Also check out the 60 minutes coverage for a great look at the fossil itself as well as conversations with its discoverers and other paleontologists: Link!!!

Check it out. Water is great.

Get ready for some more groovy sound waves to wiggle your cochleas!

Mr. John Boswell of Symphony of Science fame has put out another song. This one is a little different than the others – it’s a song of praise that addresses the system of science directly. Boswell has subtitled it “An Anthem for Science.” Tell me what you think:

-Neil

Pebble plants (Lithops salicola) among rocks. What distinguishes one from the other?

What is it, exactly, that makes a thing alive? Why do we call a rabbit alive, but not a rock? Here’s a little dialog to help clarify the problem. This is hardly comprehensive and I reserve the right to make sweeping edits in the future! But here it is, just below the fold:

Q: I’ve been wondering. What exactly is the difference between living things and nonliving things?

R: Usually this question is answered by listing a number of qualities which must be possessed for a thing to be considered alive.

Q: Like what?

R: Qualities like order, evolutionary adaptation, response to environment, self-regulation, energy processing, reproduction, and growth and development.

Q: Hm. But I can think of something which satisfies just about all of these, yet we don’t call it alive! The virus!

R: Right, we don’t call them “alive.”

Q: But why not? They reproduce, they evolve and adapt… They sure seem like living things to me. At least, they’re a heck of a lot more alive than a rock is!

R: You’re on to something here! It does seem strange that we would group viruses with rocks instead of, say, bacteria. In fact, what you’re revealing with your question about viruses is that our definitions of “living” and “non-living” matter are strictly human categories into which nature need not fit itself! The categories are far from entirely arbitrary or useless, but they are human inventions nonetheless!

Q: So you’re saying these fuzzy cases like viruses are only tricky because our categories are conceptual constructs overlaid on reality?

R: Exactly.

Q: But you did say these categories are useful.

R: I did. They certainly help organize our conceptions of the world. Breaking reality down into simpler pieces or groups (like living/nonliving) helps us to think about them and make predictions. So for instance, we classify both a frog and a tree as living things. Simply by acknowledging that both the frog and the tree belong to the same category, we can assume some things about the tree just by looking at the frog. For instance, we see the frog is made of cells, reproduces, needs energy to function, and so on. A tree has these qualities as well, and we can assume that just from their being in the same category. So the traditional definition of life is far from useless.

Much unites this Green Leopard Frog with the small plants on the surface of the water.

Q: I see…

R: And, there certainly is matter which is in many ways very different from that contained in, say, a rock.

Q: How is “living” matter different, then?

R: It’s different in a number of ways. For instance, let’s talk about it from a chemical perspective.

Q: A “chemical perspective?”

R: In terms of the nature of the molecules, the rates and variety of reactions, and so on.

Q: I see… OK, go ahead.

R: So let’s compare two things which anyone would agree are very firmly in their respective corners of the living/nonliving divide. Representing the living is a rabbit. Representing the nonliving is a common rock.

Q: Rabbit – living. Rock – nonliving. Got it.

R: Good. So the chemical behavior of these two things are VERY different. For instance, inside the rabbit, a huge variety of chemical reactions occur, including those involved in digestion, synthesis of new parts, DNA replication, and so on. However, the reactions of the rock are mostly limited to surface atoms dissolving in passing water, or being stripped away by wind or abrasion with other hard objects. The interior of the rock can react, but only under conditions of high temperature and pressure.*

Q: So what it comes down to is the variety of reactions? That’s what really separates living from nonliving?

R: Not just the variety of reactions, but also their rate.

Q: You mean how fast they go.

R: Correct. While the surface reactions involving the atoms of the rock are generally rather slow, the reactions in the rabbit proceed extremely quickly. This is because the rabbit contains enzymes – large protein or nucleic acid molecules which catalyze (or speed up) reactions by lowering the amount of energy needed for these reactions to proceed. So the rabbit and the rock differ not only in the number of different types of reaction which occur, but also in how fast their respective reactions go.

Q: Makes sense. But I have something that contradicts what you’ve just said. The organisms of the phylum Tardigrada!

R: I had a feeling you were going to bring those up…

Q: Well yes! Because the tardigrades are capable of almost totally suspending their chemical reactions and entering a state of near total inactivity! So when they’re like this, they aren’t that much different from a rock in terms of rate of reaction!

Modern tardigrades. They're very small, and exist in a huge variety of environments. They are known as polyextremophiles, because they can withstand numerous conditions that would kill most living things. These include dehydration, extreme heat, extreme cold, extreme pressure (high and low), and extreme radiation. There are probably some in your house right now!

