Culturing Science – biology as relevant to us earthly beings

Archive for April 2010

Science on the Internet: 04/29/2010 [Links]

I read, on average, 500 posts from over 180 blogs every single day.  Might as well share some of my findings with you!

  • AMAZING gallery of old-school science education models over at LIFE
  • The New Scientist covers a hypothesis about the origin of life on earth: that the RNA code we have now exists in its form due to natural affinities between nucleotides and amino acids.  Essentially, this means that once all the pieces were floating around, life was inevitable.
  • Fascinating slideshow over at BBC on research about cuckoos, the famous nest parasites which lay their eggs in others birds’ nests to avoid parental duties.  Scientists have been studying how frequently-parasited species have adapted their egg patterns to help distinguish cuckoo eggs from their own.
  • At The Voltage Gate, Jennifer writes about the current state of plastics in our environment, and how the “green” movement isn’t working too hard to stop this.
  • Will lifestyle choices you make effect your grandchildren epigenetically?  The details of a NOVA documentary on this question are over at Genes to Brains to Mind to Me.
  • The Insane Clown Posse recently doubted scientists in their song “Miracles,” specifically in the lyrics: “Fucking magnets, how do they work? / I don’t want to talk to a scientist!”  The resident physicist, Jim, over at Ghost Island gives an explanations of how magnets fucking work!
  • Cryptozoologists must mourn the discovery that the supposed 3-foot earthworm, Palouse, is less than a foot long.  Tear.  Covered on 80beats.

Written by Hanner

April 29, 2010 at 7:15 pm

Major universities write open letter in support of FRPAA, open access publishing act

Congress finds that–

(1) the Federal Government funds basic and applied research with the expectation that new ideas and discoveries that result from the research, if shared and effectively disseminated, will advance science and improve the lives and welfare of people of the United States and around the world; and

(2) the Internet makes it possible for this information to be promptly available to every scientist, physician, educator, and citizen at home, in school, or in a library.

HR 5037 2010

I’ve written previously about why I feel open access publishing of scientific research is important, and the challenges it faces.  Currently most high-profile journals are closed access, requiring a paid subscription of hundreds of dollars each year, despite the fact that most research is funded through government agencies.  Why should taxpayers have to pay twice to have access to science?

As I’ve said before, it’s a complicated question.  How do we keep productivity and quality up without the competitive atmosphere created by journal hierarchy?  How do we ensure that peer review is selective without revenue?

But I think the benefits outweigh the potentially negative outcomes of these questions.  Science will become more efficient as scientists everywhere have greater access to results and methods.  We will have more opportunities to create databases and communicate with one another.  The public will have access to the latest developments, promoting science education.  And research has the potential to fall under greater scrutiny by both the scientific and non-scientific communities.  I also just like the idea of science-for-everyone as a rule; science is not for the elite, but for the world!  (Right?)

Congressman Mike Doyle (D- Go Pennsylvania!) has revived an older bill, proposing the 2010 version of FRPAA (Federal Research Public Access Act), which would require all research institutions that spend over $100 million each year in research funding to require that the resulting research be public within 6 months of publication.  This includes all the major funding agencies, such as the NIH (National Institute of Health), NSF (National Science Foundation), CDC (Center for Disease Control), and others.

Today, major research universities – Harvard, Carnegie Mellon, UPenn (pound!), UTexas, Pitt, UCs, Rutgers, Ohio State, UIndiana, UIllinois, etc. etc. – got together and wrote a letter to Congress (.pdf warning!) in support of this bill.  They state everything I have just tried to explain above far more eloquently.

As scholars and university administrators, we are acutely aware that the present system of scholarly communication does not always serve the best interests of our institutions or the general public.  Scholarly publishers, academic libraries, university leaders, and scholars themselves must engage in an ongoing dialogue about the means of scholarly production and distribution. This dialogue must acknowledge both our competing interests and our common goals. The passage of FRPAA will be an important step in catalyzing that dialogue, but it is not the last one that we will need to take.

FRPAA is good for education and good for research. It is good for the American public, and it promotes broad, democratic access to knowledge. While it challenges the academy and scholarly publishers to think and act creatively, it need not threaten nor undermine a successful balance of our interests. If passed, we will work with researchers, publishers, and federal agencies to ensure its successful implementation. We endorse FRPAA’s aims and urge the academic community, individually and collectively, to voice support for its passage.

The internet and globalization have created opportunities for collaboration and the rapid spread of information, but the current system of publication is antiquated and is only hindering us.  I am enlivened by both the existence of this bill and its acceptance among research institutions.  I’m sure people will find fault with the 6-month waiting period, but this is a big step.

