Jeff's Lunchbreak

My wife spotted an interesting message on a sign out in front of one of the churches here in town. So, she took a picture of it and texted it to me.

For anyone that can't download images, here's the message.

IF MAN CAME FROM APES WHY ARE THERE STILL APES?

I've been seeing this as a parody of creationists for so long, that it's almost a bit surreal to see someone actually using it seriously. And it's not just some random commenter on a blog, but the message a church is putting out to the public. Even if the sign person at the church has enough freedom where the message doesn't have to get approved by someone else first, my wife tells me that the message has been up for over a week - plenty of time for someone in the congregation to say something about it.

I could just point and laugh at the sign, which may even have been enough for this entry, but that's not very productive. So, while I've covered this on the blog before, since the prior coverage was brief, I'll go through again explaining why this question sounds silly once you actually understand evolution. Since I have covered this before, some of the content below has been copied copiously from a previous post.

One of the easiest ways to see the error in this line of thinking is to use an analogy. I'll use myself as an example. My great great grandfather and grandmother on one side were German - not just of German ancestry, but born in Germany and immigrants to the U.S. So, I can quite literally say that I am descended from Germans. But it's also quite obvious that I'm not descended from any living Germans. A certain group of Germans and I share a common ancestry through my great great great grandparents. The descendants of my great great great grandparents split into two lineages - one that continued in the U.S., and one that continued in Germany. That lineage in Germany is composed of my cousins, not my ancestors.

Another way to see the error in this line of thinking is to pose it with a different group of animals. It's a bit like asking, 'If crows evolved from birds, why are there still birds?'

It's a very similar case with us and chimpanzees and bonobos. Around 6 million years ago, there was a population of apes that was neither human, chimpanzee, nor bonobo. Over the generations, this population split into multiple lineages, each of which evolved independently. Most of those lineages have gone extinct, but there are still three of us left. We are cousins. We can go back further in time and find the ancestor that we share with gorillas, and further to find the ancestor we share with orangutans, and on and on all the way back till life began. None of those ancestors will look exactly like any of their modern descendents, since evolution has been occurring in all of the lineages. (Obviously, we haven't actually found fossils of all species that have ever existed. But, in the same way that you know you must have a great great great great great great grandmother, even if you don't have any record of her, we also know that we must have common ancestors with Earth's other organisms, even if we haven't yet found their fossils.)

I think there's another misconception associated with this assertion. I think it goes back to the Great Chain of Being, where people feel that evolution is directed, and that us humans are the pinnacle. That's not the case. Much of the change that occurs in evolution is through mutation and natural selection (though those aren't the only drivers). Mutation is random. It just happens, without any conscious intent. Think about yourself - did you pick any of the mutations that make your DNA slightly different from your parents? Did you pick any of the mutations that make your children's different from yours? Natural selection isn't random. It acts like a filter - eliminating the mutations that don't work as well, while allowing the ones that do to pass through. But it's only a filter. It relies on the raw material from random mutations.

It's also important to keep in mind that mutations aren't good or bad on their own. It all depends on the environment an organism is living in, the animals lifestyle, and other factors. DNA to make gills is very useful for a fish, but wouldn't do a damn for us.

So, let's go back to that ancestral population of apes. Somehow, it got split into at least two lineages. Those lineages, once they became reproductively isolated, could no longer share DNA between each other. So, whatever beneficial mutations popped up in one population would have been available only in that population. Any mutations that made the eventual chimp lineage better at climbing trees, for example, would have been unavailable to our lineage. Likewise, any mutations that made or lineage better at walking on the ground would not have been available to the lineage that led to chimps & bonobos. So, once that population was split, the two lineages went their own separate evolutionary ways.

Environment could also have played a role. Now, I doubt the following is exactly what happened, but it's an interesting thought experiment. What could have caused that ancestral population to become split? Imagine that it was a new river, that cut through their range. Imagine that the river became so big that the ancestral apes couldn't cross it. And suppose that on one side of the river, the forest stayed largely intact, while on the other side, the forest gave way to savannah. Now, with one lineage living in forest, and the other in savannah, you can see how natural selection would have favored different mutations in each of the two lineages, causing each to evolve markedly differently.

So, once you understand a bit about how evolution works, the question 'If man came from apes, why are the still apes?' seems nonsensical, and even a bit silly.

Here's a related blog entry I wrote a few years ago:
Why Do People Have a Problem With Our Relation to Other Apes?

That entry also addresses the semantics of this a bit. In my opinion, we are just a type of ape, so saying that we evolved from apes just seems obvious.

Posted by Jeff on Tuesday, Jan 31 | Permalink | Comments (0) | TrackBacks (0)

I got a link to an interesting article recently, How many gallons of gasoline would it take to charge an iPhone?. The article was published on ExxonMobil's Perspectives blog. It was an attempt to put into perspective just how much energy there is in gasoline, and why it's so useful as a fuel.

Early on, the article presented a 'fact', without any rationale to back it up:

All of the energy concentrated in one gallon of gasoline is enough to charge an iPhone once a day for almost 20 years.

So, I thought I'd run some numbers to see just how reasonable this was.

First, what's the energy content of a gallon of gas? According to Wikipedia's Energy densities page, the energy density of gasoline is 47.2 megajoules per kilogram. A gallon of gas weighs about 6 lbs, for a mass of about 13.2 kg. Multiplying by the energy density gives 623.04 MJ in a gallon of gas.

Now, for something that took a little more work, what's the energy content of the iPhone battery. According to Wikipedia's iPhone 4 page, the battery is 3.7V at 1420 mAh. (An Ah is the "the electric charge transferred by a steady current of one ampere for one hour" - Wikipedia). So, doing a simple calculation on that, let's figure out the power the battery is putting out, and then how much energy that would be after the one hour for the Ah:

P = IV
P = 1.42A * 3.7V
P = 5.254W

As a sanity check, that's in line with what some random guy on the Internet claimed on Yahoo Answers, according to his kill-a-watt power meter.

And since energy is qual to Power times time:

E = Pt
E = 5.254W * 3600s
E = 18,914.4J

So, if we simply divide the energy content of the gas by the energy content of the battery, we get 32,940 charges. Assuming a charge every day for a year, that's 90.2 years. Now, of course, there are inefficiencies in the systems, so that's not right. Gasoline engines in cars are typically on the order of 25% - 30% efficient (per Wikipedia), and their alternators are typically on the order of 50% - 60% efficient. However, permanent alternators run optimally can have efficiencies in the high 90%'s (again, per Wikipedia). So, the claim that a gallon of gas could charge an iPhone every day for 20 years seems pretty reasonable.

An iPhone may not be huge, but 20 years is a pretty long time. It really just goes to show how much energy gasoline contains, and why it's so useful for powering vehicles.

As a side note, this is why I personally think that biofuels offer so much hope. If a way can be found to efficiently convert biomass into a gasoline like fuel (such as some of the studies on algae), we'd have a high density energy source that could take advantage of existing infrastructure. No waiting overnight to charge batteries - just a quick 10 minute stop at the pump to fill up with dead algae.

Posted by Jeff on Monday, Jan 9 | Permalink | Comments (3) | TrackBacks (0)

Around a year ago, I read Peter Wellnhofer's book, Archaeopteryx: The Icon of Evolution. I learned quite a bit, but a new paper on Xiaotingia zhengi throws a kink into archaeopteryx's relative importance in understanding bird evolution.