R: Excellent point! So the differences can’t be reduced to differences in chemical behavior.

Q: That’s what it seems to imply to me.

R: Yes, you are right. And there’s a larger point we can make while we’re here. An aside, before we move on.

Q: What’s that?

R: That the reactions of the rock and the reactions of the rabbit are actually both a part of a much larger and more intricate chemical system!

Q: Really? How so?

R: Here’s an example. Say our rock falls into a river. Over time, the rushing water knocks atoms and molecules off of the surface of the rock and they enter the water flow as dissolved ions.

Q: You already mentioned this…

R: I know! Be patient! So the rock’s molecules are now in the water as dissolved ions. Well what if these ions happen to bump into the root of a nice leafy green plant?

Q: The plant will take up the ions and use it!

R: Yes…

Q: … Making these ions a part of a living system…

R: Yes…

Q: And demonstrating that the distinction between living and nonliving cannot be applied to a given atom in itself, but only in the context of the chemical system the atom is currently participating in! Furthermore, it reveals that everything on Earth from a rock to a plant to a rabbit participates in a single chemical cycle far larger and more complex than any individual component of the system!

R: Well said!

Q: It’s like we’re two aspects of the same being.

R: Indeed! So, I trust you are satisfied now?

Q: Absolutely not!

R: No?!

Q: No!! You never resolved the Tardigrada conundrum!

R: You’re right. You know, it seems like you’re looking for some special characteristic of living matter that lets it do all these amazing things like coming back from a decade of inactivity as if nothing had ever happened – some property or quality that the matter in the rock doesn’t have.

Q: Yes! That’s exactly what I’m after!

R: Well, I think there is something that will satisfy you. Structure!

Q: Structure?

R: “The beauty of a living thing is not the atoms that go into it, but the way those atoms are put together.” – In other words, their structure!

Q: I don’t follow.

R: So in the rock, the atoms are arranged in a sort of crystal lattice. It’s more complicated than you might expect, but it’s fairly uniform. Now, in a living thing, the structure is MUCH more complex.

This is calcite, a mineral found in limestone.

Q: Why? How so?

R: Well first let me give a caveat and reiterate that the matter in a rock is the same sort of stuff as the matter in the rabbit. But the matter in the rabbit is arranged in a much more intricate manner. First of all, it is based on carbon.

Q: Carbon?

R: Yes! Our friend, element #6. Carbon’s electron configuration allows it to form long chains to which other atoms or molecules can bind. This allows for a huge variety of different compounds, each of which has its own particular chemical behavior. With the huge diversity of molecules that can be created from a carbon framework, a reaction involving carbon-based matter (and with constant energy input as we get from the sun) can develop to be far, far more complex than a reaction only involving simpler molecules.**

This is maitotoxin, a carbon-based poison. Each point where two or more lines come together represents a carbon atom. See how large and extensive a carbon-based molecule can get!

Q: Why, exactly?

R: Part of it has to do with size. Let me put the difference in size in perspective – a molecule like water, that’s got a molecular weight of about 18 atomic mass units. Not bad, but organic molecules can get huge. Really huge. How huge? Consider hemoglobin, with a molecular weight of 68,000 atomic mass units. Or the colossal protein called connectin, weighing in at 2,993,442 atomic mass units.

Basically, organic molecules can be REALLY REALLY BIG. This huge size allows a tremendous diversity of structures, and this allows a tremendous diversity of chemical reactivities. Such complexity allows structures which remind us greatly of our own mechanical contraptions. And this in turn lets them do complicated things like catalyze chemical reactions.

My friend and yours, the protein ATP Synthase. Without this fella you wouldn't be doing much of anything, because it produces the "energy currency" of the cell - ATP. It's also carbon based and shows the incredible complexity possible in organic chemistry. It should remind you of a rotor.

Q: I think I’m seeing it now… The major difference between living and nonliving matter is the structure of the molecules involved! So the Tardigrade in suspended animation is different from the rock because even when the creature’s metabolism slows WAY down, the molecular machinery is still there inside the animal in good form, ready to resume the reaction at full speed when the solvent becomes available.

R: That’s it.

Q: Wow, we’ve covered a lot of ground. Let me try to summarize. Living/nonliving is a human dichotomy which only partly reflects the real divisions among matter. These real divisions include variations in number of reaction types, the rates of these reactions, and the structure of the involved molecules. However, the traditional definition of life, which involves traits like growth and development, order, energy processing, and so on, also has its place as a way of conceptually organizing the world.

R: You got it!

Q: BOOYAH!

Questions? Concerns? Complaints? Corrections? The comments section awaits your input!