Let’s just pray now that it will easily pass in congress.  Then the real work will begin, of creating ways for us to share the public information in an organized fashion.  I’m looking forward to the day when we get to face those challenges.

(Info from GenomeWeb Daily Scan)

Written by Hanner

April 27, 2010 at 7:28 pm

Posted in Uncategorized

The alien landscape of your cells

Jessica over at bioephemera alerted the world that the GE Healthcare IN Cell Imager photo contest winners had been announced.  And looking through these photos sent chills down my spine.  (I was eating ice cream simultaneously… But, no, it was probably the pictures.)

As you can see, the pictures show various patterns of fluorescence.  A scientist can selectively stain parts of cells with fluorescent markers  – using antibodies, for example – to study their locations, or even use the brightness to measure the amounts.  (In the lab I’ve used fluorescent antibodies to stain protein residues, and I could even see the brightness without film or a microscope in a dark room.)

This here on the left is a picture of brain tissue.  The blue parts are its DNA, while the green and red are two types of neurons, or brain cells.  They’re all stringy and tangled looking so that signals can be transmitted quickly through the brain.  I’m a sucker for pictures of neurons because they look so alien compared to normal cells.

But, truly, all life on the cellular level is alien.  That’s part of what is so inspiring about viewing image collections such as this one: how can we imagine that this is what is going on inside of us?

It took me 6 years of studying biology before I truly understood that CELLS MAKE UP MY BODY.  I know, it seems like an obvious fact.  But it’s one thing to read a biology textbook and label a drawing of the parts of a cell, and another to fully grasp the concept that trillions of these things compose my body, undergoing processes of which I am completely unaware.  That once I was one cell – and now not only do I contain multitudes, but many different types.

I want to share my first moment of this realization with you.  I was a sophomore in college taking a genetics course with my main man, Stephan Zweifel.  To be perfectly honest, I was completely overwhelmed by the class.  (The thought of two DNA strands overlapping and switching their genes in a cell was way too much for me to grasp at the time.)  But one day he showed us a video put out by Harvard showing the life inside of a cell.  Maybe it was the mesmerizing music, but I was drawn in entirely, struck simultaneously by two emotions.  The first was horror at my inability to follow the video, identify a single molecule, while my classmates called them out around me.

But the horror quickly dissolved into complete and utter awe.  I sat there slack-jawed as molecules assembled and disassembled themselves into elegant stalks (actin and microtubules, the beam-like skeleton supporting the cell), a bow-legged molecule hobbled along a pole dragging a huge, watery balloon behind it (a motor protein guiding a vacuole to the transportation center of the cell), and proteins suddenly stood up erect, as if for the first time (a dramatic conformational change).  It didn’t matter that I didn’t know what was happening or why.  All I knew is that something complex was happening on screen, and that these things happened inside of me.  Constantly.  And I had never noticed.

How could my own body be so alien?  I could have been watching a sci-fi film.  And it hit me: there is beauty on this small scale.  There is art that had been perfected for billions of years, that continues to evolve.  And I had the tools to understand it if I could only apply them.

And that’s how I began my journey to try to become a science dilettante.

But seriously, folks.  Look at lots of pictures and movies about cells and molecules.  Get totally freaked out about your body and its alien landscape.  Take comfort in the fact that no one will ever fully understand it and find joy in being overwhelmed by all the things we don’t know.  That’s what being a scientist is about, as far as I’m concerned.

GE Analyzer IN Cell Photo Competition 2010
GE Analyzer IN Cell Photo Competition 2009
Harvard’s Inner Life of a Cell (music)
Harvard’s Inner Life of a Cell (narration)

Written by Hanner

April 27, 2010 at 6:10 am

Posted in Art, Link, Reflection

Octopuses doing tricks on the internet and our search for non-human “intelligence” An underwater photographer has his camera stolen by a thieving octopus, who flees with the device, filming along the way.  Sure, he was filming his own flesh, but baby’s first movie isn’t too shabby.

People love to talk about octopus “intelligence.”  The photographer specifies that the octopus wasn’t attacking him, but just wanted to steal his camera.  Why?  What use did he have for it?

If you look up “octopus” on youtube (which I hope you’ve done) you’ll come up with a billion videos of the animals solving puzzles.  (Or carrying coconuts on their heads.)  When I worked at Hatfield Marine Science Center, a story was told about the education center staff noticing that fish were disappearing from their tank, leaving no bodies but simply dwindling in number.  One night, a security camera caught an octopus crawling across the floor into the fish tank, grabbing a snack and returning to its own tank.  Whether it was intentionally trying to be sneaky or just didn’t like the conditions in the fish tank is unclear – nevertheless, stories like this are perfect fodder for support of cephalopod intelligence.