Here are some typical examples of the coverage the paper has received:

• Nature News - Archaeopteryx no longer first bird
• Internation Business Times - 'Oldest Bird' Archaeopteryx May Not be Bird After All
• Christian Science Monitor - Archaeopteryx may not have been a bird, but just a feathery dinosaur
  The tagline for that article was, "Archaeopteryx: The creature long believed to be the earliest known bird may not have been a bird at all, suggests a new Chinese fossil find."

Okay, first thing is to clear up some misconceptions. Paleontologists have not been suggesting that archaeopteryx was the first bird - only that it was the oldest known bird. In fact, if you go look at that review I wrote and look at the family tree from Wellnhofer's book, archaeopteryx is clearly shown on a side branch that went extinct, so nobody's even been arguing that archaeopteryx was a direct ancestor of modern birds. In fact, I'll just copy that family tree here:

What the new paper does call into question is how closely related archaeopteryx is to modern birds. First of all, it's clear that birds are a type of dinosaur, and archaeopteryx was obviously a fairly closely related dinosaur. But new fossils have been found of other closely related dinosaurs - some that could probably fly, and some that probably couldn't. Whereas previously it was assumed that flight probably only evolved once, and therefore archaeopteryx was a bird, all these new fossils are calling that into question.

The new paper suggests that archaeopteryx was more closely related to deinonychosaurs* than to modern birds. The problem is that deinonychosaurs can't fly. So, there are basically two possibilites:

1. Flight evolved multiple times in the maniraptorans. The common ancestor of archaeopteryx and modern birds was flightless, and each lineage evolved flight on its own. It's possible that powered or gliding flight evolved in other closely related lineages (such as Microraptor)
2. Flight evolved once in the maniraptorans. The common ancestor of archaeopteryx and modern birds could fly, but then some lineages, such as the deinonychosaurs, lost that ability (like ostriches with teeth).
3. Okay, I guess there's a third possibility. It's possible that the common ancestor of archaeopteryx and modern birds could fly, but that flight also evolved in another lineage of maniraptorans.
4. Well, I suppose there's a fourth possibility, as well - that the proposed phylogeny by Xing Xu et al is incorrect, and that archaeopteryx should still be considered a member of avialae.
5. I can't actually think of a fifth possibility, but I'm sure thre are some more possibilities I haven't thought of.

Here's the cladogram from the paper with the new proposed phylogeny:

(Click for larger image)

(Source: Pharyngula)

Paraves is the group that contains both archaeopteryx and modern birds. It also includes the deinonychosaurs, which couldn't fly. But in the avialae branch, it includes epidexipteryx, which also couldn't fly. We know from modern birds that losing the ability to fly has occured multiple times (ostriches, penguins, kiwis, dodos, etc.), so it's possible that the common ancestor for Paraves could fly and the deinonychosaurs and epidexipteryx both lost that ability. But it's also possible, like I wrote above, that flight evolved independently in the archaeopterygidae and the avialae.

So why doe this matter? Aside from trying to sort out the evolutionary relationships, I would think that this is relevant to the trees down vs. ground up debate on the origins of flight. As Wellnhofer pointed out, archaeopteryx was a terrestrial animal, not adapted for life in the trees. And it looked like its terrestrial characteristics were primitive, not secondarily derived from an arboreal ancestor. That was strong evidence in favor of the ground up hypothesis. But if flight evolved independently in archaeopteryx and modern birds, then archaeopteryx doesn't really tell us much about that evolution in birds. The trees down vs. ground up debate is back on.

So, what we have now are a bunch of fossils of very closely related dinosaurs, but it's not quite clear how they all fit together, and especially how the origin of flight fits in. I know what I would like for the truth to be, but reality doesn't care about my feelings. It's just going to take finding more fossils to fill in the family tree and make the picture more clear. Get to work on it paleontologists.**

For more information, here's a very good blog entry describing the new paper:
Pharyngula - Xiaotingia zhengi

*Okay, my nomenclature's not exactly right, but rather than re-type the whole thing, I'm just going to add this note. When I wrote 'deinonychosaurs' in this article, I was mostly referring to the dromeosaurs and troodontids, since this new analysis places archaeopteryx and related animals in with the deinonychosaurs.

**Actually, a comment from Tom Holtz in that Pharyngula thread (Holtz is a paleontologist at the University of Maryland) indicates that there are some new fossils that were recently discovered that should be coming to light fairly soon.

Updated 2011-07-31 - Added the fourth and fifth possibilities in the list, and added the note on my misuse of the nomenclature.

Posted by Jeff on Friday, Jul 29 | Permalink | Comments (3) | TrackBacks (0)

There's an interesting topic that stirs quite a bit of debate in certain circles these days - whether or not a wind powered cart can travel directly downwind faster than the wind, itself. This concept is generally known by one of two acronyms, Down Wind Faster Than The Wind, DWFTTW, or the slightly longer Directly Down Wind Faster Than The Wind, DDWFTTW.

The cart in the concept has a propeller connected to wheels through a driveshaft and transmission. You might intuitively think that this is impossible. I know I did. It sounds too much like a perpetual motion machine, with the wheels powering the propeller which pushes the wheels. So, I thought I would set out to prove it impossible with a few free body diagrams, but now that I've studied the diagrams, I find myself thinking that it might actually work.

Background

First, to get a bit of background on this concept, here are some of the websites of its main proponents:

• Faster Than the Wind Team's Official Blog
• Downwind Faster Than the Wind

To get an idea of just how much passion this concept evokes, take a look at some of the discussion threads arguing over it:

• JREF Discussion Forum, Thread 1
• JREF Discussion Forum, Thread 2 (this one's still active)
• Mythbusters Fan Club Forum
• SkepticBlog
• Good Math, Bad Math

As one last link before getting into my own discussion, the Faster Than the Wind Team claims to have built and tested a car that demonstrates the concept. The North American Land Sailing Association (NALSA) witnessed and authenticated the event. While some might think that would be enough to convince doubters, many remain skeptical of the claims and suspect foul play or incompetence (such as not running directly downwind or measuring windspeed incorrectly in the more generous accusations).

• NALSA's Direct Downwind Record Attempt Page

Here's some video of the record claiming run.

Main Issues

There are two big discussions in this debate, whether a DWFTTW car is even possible, and second, whether the widely circulated 'Treadmill Experiment' is useful in demonstrating its validity. Since the first claim is more interesting, I'll address that first.

Is DWFTTW Possible?

To address this, I drew up some free body diagrams. All the diagrams are shown in an assumed steady state condition. For simplicity, the vehicles are all simplified as just a single wheel, a prop/turbine, and a transmission connecting them.

Let's start with something that we know works, an upwind vehicle.

In this case, V_wind will be greater than V_ground. The prop/turbine will be acting as a turbine, so it will be creating drag. The wheel will be driving the vehicle, so F_ground will be in the forward direction. Since the vehicle is in equilibrium:
F_ground = Drag

To calculate the power from the turbine and the power from the wheel:

P_turbine = Drag * V_wind
P_wheel = F_ground * V_ground

Since Drag = F_ground, if V_wind > V_ground, then P_turbine > P_wheel. That's what it needs to be to overcome transmission losses and the vehicle wind drag that I didn't account for. So, the diagram and analysis agree with what we expect from reality.

Next, let's move on to a case that we know doesn't work, a vehicle with no wind.