-Neil

*We should also note that in inorganic liquids and gasses, the full volume, not just the surface, is available for reaction.

**Silicon has a similar chemical behavior, but on Earth it seems to be mostly tied up in rocks. Still we can’t preclude the possibility of silicon based life elsewhere!

The man himself! Sir David Attenborough.

The unparalleled naturalist David Attenborough has participated in a huge number of fantastic nature documentaries over the year, and it turns out a fair number of these are available on youtube! Having stumbled on these yesterday and spent several hours enjoying them, I felt compelled to share them with you, the public hungry for knowledge!

Youtube user akhilind has posted many of these videos so I direct you to this person’s channel. He’s got the Private Life of Plants, which makes extensive use of time lapse photography to bring slow (but fascinating!) plant behavior into the realm of human perception. He’s got the classic Planet Earth, a practically pornographic (in the lushness of the visuals, I mean!) look at our planet from pole to pole. He’s got Blue Planet, which focuses on the watery parts of our globe. He’s also got a wide variety of other documentaries, with the emphasis seeming to be on environmental preservation and appreciation. So give it a look!

As a personal recommendation, let me suggest the episode of the Private Life of Plants called Flowering, which provides many many examples of unique and wonderful flower/pollinator relationships. Here’s the link: http://www.youtube.com/watch?v=r96hhTmNCX0

[[EDIT: These episodes of the Private Life of Plants have been taken down as of Feb. 20, 2010. Try user shienlen for some the regulators seem to have missed (http://www.youtube.com/user/shienlen).]]

Now keep in mind this is just one person’s channel! There are many other users who have uploaded many other entertaining and informative videos from all kinds of different productions. Just search around for a topic of interest and you’re sure to find some material you’ll enjoy. Youtube is an excellent resource for education, and if you can for a moment gently push aside the videos of obese men eating pizza or small mammals rapidly turning their heads, you can discover a treasure trove of wonderful things. Sometimes people complain that the internet is not used to its full potential as an information disseminating medium, but that is hardly the fault of the internet! It’s simply ours. The material is there, waiting to be viewed. It’s only up to us to click the link!

So go look! Go on! I promise you’ll find something you like.

-Neil

Until next time!

-Neil

The matter of the Chimpanzee and the matter of the stone are not so different...

Today I want to discuss something more philosophical than usual. This post contains personal thoughts that are not scientific and upon which there is not a consensus opinion. But I find the topic very, very interesting and I felt like sharing. So here we go.

The topic is Emergent Phenomena.

Let us start with a neuron.

A neuron is a fantastic thing! It is a cell with many remarkable characteristics. In terms of its shape, the neuron is very long and spindly. It possesses long branches on either end of its body which allow it to interact with a multitude of neighboring neurons. On a molecular level, its membranes are studded with channels which permit ion flow into and out of the cell. These channels can be activated by a contact with certain molecules or by a sufficiently strong electric current. A neuron is certainly an amazing thing, yet if enough neurons are arranged together in a particular way, phenomena far more incredible emerge. Consciousness, emotion, thought, love, fear, anger, regret, joy, creativity, invention – all these are the product of neurons acting in concert. Yet if we examine the single neuron, we see nothing of any of these. Where is the consciousness in a neuron? What in a neuron accounts for love? What in a neuron accounts for the flash of insight that accompanies the conception of a great invention? Nothing! There is nothing in a single neuron that can account for any of these. Yet with sufficient numbers and a certain arrangement, these complex phenomena emerge. This is the idea of the emergent phenomenon – the thing which is greater than the sum of its parts.

The neuron itself – or more broadly the living cell – is also an emergent phenomenon. It is a living thing, comprised of nonliving molecules. How can this be? How can all the properties of life – mobility, reproduction, metabolism, adaptation, and so on – arise from molecules which have none of these? Again, it is the number, variety, and arrangement of the molecules which leads to the emergence of a new and more complex phenomenon.

Let us go deeper still. The molecules in a living cell are no mundane matter! They themselves are examples of emergent phenomena. Take an enzyme like lactase, which cleaves the milk sugar lactose into its constituent sugars, galactose and glucose. Lactase enzyme is a protein, a molecule comprised of many smaller molecules called amino acids. These amino acids are individually incapable of splitting lactase. Yet if you gather enough of them together in a specific order and structure, an enzyme emerges fit for the task.