I’m clearly opening a huge can of worms here – or perhaps a jar of crabs – but can an octopus actually be described as “intelligent?”  What is intelligence?

I’m on a cephalopod email list where there is an active discussion on the use of the word “intelligence” in reference to octopuses.  One contributor, David Hill, wrote that one issue with the use of the word is its multiplicity of meanings depending on the circumstances.  Here are some of his own examples of varying definitions:

1) Solves complicated problems
2) Integrates multiple sensory inputs into a behavioral sequence
3) Uses complex information to determine behavior
4) Displays ‘insight’ (?) when approaching a novel situation
5) Has a lot of neurons, or ‘higher’ interneurons
6) Demonstrates functional mastery of ‘difficult’ concepts
7) Behavior is highly visual, or otherwise a lot like human behavior
8) Uses a lot of longer-term memory, or can demonstrate this memory
9) Can communicate complex ideas to other members of the species
10) Has a complex communication system
11) Can communicate with people

Throughout this list, there are two main criteria: language and access to memory.  However, the requirement for these two is consciousness.  It’s hard to imagine storing and accessing information in the brain without having some sense of your own self.  It’s consciousness that differentiates an automatic, mechanistic reaction by instinct from a thought-out (even if briefly) decision.

How can you qualitatively or quantitatively describe consciousness?   We have no real language for this purpose because consciousness is purely experiential.  For all I know, I am the only conscious being and you are all robots and this is some sick game.  If we can’t even generalize across our own species, trying to imagine or articulate other levels of consciousness – a different mixture of thought and instinct – is nearly impossible.  How can we know the self-awareness of a monkey or a dog?

In 2005, scientists from the Institute of Neurobiology in San Diego came up with a list of criteria for mammalian consciousness (article here).  Now, I’m no neuroscientist, nor am I going to go through their entire list, but here are some of the most important physical brain criteria for determining consciousness:

  1. Variable EEG (electroencephalography) activity. An EEG is a test to measure the levels of electrical activity in the brain.  An awake human has EEG levels of 20-70 Hz, while humans in unconscious states (sleep, under anesthesia, vegetative coma) have EEG levels of 4 Hz.  If an animal has 2 different EEG states, it is presumed that they have some level of consciousness above zombie sleep.  All mammals tested thus far exhibit this.
  2. Thalamocortical system.  Many parts of the brain can be removed or damaged without loss of consciousness; not the thalamus or the cortex.  These two parts of the brain (see colored portion of figure above) are well connected and significantly larger in humans than other mammals with similarly sized brains, leading scientists to believe that they are linked to consciousness.
  3. Widespread brain activity.  When humans are actively thinking through a problem, there is activity all over the brain.  However, when we’re performing tasks that have become routine or automatic, activity is restricted to smaller areas.  Thus we could measure the brain activity of animals to see if they have different states of activity extension depending on comfort with a certain activity.

The authors suggest that these parameters, and 14 others that I’ve left out, can be tested in mammals to determine whether they are conscious, giving us information on the evolution of consciousness as well as supporting our constant anthropomorphization of cats, dogs, and walruses all over the internet.

All mammals are in the same class and show a great deal of homology between species, making it easy to compare them to our only known instance of consciousness, ourselves.  Birds are more complicated because they have a different brain structure.  However, as vertebrates, we are pretty closely related to birds.  Studies have been able to map the bird brain onto the human brain, and the study of their consciousness is ongoing.

Octopuses, however, are a whole different ballgame.  They don’t even have bones!!  We clearly departed from the evolutionary pathway of octopuses a long time ago.  Let’s quickly go over the 3 criteria above for mammalian consciousness to see if they apply for cephalopods.

  1. Variable EEG activity.  In 1991, Bullock and Budelman measured EEG potentials in cuttlefish and found variation similar to humans, suggesting that cephalopods have multiple levels of consciousness.  While this is the only study of its type and should be repeated, it is the strongest evidence thus far to support consciousness in cephalopods.
  2. Thalamocortical system.  Clearly octopuses do not have a thalamocortical system.  Humans and octopuses have very similar nerve cells, but their brains evolved separately so we will not find homology.  The octopus does however have a central nerve cluster (“brain”) in its head, which is lateralized like vertebrates’ brains.  It is about the size of the brain of a small vertebrate, and has huge optic nerves to support its fabulous eyes.  No study has looked for a consciousness center, as we simply don’t know enough about the cephalopod nervous system yet to look for something that specific.  Humans and octopuses do share some neurotransmitters, giving hope that we can do experiments using these as tools in the future.
  3. Widespread brain activity.  Humans have a central brain with fewer nerve cells spread throughout the body.  Surprise, surprise: octopuses have the opposite!  Octopuses actually have more neurons in their tentacles than in their central brain.  We humans visualize all our thinking as happening inside our heads – can we even imagine thinking in our arms?  An octopus potentially having sensory nerves entangled with its “brain” nerve cells in its tentacles makes measuring electrical activity very complicated, don’t you think?