Once again, to maintain equilibrium:
F_ground = Thrust

Since I labeled the forces slightly differently, here are the power equations:

P_prop = Thrust * V_wind
P_wheel = F_ground * V_ground

Since Thrust = F_ground and V_wind = V_ground, then P_prop = P_wheel. That doesn't work, since transmission losses will sap the energy out of that system, as will the air drag. I think it should be obvious enough that if you reverse the drive direction (i.e. a turbine powering the wheels), that it still comes out to P_turbine = P_wheel, which doesn't work. So again, the diagram and analysis agree with what we expect from reality.

Now, let's move on to the DDWFTTW case.

Once again, to maintain equilibrium:
F_ground = Thrust

The power equations are the same as the previous case:

P_prop = Thrust * V_wind
P_wheel = F_ground * V_ground

Since Thrust = F_ground, if V_ground > V_wind, then P_wheel > P_prop. Like the first case, that's what it needs to be to overcome transmission losses and the vehicle wind drag.

So, it seems counter-intuitive, but unless I've made a mistake somewhere, it looks like it should work. Maybe there is something to what the propenents have been saying, that the differential velocities are the source of energy, and why this isn't a perpetual motion machine. As the diagrams show, if there's no wind at all, then the vehicle doesn't run.

The Treadmill Experiment

An early proof of concept experiment that made its rounds on the Internet was to put one of these carts on a treadmill and see what happened. The video is included in the links I gave at the start of this entry, but I'll embed it here to make it easier for you.

The treadmill experiment prompted two big questions - is it representative of a cart moving downwind over the ground, and does it demonstrate the validity of the DWFTTW concept?

The answer to the first question is a clear yes. The treadmill is an equivalent reference frame. That's how wind tunnels work – it's all about relative velocities. If a treadmill is moving at a steady 10 mph in still air, it's the same as the ground being stationary with a steady 10 mph wind.

Consider this. The Earth's surface is not stationary itself. Given a circumference of approximately 25,000 miles, and a rotation period of 24 hours, the ground is moving at just over 1000 mph at the equator (and that's ignoring the Earth's motion around the Sun, the Sun's motion around the Milky Way, and the Milky Way's motion about the local galactic cluster). In other words, the Earth could be considered a giant treadmill. But we can safely neglect that if we use a frame of reference that moves along with the earth. It's the same thing with the treadmill. As long as all the relative velocities are equivalent, then your reference frames are equivalent.

But, did the experiments in the video demonstrate the validity of DWFTTW? I think the answer is yes to that as well, but I also have an idea for another experiment.

My initial skeptical thought was that by physically holding the cart stationary on the treadmill before releasing it, they were storing energy by spinning up the propeller on the cart. When they released the cart, it would surge forward using that stored energy. It's just like a toy helicopter where you pull a string to make it take off. There's nothing surprising about that.

But, if you watch the video, once the cart is operating, they aren't holding it against the treadmill, they're holding it back against its own thrust. That, to me, is indicative that the cart wants to run faster than the treadmill. Unfortunately, given the short length of their treadmill, the videos never show the cart reaching a steady state.

My suggestion for a better experiment (aside from the full size human carrying cart) is to build a long treadmill inside a building, and put their cart on that with some guides to keep it from running off track. If it achieved a steady state forward velocity relative to a stationary observer (and was well documented by independent observers), then I'd think most reasonable skeptics would be convinced. Alternatively, the cart could be placed on the treadmill before the treadmill was started in motion, so that it wouldn't be touched by human hands at all once the experiment started. Judging by the Faster Than the Wind Team's human carrying cart, I would think they have the means to carry this out, and all remaining doubts could be put to rest.

Alternate Explanation 1

I think a better way to understand this vehicle, is rather than thinking of it as a ground vehicle powered by the wind, think of it as an aircraft powered by the ground. I have a little thought experiment that might help. Envision the vehicle suspended on some rails, with the prop aligned to propel it down the rails, and with the wheel hanging below on a caster that enables the wheel to face any direction. If you put a conveyor up to the wheel with the conveyor running sideways relative to the vehicle, it's obvious that the conveyor will turn the wheel, which will drive the propeller and push the vehicle down the tracks. Now, if you start rotating the conveyor to more closely align with the tracks, it will continue to drive the wheel. The more closely it aligns with the tracks, the higher the drag load that it will impart, but it will continue driving the wheel.

So, think of the cart as an aircraft that with no other forces acting on it would want to be 'at rest' with zero relative windspeed. But, once the ground starts moving relative to the aircraft, it provides a power source that the aircraft can tap into to propel itself.

Alternate Explanation 2

Consider a cart where one set of wheels is turning a generator used to power another set of wheels driven by motors. This obviously won't work. Since both wheels are moving over the ground at the same speed, if the force at each wheel was of equal magnitude, then the power created by the generating wheel would be equal to the power being used by the driving wheel, which doesn't work when you account for losses.

If a cart with a propeller was moving through still air, then it would be the same thing. That was what I tried to explain with the no wind case. When forces are equal and velocities are equal, then powers are equal.

What makes the downwind case work, is that the wheels and the propeller are operating in two different media at two different speeds. For a propeller, we typically look at the thrust generated for a given power, since that's the way engines operate. It's well understood that for a given power, thrust drops with airspeed. But looking at that a different way, it means that to generate a given thrust, the power requirement goes up with airspeed. So, using the no wind day as a baseline, when the thrust from the prop and the drag from the wheels are the same, the input and output powers are the same (which doesn't work because of losses). Now, if you add a little bit of tail wind, it means the propeller is not travelling through the air as fast. If you maintain it at the same thrust, it means the power requirement goes down. So, now we're getting into a regime where the power generated by the wheels is higher than that required by the prop. With enough of a tail wind, the power differential can get big enough to overcome the inefficiencies and make the system actually work.

Conclusion

So in the end, once I gave this a little thought, I surprised myself. I think my initial gut reaction to this concept was wrong, and that the DDWFTTW proponents are right. That's all part of honest skepticism - knowing when to admit you were wrong and to change your views based on new reasoning and evidence. It's certainly nice to know that the Faster Than the Wind Team is most probably honest, and that the videos probably aren't a hoax. Congratulations to them for their achievement.

Now that I've had my say, and hopefully convinced people that this is possible, here's a good article on it:

• Wired - A Long, Strange Trip Downwind Faster Than the Wind

I'll also add that the nice thing about this question is that it's testable. If I get a chance, I'll build a little cart myself. If enough people do this and test it, it should be confirmed pretty quickly. If you're one of the people that feels really strongly about this, go do a test for yourself.

Added 2011-06-13

I figured it might be fun to throw in a few real numbers to get a feel for how this would work. So, I pulled some numbers out of the air to see how the calculations come out.

I started out with a ground speed of 30 ft/s (~20.5 mph). Assuming 100 pounds of drag on the wheels, this works out to 3000 ft-lb/s of power (~5.5 HP). Assuming a 90% efficient drive train, there's 2700 ft-lb/s going into the prop. Now, the next step requires a little understanding of propellers which I've explained on my static site (Theoretical Max Propeller Efficiency). Assuming a figure of merit of 0.9*, and a propeller diameter of 15', the prop will create 170.5 lbs of static thrust. So, at the state where ground speed matches wind speed, the thrust created by the propeller will be greater than the drag on the wheels - the cart will accelerate forward. And since the cart is at zero relative airspeed at that condition, there's no aerodynamic drag to consider. Also note that there's no stored energy from a flywheel effect in this analysis, so the steady state condition will necessarily be at some speed where the cart is going faster than the wind speed.

