The question: is this hybridization significantly changing the DNA of the native species?

To investigate this question, the researchers identified an introduction site at a pond in central California, and took samples of over 200 salamanders (by clipping the end of their tail and immediately releasing them) at this site and others within a region 200 km north.  Using salamanders of each species from non-invaded ranges, they determined the baseline genetic makeup of each species.

They scanned the genomes of the sampled salamanders (say it 10 times fast) for 68 genetic markers to see if any of the invasive genes had “taken over” the native genes.  They saw no real difference in 65 of these species — that is, the salamanders retained their native genes.  However, they saw a drastic increase in 3 of the genes.  In the figure below, taken from their paper (click on image for larger size),  the little “thermometers” measure the DNA differences at different sites, native in white and invasive in black, with the introduction site indicated by the red arrow.  The upper left (A) shows the big picture: of the 68 gene markers studied total, invasive genes are only apparent at the introduction site.  The other 3 boxes (B, C, D) show the three genes that have spread — and as you can see, they have spread far and deep, despite their invisibility overall (A).  The authors were thorough: they tested whether this pattern was due to either sampling error or random genetic drift without natural selection, and neither of these biases accounted for the pattern of these 3 genes.

The function of these genes is unknown.  However, by studying the behavior of the animals, it seems they are related to reproduction.  The hybrids have larger larvae with greater survival and develop more quickly, ever hastening their dispersal.  This raises a few questions:

1.  If these invasive genes are helping survival, then who cares if they invaded?  It is easy to look at this as actually beneficial to the threatened native salamanders.  However, it has unknown impacts on the surrounding ecosystem.  These bigger larvae eat a lot more, impacting the populations of their prey species through indirect effects of the invasion.  A change in the abundance of one species affects all others – what seems to be an immediate benefit can be incredibly harmful in the long run.

2.  How do we define a species?  The native salamanders are a threatened species.  If they have received genes that increase their numbers through hybridization, is this a comeback?  Are they still A. californiense?  Do these 3 genes alone make them A. mavortium?  Are they an entirely new species?  Is it possible to stop the invasion of these genes throughout the state without killing off a threatened species?

I don’t have the answers to these questions.  We human beings are drawn to classification: we want to put all of the animals in neat little piles and call it fin.  But the truth is that species are eternally evolving — as Peter and Rosemary Grant have shown with their Galapagos finches, most recently in November 2009.  The monkeys that live on one side of a jungle can have a different genetic makeup than the ones on the other side even if they can still mate.

Clearly the introduction of these salamanders, which was just an innocent attempt to raise some bait locally, has had unforeseen impacts on the ecosystem.  Humans’ ability to travel has meant that we are bringing animals together that have not evolved to live together, or have evolved apart millions of years ago.  In some ways it feels like what is done is done — and I am not enough of an expert on habitat restoration to tell you otherwise.  But try little things: wash the mud off of your boots before you go hiking in another state or country, don’t release your foreign pets locally (as my roommate Erinrose and I have been tempted to do with our pet turtle, Nicolas Cage), volunteer at your local wildlife refuge.  Biodiversity is important.

How can we save our planet?

Fitzpatrick, B., Johnson, J., Kump, D., Smith, J., Voss, S., & Shaffer, H. (2010). Rapid spread of invasive genes into a threatened native species Proceedings of the National Academy of Sciences, 107 (8), 3606-3610 DOI: 10.1073/pnas.0911802107

Written by Hanner

March 2, 2010 at 9:43 pm