As you can see, it is very hard for us to draw conclusions about octopus consciousness based on anatomy.  This is another example of how we humans only really know ourselves.  It sometimes feels impossible to study organisms which have systems which don’t reflect our own; we don’t really know where to start.

But let’s get back to David Hill’s list of intelligent characteristics above: the two themes were memory and language.  As the many videos on the internet show us, octopuses can learn.  Scientific studies have demonstrated their ability to learn from experience and hold onto this knowledge as long as regularly presented with a similar challenge.  (They do forget within just a few weeks if not required to utilize their learn skill again.)

Language is trickier.  Octopuses and other cephalopods are solitary animals, interacting for territory and mating.  They have an incredible ability to change the color and texture of their skin for camouflage and also use this for mating.  Caribbean reef squid will flash different colors to signal enemies and mates.  They will even halve themselves, each half painted a different color, to simultaneously signal to a female on one side and a competitive male on the other (see photo above and video here).  But, once again – is this form of communication a conscious use of a physical language or instinct?

I have no answer here.  I don’t know if octopuses are conscious, or are “intelligent.”  They have many neurons; they can experiment, learn to solve problems and remember the solutions; they signal to one another through color; they use tools.  What I think is more fascinating is our human need to find other organisms that are conscious.  We constantly attribute empathy and emotion to animals that may not have the capacity.  Maybe it makes us more kind to animals to imagine them as human-like, maybe it creates a space within which we can interact.  Or maybe we just feel so alone in this big world… (Cue Bright Eyes now.)

In the end, I have a scientific brain: I was born to be skeptical of everything.  So I do fall on the side of being skeptical about animal intelligence.  We seem bred to seek intelligence in creatures and thus are predisposed to see it where it doesn’t exist.  On the other hand, there wasn’t a switch flipped inside humans alone that turned on consciousness; there must be some continuum through the “lower animals.”  (Oy, I hate that sort of language.)  The truth is that we have no idea what a “lower level” of consciousness would feel like  (or a higher one for that matter), or to have only a partial sense of self.  I think it is a fascinating search and I commend it, but I don’t know if we will ever come up with an answer to any of these questions.

Edelman, D., Baars, B., & Seth, A. (2005). Identifying hallmarks of consciousness in non-mammalian species Consciousness and Cognition, 14 (1), 169-187 DOI: 10.1016/j.concog.2004.09.001

Mather, J. (2008). Cephalopod consciousness: Behavioural evidence Consciousness and Cognition, 17 (1), 37-48 DOI: 10.1016/j.concog.2006.11.006

Seth, A., Baars, B., & Edelman, D. (2005). Criteria for consciousness in humans and other mammals Consciousness and Cognition, 14 (1), 119-139 DOI: 10.1016/j.concog.2004.08.006

Written by Hanner

April 20, 2010 at 9:50 am

Carnival of Evolution #22 – Check it out!

I forgot to mention – the 22nd Carnival of Evolution is going on at Beetles in the Bush.  Head over there to see some great recent posts on evolutionary biology, on topics including human and primate studies, microbiology, theory, and sex.  (You might spot me among the 26 fabulous submissions…)

Written by Hanner

April 7, 2010 at 5:03 pm

Posted in Uncategorized

Animals without oxygen and their implications for the evolution of life

ResearchBlogging.orgIt’s been a slow few weeks around here at Culturing Science.  It’s due to a little bit of writer’s block, but mainly it’s just the beautiful weather keeping me outdoors and away from the computer.  Hopefully you’ve been outside so much that you haven’t noticed.

But today my dream article was published: microorganisms, extreme environments, evolution, and daydreaming all rolled into one.  I couldn’t resist but write it up in an excitement-driven fury.  (The 90 degree weather in Philadelphia is also a little too hot for my taste.)