You can play around with those numbers if you want to. For the given efficiencies and prop diameter, the break even point where thrust = drag is around 495 lbs (27 HP @ 30 ft/s). If you hold the efficiencies and drag constant, the break even point on thrust & drag occurs for a 6.7 ft diameter propeller. All of these numbers appear to be fairly reasonable, giving me yet further confidence that the Faster Than the Wind Team probably achieved what they stated.

* This figure of merit is a measure of how much of the power is going into accelerating the air. This is a more useful measure than efficiency for low speeds, since by definition, propeller efficiency is equal to zero for static thrust. A figure of merit of 1 is the theoretical limit. The propellers I've designed at work typically achieve figures of merit of 0.92 to 0.94 for static thrust.

Posted by Jeff on Monday, Jun 13 | Permalink | Comments (0) | TrackBacks (0)

This entry is part of a series. For a bit of an introduction and an index of all entries in the series, go here.

This installment covers Chapter 15, Chromosomes and Genes.

Darwin used artificial selection (breeding) as an analogy to natural selection. Here, McCann tried to cast doubt on that analogy.

Artificial selection selects exceptional, most widely divergent characters which appear only in a few individuals, whereas natural selection is a selection of slight differences appearing simultaneously in many individuals. Artificial selection often leads to morbid or exaggerated development, to a sickly disposition, to an undermining of the whole constitution, whereas natural selection effects no injury to the whole constitution but on the contrary strengthens and betters it. Artificial selection results in lack of stability. Natural selection remains constant.

"In the light of this truth," says Morgan ("Evolution and Adaptation," 1903) "the relation between the two selective theories may appear quite different from the interpretation that Darwin gives it." (McCann 195)

Artificial selection is still a very good analogy to natural selection. In fact, they're pretty much the same thing. It's just that the selection pressures can so heavily favor single traits in artificial selection, or become extremely relaxed for traits that domestic animals no longer need. For example, let's look at modern chickens. They're extremely exaggerated compared to wild chickens. They're little more than meat factories with the bare minimum of life support to grow that meat (more info). But selection explains exactly why they got that way. Farmers chose the most muscle bound chickens to breed, so they created the most offspring. Scrawnier chickens were sent straight to the slaughterhouse without a chance to make any baby chicks. Farmers have just become a new selection pressure compared to what wild chickens see.

I don't want to criticize McCann too much for misunderstanding genetics, since it was still a fairly young science in his time, but here is a perfect case of what the modern synthesis would bring to the theory of evolution.

Here the biometrician and the Mendelist part company. The biometrician says: "Selection is the process of accumulating infinitesimal differences through gigantic periods of time." The Mendelist says: "Selection is a process of combining and sorting out genes." The biometrician says: "Selection is creative, actually producing new characters." The Mendelist says: "Selection merely assorts, and such effects of variation as are sometimes said to be found are merely due to new combinations of characters that were already present." (McCann 196)

When McCann quotes an actual scientist immediately following the above paragraph, he can make a good point.

De Vries himself says ("Darwin and Modern Science," p. 70): "Natural selection acts as a sieve; it does not single out the best variations but it simply destroys the larger number of those which are from some cause or another, unfit for their present environment. In this way it keeps the strains up to the required standard, and in special circumstances may even improve them." (McCann 197)

We now know that both points of view presented above are right. Random mutation is the ultimate source of the genetic variation in a population, and mutation occurs all the time. Current estimates for human mutation rates are around 100 mutations per individual. Obviously, most of those are neutral, but some will be advantageous or deleterious, and even that will depend on environment.

So, thanks to mutation, you have populations of organisms with quite a bit of genetic diversity. Natural selection acts on that existing diversity - it doesn't create new characters. Go back to my hypothetical population from a previous entry, where an environmental change favors animals that can browse from the tops of trees. Natural selection never creates an individual with a longer neck. Random mutations create animals with longer and shorter necks than their parents, and natural selection describes how those animals with the longer necks survive and reproduce more. After many generations, the population will be composed of animals with much longer necks than the founding population, but it was random mutation that created the longer necks in each generation.

To anyone who's spent any time following creationism, the argument that genetic mutation can only cause the loss of information, and not create anything new, is a familiar argument. After reading McCann, I now realize that this argument is nearly as old as genetics itself.

But science is not looking for losses along the path of evolution. On the contrary science insists she is looking for gains, additions.

It is for this reason that so many scientists are reluctant to admit that characters which look like additions in domesticated or cultivated forms are really due to the LOSS of something which in the past has prevented the appearance of the hidden factor. (McCann 197-198)

I'll once again use Richard Lenski's experiment, where e. coli developed mutations that gave them the ability to digest a new food source (citrate), as an example of how random mutations can result in new functions. I'll also link to an article by Richard Dawkins, The Information Challenge, which explains the processes of how information can be added to the genome.

With the way so many people today use the term 'Darwinism' synonymously with evolution, it's interesting to see it used in a slightly different (and probably more accurate) context.

"Klebs, the eminent plant physiologist," says Kellogg, "keenly criticizes the mutation theory. Copeland finds in the mutations of De Vries nothing radically different either in character or behavior from the Darwinian fluctuating variations." (See "Darwinism Today," 1907, pp. 372-373). Having abandoned Darwin and come to De Vries, there would thus seem to be a desire to return to Darwin. On this point Kellogg is clear and emphatic. He says, under the caption, "The Deathbed of Darwinism," in the introduction to "Darwinism Today," 1907: "... Numerous books and papers are appearing now in such numbers and from such a variety of reputable sources as to reveal the existence among biologists and philosophers of a widespread belief in the marked weakening, at least, if not serious indisposition of Darwinism. A few of these books and papers from scientific sources even suggest that their writers see shadows of a deathbed. (McCann 199)

So, Darwinism here isn't simply evolution. It's contrasting Darwin's evolutionary theories with De Vries' evolutionary theories.

With how much we take for granted our knowledge of genetics today, it's interesting to see this.

The remarkable fact has now been established that every species of plant or animal has a fixed and characteristic number of chromosomes. In many of the lower animals the number of chromosomes to the cell has been determined positively. With respect to man the number is now thought to be twenty-four. Wieman (1917) asserts that the number in both negro and white spermatogonia is twenty-four, thereby agreeing with Duesberg's (1906) count. (McCann 199-200)

The vast majority of people have 24 chromosomes. However, the number's not exactly fixed. Mutations involving fusions are so common that they have their own name, Robertsonian Translocations. Those people only have 23 chromosomes, and they get along just fine, though their children carry a higher risk of Down Syndrome and other similar disorders.

If only McCann could have actually seen the research he was wondering about.

At this writing, 1921, no scientist may foretell what a contrasted examination of the chromosomes of the chimpanzee, gorilla, orang, gibbon and man will reveal, yet the old dogmatic certitude of the evolutionists, who have heeded none of the bewildering complexities involved in this study, persists, as if it were indeed a thing upon which the freakish Trinil Ape-Man, Piltdown Ape-Man and Neanderthal Ape-Man might look with profound contempt. (McCann 201)

There's a very good comment in Pharyngula, that I often link to in these discussions (I have a local copy on this site it's so good). It discusses the very thing McCann mentioned - "a contrasted examination of the chromosomes of the chimpanzee, gorilla, orang, gibbon and man". We're related. Chimpanzess and bonobos are the most closely related of the great apes, and are next most closely related to humans. Our DNA is more similar to a chimp or bonobo than is that of a gorilla or orangutan.

We do have a different number of chromosomes than the other great apes, but when you look at our chromosome 2, you find telomeres and centromeres exactly where you'd expect if two chromosomes had fused together in one of our ancestors. And when you compare our chromosome 2 side by side with chromosomes 2p and 2q from the other great apes, you see marked similarities.