We can go further still, to the atom! We have discussed water at great length on this site, and for good reason. If we examine oxygen and hydrogen, we see atoms comprised of nuclei and electrons, oxygen with its particular properties and hydrogen with its particular properties. But if you get them together, and pair two atoms of hydrogen to an atom of oxygen, you get a substance with many peculiar traits, among them cohesion, adhesion, a solid form less dense than its liquid form, a high specific heat, and so on. One would never expect all these remarkable traits simply by looking at the isolated oxygen or hydrogen atoms. Certainly, no one would predict such properties from the examination of a proton or electron! And yet here they are, molecules of inconceivable variety, each arising from a particular arrangement of protons, neutrons, and electrons.

I want to be careful to point out that for the emergent phenomena detailed above – consciousness, the cell, the enzyme, the molecule – the properties of the simple are not irrelevant to the properties of the emergent. They are in fact totally responsible for the properties of the emergent. Working our way from lowest to highest:

The properties of the water molecule are a result of the different electron arrangements of hydrogen and oxygen, as well as their relative electronegativities (affinity for electrons). These properties are in turn a result of the number of protons and neutrons in the nucleus of the atom.

The properties of the enzyme are a result of the interacting properties of the amino acids which compose it. One amino acid might contribute a negatively charged site to the molecule, another might contribute a positively charged site, while the pairing of a third and fourth amino acid might introduce a structural “kink” in the amino acid chain which brings the two in close proximity.

The properties of the cell are also a result of the interacting properties of the simpler things which compose it. In each cell there is a huge variety of large molecules which compose it.  The neuron’s ability to send messages depends entirely on the type and abundance of molecules which make it up. If it did not have the ion channels discussed above (themselves proteins like the enzyme lactase), it could not accomplish this feat. And of course, if it did not have nucleic acids like DNA to direct the synthesis of these molecules, it also would be incapable of performing its role in the body.

Lastly, the fantastic phenomena of the human mind are traceable to the properties of the neurons, and their ability to transmit signals rapidly among their kind.

So it is that emergent phenomena are entirely unexpected, but not entirely unexplained. We do not expect consciousness to arise from neurons, or neurons to arise from molecules, but once we see that they do, we can see why. Each level possesses properties whose interaction creates the properties of the next level. The interactions of the properties of that level in turn create the properties of the following level, and so on. Atomic structure determines chemical properties, which determine molecular structure, which determines molecular function, which determines cellular function, which finally determines organismal function. I want to emphasize that structure – the relative position of things in space – is of critical importance in understanding emergent phenomena. As I have mentioned, it is the interactions of the different properties at each level that determines the properties of the next level. For matter, and especially for larger molecules, the importance of structure cannot be overstated. For instance, in a protein, it is the arrangement in space of the amino acids which determines the function of the protein. Move one bit around, and it will no longer perform the same way. It’s function and its form are totally inseparable. Likewise, the particular properties of water depend on its being a molecule with a “bent” shape. If water was linear, with all three atoms in a row, it would not have its remarkable properties.

I wanted to write about this because I find it so interesting. Because it is so unintuitive to think that I, the breathing, thinking, moving, shouting, clapping me, am composed of simple atoms. How can this be! It baffles any attempt by the intuition – it appears that atomic structures and my love of singing, for instance, are totally irreconcilable! Yet this is not the case! The atomic structure of carbon is intimately tied to the good feeling I get when I sing. If we remove that piece, the whole thing collapses. Likewise I could hardly sing if I did not have hemoglobin, the molecule I rely on to transport oxygen and carbon dioxide around my body. And so while it seems absurd to attribute my love of singing to say, the atomic structure of oxygen, it is absolutely accurate, and if we carefully examine each level of emergence, it is not so hard to see.

There is some beauty that comes from this understanding. For example, this idea of emergence seems to erode the boundary between living and nonliving matter. The oxygen in me is no different in terms of its chemical properties from the oxygen in the atmosphere. Indeed, by the end of the day, many of the atoms in me now will be no longer, and many of the atoms previously “nonliving” – in the air I breathe or the water I drink – will be incorporated into this body, will be living. If we were to take this line of thinking further, we might raise serious questions about what it means for matter to be alive, or how to define a thing which is constantly in flux with its surroundings, or if it is even accurate to define an organism and the surrounding environment as separate things.

I am very interested to hear what others think of these ideas, as they are very intriguing to me. Please, comment at length!

Until next time,

Neil

Oh, and Happy New Year!

Go!

Two majestic marine mammals

Greetings, faithful blog readers!  My name is Sam and I’m going to take you on a fascinating tour of the animal kingdom over my next few posts, as well as whatever other scientific topics strike my fancy.  Today, I’d like to talk about our fishy friends, the whales (not actually fish, though we’re sure you knew that), and the fascinating topic of animal intelligence.