Are you sitting down?  Today scientists from the Polytechnic University of Marche (Ancona, Italy) and the Natural History Museum of Denmark published their discovery of the first multi-cellular animals found to survive without oxygen.  You’ve probably heard of Archaea or Bacteria species which are able to survive in extreme temperatures, acid, or sulfur-rich environments – places we wouldn’t dream of living.  And the world at large is fascinated by them for this reason.

For this study, the scientists collected sediment core samples from the L’Atalante basin in the Mediterranean.  This basin is completely anoxic (oxygen-free), with a salty layer of brine above forming a physical barrier preventing any oxygen from reaching the area.  In the sediment, they found traces of animals from three phyla:  Nematoda, Arthropoda and Loricifera.

However, as all the animals were dead upon analysis, they had to confirm that these animals were in fact living in the sediment, and hadn’t simply settled there in a “rain of cadavers”  (What poetry!) from oxygenated areas of the sea.  They treated the specimens with a stain that binds to proteins – presumably dead animals would have fewer proteins due to decomposition.  In the figure to the right, we see little protein in the Arthropoda (a) and Nematoda (b) images.  However, the Loricifera (c) specimen is bright pink, indicating protein.  The arthropod and nematode species are thus probably dead bodies or shed exoskeletons – but the Loriciferan (unstained in f) shows promise of actual life in the oxygen-free sediment.

After staining more specimens, the researchers also noticed eggs (d and e) within the bodies of the Loriciferans.  This is a novel find because it suggests that these animals do not just spend part of their lifecycle in the anoxic sediment, but live without oxygen for their entire lives, including reproduction.  They additionally found exoskeletons from young Loriciferans (g) suggesting that these eggs grow up in the sediment as well.  While it would still be a new discovery to science if we found animals that live part of their lives in anoxic conditions, the fact that they spend their entire lifecycles down there raises many more questions and expands our definition of life on this planet.

To further confirm that these bugs are living in the sediment, the team gathered fresh sediment samples and added radioactive protein to see if the Loriciferans would eat it.  They traced this radioactivity and found that the animals had incorporated the radioactive substrate into their bodies providing final evidence that these guys are in fact living without oxygen.

So what’s the big deal about a multicellular organism living without oxygen?  Why am I nearly peeing myself over this?  We already know about single-celled organisms can live in extreme conditions.  Why is this so exciting?

It makes sense that single-celled organisms would be more likely to survive in weird places because they can adapt to environments more easily.  They only have one cell to take care of, so if that one cell is viable, they’re fine.  In addition, single-celled organisms are more likely to transfer genes between one another, allowing adaptations to spread more quickly.  But it was assumed that we don’t find multicellular life in extreme conditions because more complex life simply could not exist there.

But now we have found a multicellular animal that can survive without oxygen.  And the million dollar question: how did it evolve that way?  In their findings, Danovaro et al. mention that the Loriciferans don’t appear to have mitochondria, which are found in oxygen-consuming animals, but rather hydrogenosomes, which are found in some single-celled organisms living in extreme environments.  This presents the possibility of endosymbiosis – or the incorporation of one organism into the other.  Endosymbiotic theory is widely accepted to explain mitochondria and chloroplasts in cells; perhaps this occurred another time for the hydrogenosomes of the Loriciferans.  This suggests that maybe this is not as rare of an event as we thought – who knows what other organelles have evolved this way, including ones we haven’t identified yet.

This finding has implications for how we think about the evolution of life on earth.  We humans are obsessed with ourselves; since we breathe oxygen, it’s often assumed that life on earth evolved once oxygen was around.  The discovery of these non-oxygen-breathing animals provides evidence that multicellular life could have risen prior to oxygen, supporting evidence that early life evolved in highly acidic conditions.  (For more on this, see Marek Mantel and William Martin’s commentary on this paper.)

But let’s get down to the real business: let’s talk about space and aliens.  Thus far, we have been primarily searching for alien life based on oxygen because we have lacked proof that complex life can exist that isn’t oxygen based.  The only life we know – us – is oxygen based, providing no other models of life besides planets with oxygen.  The prior knowledge of only single-celled organisms living in non-oxygen based environments suggested that intelligent life cannot exist in those systems.  And while I wouldn’t consider Loriciferans (also known as “brush-heads”) intelligent, they do suggest that non-oxygen substrates can support higher life.  So when looking for aliens, let’s stop being so anthropocentric.  Life can survive without oxygen.

Danovaro, R., Dell’Anno, A., Pusceddu, A., Gambi, C., Heiner, I., & Kristensen, R. (2010). The first metazoa living in permanently anoxic conditions BMC Biology, 8 (1) DOI: 10.1186/1741-7007-8-30

Written by Hanner

April 7, 2010 at 2:41 pm