There's no doubt that all of us great apes are related.

Proceed to Chapter 16

Posted by Jeff on Friday, May 20 | Permalink | Comments (1) | TrackBacks (0)

I've just finished reading Jerry Coyne's book, Why Evolution Is True. This is one of my new favorites for introducing evolution to people who don't currently understand or accept it. It contains a great balance of theory and evidence, or in other words, explaining how evolution works, as well as showing the evidence of how we know that.

The book covered a wide range of topics, and did it well while keeping the book to a manageable length. It started with an explanation of what evolution actually is. This was a pretty important chapter, given how much many people misunderstand evolution. He then moved on to fossil evidence for evolution, followed by discussion of vestigial organs, embryological evidence, evidence from poor 'design', and biogeographical evidence. Following all that was a discussion of natural selection and sexual selection, and then a discussion of speciation. The penultimate chapter focused on recent human evolution (recent as in after the chimp & bonobo lineage diverged from ours). Finally was a chapter to wrap it all up, which also discussed what some people believe to be implications of evolution (i.e. if it says we're just animals, why not act like animals). Of course, by covering such a broad range of topics, Coyne couldn't delve too deeply into any single one, but I think it was very good for an introductory book.

Why Evolution Is True was written not just to explain evolution, but also as a counter to creationism. In many places, he pointed out why evolution was a more reasonable explanation to certain pieces of evidence than creationism. When I read Richard Dawkins' book, The Greatest Show on Earth, I'd mentioned that he hammered too hard on creationists, and that it was a bit of a distraction. In contrast, Coyne seemed to spend just enough time discussing creationism without it becoming too distracting from the far more interesting story of evolution itself.

Coyne was also very balanced in his discussions of controversial areas, or areas where the evidence isn't conclusive. For example, in the discussion of sexual selection, he mentioned both the good genes hypothesis and the perceptual bias hypothesis, as well as studies that provided evidence for both.

In short, this book is a great introduction to people who don't understand evolution. Donald Prothero's Evolution: What the Fossils Say and Why It Matters may have a more detailed discussion of the fossil evidence, and Carl Zimmer's The Tangled Bank may have a more detailed discussion of the mechanisms, but Coyne's book has just the right balance of theory and evidence, especially evidence from a broad range of disciplines.

For a great review from Amazon, go here.

Updated 2011-11-02 Fixed link to Zimmer's The Tangled Bank.

Posted by Jeff on Tuesday, Mar 8 | Permalink | Comments (3) | TrackBacks (0)

This entry is part of a series. For a bit of an introduction and an index of all entries in the series, go here.

Today's entry will cover Chapter 2, The Trinil Ape-man.

McCann seems to be one of the people that would ask, "If evolution is true, why are there still monkeys?" He doesn't seem to understand phylogeny.

Out of all this "proof," dignified as the palæontological evidence of man's descent, Professor Osborn draws so many shreds of secret doubt that he must protect himself against the difficulties in his path by admitting ("Guide Leaflet," series No. 52, p. 4) "Man is not descended from any known form of ape, either living or fossil." This confession is not original with Osborn nor is it new with any of the monkey evolutionists. You will find it back in 1871 on Darwin's lips: "But we must not fall into the error of supposing that the early progenitors of man were identical with or even closely resembled any existing ape or monkey." (See 'Descent of Man,' 1871, vol. I, p. 158.) (McCann, 22)

Neither Darwin nor Osborn were making any type of 'confession'. They were explaining a point about the history of life that's too often misunderstood. The easiest way to see the error in McCann's line of thinking is through analogy. I'll use myself as an example. My great great grandfather and grandmother on one side were German - not just of German acenstry, but born in Germany and immigrants to the U.S. So, I can quite literally say that I am descended from Germans. But it's also quite obvious that I'm not descended from any living Germans. A certain group of Germans and I share a common ancestry through my great great great grandparents. The descendants of my great great great grandparents split into two lineages - one that continued in the U.S., and one that continued in Germany. That lineage in Germany is composed of my cousins, not my ancestors. It is a very similar case with us and chimpanzees and bonobos. Around 6 million years ago, there was a population of apes that was neither human, chimpanzee, nor bonobo. Over the generations, this population split into multiple lineages, each of which evolved independently. Most of those lineages have gone extinct, but there are still three of us left. We are cousins. We can go back further in time and find the ancestor that we share with gorillas, and further to find the ancestor we share with orangutans, and on and on all the way back till life began. (Obviously, we haven't actually found fossils of all species that have ever existed. But, in the same way that you know you must have a great great great great great great grandmother, even if you don't have any record of her, we also know that we must have common ancestors with Earth's other organisms, even if we haven't yet found their fossils.)

Where the quote from Darwin is a bit misleading is that word 'closely'. We should expect the common acestor of us, chimps, and bonobos to resemble the three of us. We share many features with our cousins, and the most likely reason is because those features were present in our common ancestor (See here for a look at just how similar we are to bonobos).

To be honest, the main reason I included the following quote is because I thought "ape-manologist" was pretty funny.

Hence Virchow's word of caution to the all-too-eager ape-manologists, urging them in their elaboration of missing links to wait until they can get hold of a real skeleton, a complete skeleton, to take the place of their few fragments of broken bones. (McCann, 25)

This is one of the areas where I do have a bit of smypathy for McCann. In his time, we just hadn't discovered as many fossils as we have now. In the present, though, we certainly do have hominid fossils. Two classic examples are Lucy and Ardi, but they certainly aren't the only hominid fossils we have. (See here for an interesting discussion on how modern day creationists try to deal with those fossils.)

Just a little later on the same page, McCann showed that he didn't realize common descent applied to all life on this planet.

He [Osborn] might have said, speaking of resemblances, "In the hand of man the same bones are to be seen as in the tortoise. The elements in the foot of a lizard are the same even in the highly modified human foot." He would have found the words quoted on page 371, "Human Embryology and Morphology" by Arthur Keith, M.D., F.R.C.S., 1910, Royal College of Surgeons, University of Aberdeen, University of Cambridge, London Hospital Medical College, etc., etc.

From all this are we to have a "Tortoise Theory" or a "Lizard Theory" or are we to go right on, shattering "resemblances" only when they fail to come to our aid in support of something "pre-human"? (McCann, 25)

We fully expect from universal common descent for there to be broad similiarities among life, and for there to be more similarities between more closely related species. For example, consider Tiktaalik Rosaea, which lived around 375 million years ago. Now, this animal probably wasn't our direct ancestor, but rather a close cousin to our ancestors (remember that fossils are rare, and that most species end up going extinct, so we're pretty unlikely to find direct ancestors of any particular organisms). Still, in Tiktaalik we can see many features that all tetrapods share. In its forelimbs, it had a humerus, radius, ulna, and many of the bones that we have in our wrists and hands. It's close cousin, our director ancestor, shared those same bones. Our ancestor passed those traits on to its descendants, which passed them on to their descendants, and on through the generations down to all of the tetrapods alive today. That is why we have the same bones in our hands as tortoises and chimps, because we're all descended from that cousin to Tiktaalik. Since chimps and us share a more recent common ancestor, our bones are more similar to each other than to tortoises.