Everyone knows that the dolphins at SeaWorld can learn tricks, but the assumed limits of whale intelligence are being shattered regularly.  Dolphins are capable of recognizing their own reflections (a sign of self-awareness), singing the “Batman” theme song (reproducing rhythm and pitch) and most recently, hunting with sponges to protect their noses (tool usage).  Clearly, the cognitive ability of our marine amigos is not to be underestimated!

But let’s backtrack for a second, and understand what’s going on inside a whale’s head.  Toothed whales – like sperm whales, orcas and dolphins- use echolocation as one means to find food in their habitat.  Echolocation is a process by which sounds generated by the animal are sent out and the returning echoes allow the animal to interpret a three-dimensional rendering of their surroundings.  This is particularly useful in the water, where there may be little light, and sound travels faster than in the air.  In fact, the sounds generated by the sperm whale are the loudest sounds made by any animal on the planet.

Sound is passed through the phonic lips and modulated by the melon, a fatty organ (red lines). Incoming sounds (green) are passed through the lower jaw and transmitted to the ear.

The implications of this are astounding: a whale’s brain can interpret three-dimensional images of its surroundings.  Really, “images” isn’t even the right word for this ability, because “images” implies two-dimensions; whales are processing their environment as a fully-rendered space in a way that we cannot conceive.  Incredible!

This brings me to my main point: the whale brain. The sperm whale has the largest brain of any known animal, modern or extinct: it weighs nearly 20 pounds.  For reference, this is about the weight of a car tire.  That’s a big brain!  The zombies would have a feast.  Dolphins have one the highest brain size to body ratios outside of humans, which is a particularly strong indicator of intelligence.  They also exhibit immense problem-solving abilities, and are capable of reasoning, planning, thinking abstractly and learning from experience.

Whales undoubtedly have culture, as well.  They travel in nomadic pods, and because they have no hands and spend their lives constantly swimming, they have no permanent possessions or residences.  Thus, their social groups are the only consistent feature in their lives.  The parts of dolphin brains that are involved in processing social relationships and emotions are extraordinarily complex.  Two whale populations, while genetically similar, may exhibit vastly different behaviors within their groups and in how they interact with their environments.  For example, different pods of genetically similar orcas may subsist on different diets or use a different set of sounds to communicate with one another.  Because of the uniqueness of a whale’s lifestyle and brain, their intelligence and relationships may be inconceivably distinct from our own – more on this below!

What could this benthic behemoth be thinking about?

For contextualization, it is worth noting that whales are particularly far removed from primates in the evolutionary scheme of things.  Their brains are very different from ours, and as a species, acquired their intelligence along a different course of environmental pressures.  Their unique intelligence is actually older than our own – if aliens had come to earth before about 1.5 million years ago to communicate with the brainiest animals, they would have chosen dolphins, not apes.  Therefore, with cognitive abilities that have developed so independently and uniquely, it is difficult to even know what we should be testing for when we measure cetacean intellect, as accurate markers for what humans perceive as intelligence may actually have little bearing on marine mammal minds.

The social and intellectual abilities of whales is incredibly interesting, as it implies that as a species, we may be far less alone in the universe as intelligent life.  I wonder:  as whales transmit and process three-dimensional renderings directly into one another’s large brains what information could they be sharing?  Ocean maps?  Cultural practices?  The possibilities seem limitless.  This revelation also brings to light the horrifying implications of nearly hunting these creatures to extinction over the past few centuries.  Be sure to cherish our briny brothers!

And finally, dolphins have been used by militaries across the world for mine-deactivation, diver rescue and even, potentially, offensive purposes.  The Soviet dolphin hit squad was recently sold to Iran, undoubtedly marking the first animal mercenaries in history.  I’m not kidding.

Further Reading:

Dolphins and Singing: http://www.abc.net.au/science/news/stories/s1473208.htm

Dolphins and Tools: http://www.timesonline.co.uk/tol/news/environment/article5439491.ece

Whales and Identity: http://www.wired.com/wiredscience/2009/06/whalepeople/

Whale Culture: http://www.wired.com/wiredscience/2009/06/whaleculture/

Orca Pods and Culture: http://www.orcanetwork.org/nathist/fins.html

Tree of Life of placental mammals, showing the distance between cetaceans and primates: http://tolweb.org/Eutheria/15997

Dolphin Mercenaries: http://news.bbc.co.uk/2/hi/world/middle_east/670551.stm

A flashlight fish, one of the many denizens of the deep.

Top DTC reporter Sam alerted me this morning to a press release by the Census of Marine Life with some new photos of deep sea critters. Go to their site and have a look! The organization has lots of photos of amazing creatures, and video too!

There’s some seriously cool stuff down there.

-Neil