Image of Tiktaalik from Donald Prothero's Evolution: What the Fossils Say and Why It Matters

Obviously, new features do sometimes appear, or else we'd all still be single celled organisms. But it's much easier for evolution to modify existing features than to create new ones. That's why most tetrapods alive today are variations on a plan, and none have sprouted extra sets of limbs. (When I say 'easier', I mean 'much more likely to happen' or 'tends to happen more often'. Natural selection is not a conscious process, so there is no easy or hard in that sense. Strictly speaking, anthropomorphisms like the one I just used aren't accurate, but they do make for more concise writing as long as people recognize that they are euphemisms.)

McCann, like many creationists still, seems to be stuck thinking in terms of the Great Chain of Being, and that evolution predicts a steady progression towards perfection.

One of the stumbling blocks created by Professor Osborn himself, but nowhere referred to by himself, is found in the fact that these old palæolithic skulls, described as Neanderthal, although said to be 50,000 years old, had an average capacity of 1626-1635 c.c. Some of them measure up to 1700 c.c. These figures knock the bottom out of the evolutionary procession which, for the sake of plausibility, must ever move from a low figure to a higher figure, and certainly where brains are to be considered must never move backward like Hamlet's crab. (McCann, 32)

Why should evolution cause a steady increase in brain size from generation to generation? Evolution has no goal. It only optimizes populations for their environment, and the environment changes over time. Plus, there are tradeoffs for just about every feature of an organism. If individuals with larger brains produce more offspring in a certain environment than individuals with smaller brains, then larger brained individuals will become more common in the population. But larger brains don't come for free. In modern humans, for example, our brains are about 2% of our body weight, but they consume 20% of our energy. 1 lb out of every 5 that we eat goes straight to our brain. That's a lot. If selection pressure for intelligence were reduced, it's not hard to see that there would be an advantage for smaller brains, because those individuals either wouldn't need as much food, or could 'spend' those resources on larger muscles, better immune systems, or some other trait.

This type of adaptation to changing environmental conditions has been clearly documented by Peter and Rosemary Grant in their studies of Galapagos finches. One of the populations they've studied are the medium ground finches that live on an island named Daphne Major. The plants on the island provide them with a choice of big hard spiked seeds or small soft seeds. Back in 1977, there was a drought that killed 85% of the birds. The drought resulted in their diet being limited mainly to the hard seeds. When the population had recovered to pre-drought levels, it had shifted to larger beaked individuals that could eat those hard seeds. In the 80s, heavy rains on the island caused a proliferation of the small soft seeds, and the population shifted the other way, to smaller beaks. Also in the 80s, a new species arrived on the island, large ground finches. These birds had large beaks well suited to the hard seeds. They created a new aspect to the environment on Daphne Major. When another drought hit in 2004, the large ground finches outcompeted the medium ground finches for the limited amount of hard seeds, so the medium ground finches with smaller beaks did better this time, and the population shifted towards smaller beaks.

There is no eternally perfect form that evolution strives for, no progression towards an ideal goal. There are traits better or lesser suited for given environmental conditions, and as those conditions change, it changes which traits are most favored.

While we're on the subject of Neanderthals, let me back-track a little bit, and pull a quote from Chapter 1. McCann was making the argument, still being used by creationists, that Neanderthals fell within the variation of modern humans, so there's no reason to think they were a separate species. He devoted quite a bit more space to this than just the two quotes I'm using. This first one gives the gist of his argument.

At this point one would think the materialistic evolutionists would pause in their persistent efforts to bolster their pet theory enough to make it comfortable. Even though complete skeletons, instead of fragments fancifully reconstructed, could be found, they would mean absolutely nothing unless the absurd conclusions that all men are cast in the same uniform mould, and that, therefore, the measurements of any one of them apply with equal accuracy to all the others, are to be gratuitously accepted. (McCann 14-15)

The following quote shows McCann explicitly stating that Neanderthals were humans.

The receptive school teachers who visit this famous Hall will not be flattered by the realization of the fact that their brain capacity corresponds almost exactly with the brain capacity of the Neanderthal restorations. Either Professor Osborn has all but made monkeys of the school teachers, or as far as skulls are concerned the Neanderthals were just as human as any other human being is supposed to be or can be. That is precisely what they were! (McCann 31-32)

This still a common argument from creationists, but there's nothing surprising about different closely related species overlapping in characteristics. Look at horses and zebras. With the variation among horses, from miniature horses and ponies, on up to Clydesdales and Shire Horses, zebras obviously fall within the natural variation of horses. But that doesn't make them horses.

Remember that evolution is gradual. Big changes take a while to happen. A good example of this, relevant to the discussion of Neanderthals, is this comparison of hominid skulls on the TalkOrigins website. When you compare the Australopithecus africanus from the top left to the modern human on the lower right, it's easy to see that we're separate species. But if you only move over one picture at a time, the differences become less pronounced. It's like the old conundrum - if you start off with one grain of sand, and add only one grain at a time, at what point does it cease to be a few grains of sand and become a pile? We don't expect there to be clearly defined demarcations for gradual processes.

As one last note on Neanderthals (for the time being), we now know that Neanderthals were mostly a dead end. They went extinct, and at most only a few Neanderthal/human marriages contributed any genetic material to the human lineage in Europe. So, their brain size was irrelevant to our own evolution, anyway. In McCann's defense, though, the place of Neanderthals in our family tree had been contested for a long time, and it's really only with modern genetics that the picture is finally being sorted out.

Proceed to Chapters 3 & 4

Posted by Jeff on Friday, Mar 4 | Permalink | Comments (0) | TrackBacks (0)

I've gotten permission from The Skeptics Society to post one of their old articles on this site. The article is:

The Double-Blind Gaze: How the Double-Blind Experimental Protocol Changed Science.

If you've never read this article before, I highly recommend that you do so now. It focuses mainly on medicine, but also shows how it can be difficult to determine the truth of reality, and why the scientific method is so important.

Posted by Jeff on Wednesday, Feb 16 | Permalink | Comments (0) | TrackBacks (0)

Last night, there was a total lunar eclipse visible to all of us in North America. It happened to fall right on the winter solstice, which is a pretty rare event. In the past 2000 years, it had only happend once, in 1638, prior to last night. It won't happen again until 2094.

Circumstances were just right for my family and me to watch it. Every year since we've moved into our new house, I've decorated the big tree out front for Christmas. It takes a while, and depending on how busy I am with work and other things, I don't always get it done as early as I'd like. So, I'd already set myself last night as the deadline to get the tree done before Christmas. Which meant - I was already going to be outside for much of the night, giving me the perfect opportunity to occasionally glance up at the moon to see when the eclipse started and how it was progressing. My wife helped out some with the tree, put up a few lights of her own, and ran out to Wal-Mart to buy a few more lights for me, so she was up, too. And since Christmas break had already started for my daughter, she was already going to be staying up late watching T.V., so she could pop out from time to time to check on the eclipse.

Once the eclipse got started, my daughter brought out the telescope so she could track the eclipse with that (I didn't break out the Celestron NexImage camera because I was so busy with the lights). My wife brought out her camera and tripod, and snapped a few pictures. She'd never tried taking pictures of the moon before, so she had to experiment with the settings a bit. Below is a composite of some of the pictures she took (you can see how they got better towards the end as she zeroed in on the right settings).

I couldn't decide on what resolution to provide to readers, so I gave you several choices if you want to see that image bigger:

• 800 x 414
• 2000 x 1035
• 3822 x 1978

I called my parents to let them know about the eclipse. They watched part of it, but then it got blocked by clouds. So, I guess we were lucky to have a clear night down here in Texas. I should also note the weather. We had a warm front come through, and I was doing my work wearing shorts and a t-shirt - not bad observing conditions for late December.

All in all, it was a good time, and a nice little distraction after a long night of hanging Christmas lights.

Posted by Jeff on Tuesday, Dec 21 | Permalink | Comments (0) | TrackBacks (0)

Every year, I get an Amazon gift card from my mom for my birthday. This year, I used it (along with some of my own money) to buy the Celestron NexImage Solar System Imager - an attachment for a telescope that lets you digitally capture what you would normally see through the eyepiece. It also comes with software that lets you 'stack' frames from a recorded video, and then the software will clean that up to give you a good still image.

I took it out to play with for the first time last night. I still have a lot of learning left to do, but at least I could see on the monitor something resembling what I saw through the eyepiece. Just for the hell of it, I decided to post two of the videos I captured last night. The cool thing these videos show is just how fast the Earth is moving. I wasn't moving my telescope at all (except for the big jumps and the one change of focus). The motion of the objects across the frame is due solely to the Earth's rotation.

In case you haven't figured it out, what you're seeing in the two videos above is Jupiter and some of its moons. The second video is with the NexImage directly where the eyepiece would normally go. The first is with a 2x barlow lens. For reference, I'm using an Astroscan telescope (which explains the jumpy movement when I have to re-aim).

Like I said, I still have some learning to do. Those videos are definitely overexposed - through the eye piece, I could just make out one of the bands on Jupiter, and I could make out the overall color better. I've found some info on websites with some helpful tips. So, one of these nights, I'll get out there and try them out, and hopefully get some better video. Once I have that, then I'll start playing around with the video processing software to see how good of a still I can get.

Posted by Jeff on Wednesday, Nov 10 | Permalink | Comments (2) | TrackBacks (0)

On a recent trip to the Houston Museum of Natural Science, I bought a ticket to see the the exhibit, Archaeopteryx: Icon of Evolution (related link). The exhibit was a fascinating collection of fossils from the Solnhofen region of Germany, with an archaeopteryx known as the Thermopolis specimen as the centerpiece. The archaeopteryx fossil was very interesting, but there were two things about it, in particular, that I was struck by. First was the size. For some reason, in my mind's eye, archaeopteryx had always been a big bird, something along the lines of an eagle. The archaeopteryx fossil at the museum was about the size of a crow (more on this below). Second was the level of detail in the feather imprints, which photos just don't do justice to. It's not that the feathers were imprinted perfectly in their entirety, but in the regions where the preservation was best, it was very obvious that you were looking at an actual feather.

The Thermopolis Archaeopteryx, With a Hand for Comparison to Show Size

So, after I left the exhibit, I went to the museum gift shop to find a souvenir. About the only thing they had that was appropriate for an adult was the book, Archaeopteryx: The Icon of Evolution, by Peter Wellnhofer*.

Before I get started with my own review, let me note that the publisher has a great section for the book. Perhaps best for someone considering buying the book is the section of sample pages. The pages shown are not anomalous - nearly every page had many illustrations, which was great. Also note the small text size and amount of text per page. Even though the book was only 208 pages, it was an information packed 208 pages.

The book was divided into several sections. The first was a short description of the locale where the fossils were found, the Solnhofen region of Bavaria, in Germany. It was the sort of description you'd expect from a chamber of commerce.

Next came a brief description of the geology of the Solnhofen region, and what this tells us about the ancient environment of the area. All of the archaeopteryx specimens found so far have come from Solnhofen Jurassic limestone deposits. It turns out that these deposits were from lagoons in shallow seas. The water was apparently fairly calm, and formed stratified regions with very low oxygen levels at the sea floor - no multicellular life could survive in those anoxic conditions. The mainland was not very close, but it's possible there were islands nearby. So, the limestone deposits were necessarily not the native habitats of any of the terrestrial animals found there. It's possible that the archaeopteryx were blown out to sea during storms, and didn't have the strength to fly back to land (the fact that all archaeopteryx found thus far are juveniles supports this idea).

Death March of a Horseshoe Crab, Which Died after Wandering into an Anoxic Lagoon

After that came a discussion of the history of fossil discovery in the Solnhofen. Obviously, being a marine environment, most of the fossils from the region are from sea creatures, with the fossils of terrestrial animals being very rare. Because of the way the fossils were formed, the preservation is excellent, and Solnhofen fossils have been prized for centuries. They were regular inclusions in the curiosity cabinets of medieval Europe, which emerged in the 16th century (some of the best collections served as the start of modern museums).

Next came the heart of the book - 83 pages discussing the known archaeopteryx specimens in detail. If you think 83 pages of discussion sounds like a lot - it was, and it was a bit dry. I think of myself as a fairly knowledgeable layperson when it comes to evolution and biology, but much this section was a bit advanced for me. The fossils were described in technical terms (radius, ulna, meta carpal, flexor tubercle, pneumatic foramina), which would have made a firm grounding in anatomy useful in understanding this chapter.

This section started with a discussion of how the urvogels (a common name for archaeopteryx from German, meaning proto bird) likely became fossils - they floated in the sea for a few days before sinking to the sea floor, where they were covered with a microbial film before being covered by sediment. One fact I found interesting is that the feathers formed an imprint in the sediment before decomposing, and then this imprint was transferred to the adjacent layer of sediment after the feather decomposed. So, when a slab containing an archaeopteryx is split, both new slabs show only one side of the feathers.

After discussing fossilization, this section moved on to the controversy in the nomenclature and taxonomy of archaeopteryx. The rules of taxonomy state if a species is named twice, the first description has precedence, even if it was obscure and few people heard of it, or if the type specimen wasn't as complete as the later one. (This, for example, is why brontosaurus is now referred to as apatosaurus, since apatosaurus was the first name used, even if it wasn't as widely known). An early archaeopteryx specimen, not being recognized as a bird, was named Pterodactylus crassipes, so crassipes should be the species name. But before that specimen was recognized as a bird, a fossil feather was discovered and used as the original type specimen for Archaeopteryx lithographica. Once subsequent archaeopteryx were discovered, they were named after the feather, even though it's not certain if the feather is actually from the same animal. Another ealy genus name was Griphosaurus. In the end, most people referred to the animals as archaeopteryx, so a special petition was made to the International Commission on Zoological Nomenclature in 1977 to make the London specimen the type specimen, and to make Archaeopteryx lithographica the official genus and species names.

There is, however, some controversy as to whether the archaeopteryx specimens found so far are actually all from the same species. Most notable is the size difference between the specimens, but there are also differences among the details of the anatomy. The size and some of these differences could be explained by the urvogels being different ages at their times of death, along with individual variability, or even sex differences. But, it's possible that the fossils represent more than one species.

Size Comparison of Archaeopteryx Specimens

Next came the discussion of each fossil. For each fossil, Wellnhofer gave a brief overview of how the fossil was discovered and brought into public light, followed by a detailed physical description, which as I already mentioned, was rather technical when it came to anatomy. Besides the feather (which may or may not be from an archaeopteryx), there have been 10 archaeopteryx specimens discovered so far, of differing levels of completeness and preservation. Most are now housed in museums, and are known by the city in which they're permanently located. In order of discovery (though not necessarily public knowledge), the specimens are the feather, London, Berlin, Maxberg, Haarlem, Eichstatt, Solnhofen, Munich, Burgermeister-Muller, the 9th, and Thermopolis specimens.

The first, and one of the most complete, was what is now known as the London specimen. It was discovered in 1861, just two years after Darwin published On the Origin of Species, and made quite a stir being such an obvious transitional form. Also notable is the Maxberg Specimen, which has gone missing since its owner's death. Luckily, casts were made of the fossil before it was lost, but casts are not as useful as the real thing.

Once all the fossils had been described, the next section was a sort of synthesis, describing as much as we can know about archaeopteryx from the fossils we've found. Wellnhofer started with the subject with the most certainty, the skeleton, and moved on from there through less certainty and more conjecture - plumage, physiology, then lifestyle.

The remaining four chapters were all related - discussing early bird evolution, and the role of archaeopteryx in understanding that story. Archaeopteryx is, after all, the oldest bird yet known (though not the first bird, as is too often mistakenly said). Wellnhofer discussed some of the leading hypotheses on the ancestor of birds, including the thecodont hypothesis and the crocodile hypothesis, along with a few more 'imaginative' theories. But the leading hypothesis, which is pretty much certain, is that birds are a lineage of dinosaurs, closely related to the maniraptoran theropods. They're so similar, actually, that there's some discussion as to whether some animals traditionally classified as non-avian dinosaurs are in fact birds that have secondarily lost the ability to fly (in the same manner as ostriches, but back when birds still had teeth and clawed hands).

One of the things that struck me is just how much more dinosaur-like than bird-like archaeopteryx was (yeah, yeah, I know - birds are dinosaurs, but I think my meaning is clear enough). In fact, the Solnhofen Specimen was originally mistaken for a Compsognathus theropod by an amateur collector. I've included two pictures from the book below to dramatically illustrate this (I apologize for the quality of the scans, but like I said in another review, I wasn't about to ruin the binding on my book just to make it lay flat in the scanner).

Comparison of Bambiraptor, Archaeopteryx, and a Modern Chicken - not to scale

Comparison of Archaeopteryx to a Modern Eagle - not to scale

Take a close look at those skeletons. If you had to pick which other animal archaeopteryx was most closely related to, it seems pretty obvious that it would be the bambiraptor. Archaeopteryx still had clawed hands, a hyperextensible 'killer' claw on its foot (though not shown in the above reconstruction), a long bondy tail, gastralia (the bones under the stomach), a more theropod pubis, and teeth in its mouth. Just as important is what archaeopteryx didn't have - a pygostyle, a keratinous beak, a large keeled sternum, fused hand bones, a fused tibiotarsus, or a fused tarsometatarsus. It also seems pretty likely that archaeopteryx lacked a bastard wing. And those are just some of the differences between archaeopteryx and modern birds.

I hadn't realized just how many ancient birds have been discovered that are younger than archaeopteryx. There are quite a few. In fact, the evolutionary story of birds following archaeopteryx is pretty well understood. The family tree below illustrates this. Note that archaeopteryx is most likely not actually the ancestor of today's birds. Like most animals, it was in a lineage that went extinct, which means it had a few traits it had evolved that set it apart from the surviving avian lineage. However, it's still a very valuable specimen for understanding what early birds were like.

Avian Family Tree

This discussion also helped to put into perspective the K-T mass extinction. You often hear that birds were the only lineage of dinosaurs to survive that event, which makes it seem like there must have been something extra special about birds. But look at that phylogenetic tree. Most birds died at the end of the Cretaceous along with their non-flying relatives. There may have been some advantage that the surviving lineage of birds possessed, or they may have just gotten lucky (similarly, most mammals also died out at the end of the Cretaceous).

Despite there not being any known birds older than archaeopteryx, in recent years, paleontologists have discovered quite a few feathered dinosaurs. The book discussed a few of those dinosaurs, and compared the structure of their feathers to those of archaeopteryx and birds. The dinosaur feathers are more primitive. Some are just a downy covering, but some more advanced feathers do resemble the flight feathers of birds, only lacking the asymmetry. While the downy feathers were likely used for insulation, the function of those flight-like feathers is still uncertain.

Wellnhofer also covered the ground up versus trees down debate on the origin of flight. Up until I heard of this debate a few years ago, I'd always assumed that avian flight must have evolved from the trees down. It didn't seem plausible that it would have developed any other way. But many people have made compelling arguments for how it could have evolved from the ground up, where the wings would initially have been used for balance, and then maybe flapped for extra thrust to increase running speed, before fully developing flight. It's interesting that the flapping motion of a bird wing is very similar to the motion possible in a maniraptoran arm (most likely used to capture prey).

Perhaps the best evidence for the ground up hypothesis is that archaeopteryx very strongly appears to be a fully terrestrial animal, with no special adaptations for an arboreal lifestyle. Since archaeopteryx wasn't the first bird, it's possible that archaeopteryx secondarily evolved a terrestrial lifestyle, but given its similarities to the theropods, this seems unlikely. One proposed evolutionary stage in the ground up scenario, wing-assisted incline running, is supported by observation of living birds. The idea has also been proposed that flight may have evolved from jumping and parachuting from cliffs or other elevated points, followed later by gliding, as a sort of reconciliation between the trees down and ground up hypotheses, but eliminating the trees.

The ground up hypothesis certainly seems to be the more likely at this point, but as Wellnhofer pointed out, all ideas on this are speculative for the time being, since we haven't found the fossils of earlier birds.

Archaeopteryx: The Icon of Evolution was a very interesting book. It's very informative and detailed, and I learned quite a bit from it. I wouldn't recommend it for everybody, though. The target audience is quite a bit higher than the general layperson. Although some sections would probably be interesting to many people, if you only have a passing interest in archaeopteryx, maybe Wikipedia is a better choice. But if you happen to have a really strong interest in avian evolution, and don't mind reading technical jargon, then this is the book for you.

Update 2011-08-02 - A new fossil, xiaotingia zhengi, has been found that sheds further light on the evolution of archaeopteryx like animals. A cladistics analysis using this fossil suggests that archaeopteryx might not be quite as closely related to birds as previously thought. You can read more about it in a new entry, Is Archaeopteryx Still a Bird?

Update 2010-09-28 - I reworded several sections to make them more clear, particularly the section on the origin of flight. I also added a bit of information to the section on the origin of feathers.

* Although I commonly buy books as souvenirs from museums, this one was a little more expensive that I was willing to pay, so I walked out of the museum without it. However, my wife and daughter, seeing how interested I was in it, bought it without me noticing, and gave it to me later as a Father's Day present. Actually, it was my daughter's girl scout troop leader who bought the book, who then gave it to my wife when I wasn't looking. The full story is that we were at the museum as part of a girl scout trip. My wife was an official full time chaperon for the trip, and although I helped with chaperoning duties for most of the time, since I wasn't officially one, I was free to go off and do my own thing if I wanted to. Since the tickets to the archaeopteryx exhibit cost extra, it was out of the budget for the girls, so I went through the exhibit by myself. I would have liked to have taken the girls, but to be honest, I think they were all fossiled out after the museum's main exhibits. At the least, they definitely wouldn't have taken as much time as I had.

Posted by Jeff on Friday, Sep 10 | Permalink | Comments (2) | TrackBacks (0)

I got into a discussion with a few co-workers last week on a topic that I'd thought most educated people agreed upon to a large extent - the limits of genetic determinism. In the old argument of nature vs. nurture, I thought most people realized that who we are is a combination of both influences. However, in that conversation, I was the only one who thought environment played a big role, while the other two thought it was mostly down to genetics. Anyway, a few days after our conversation, I sent them an e-mail explaining how environment can contribute to our traits, and decided that it might be worth posting a modified version of it here on the blog. So, to anyone who puts too much stock in genetic determinism, here's some information on how environment also plays a strong role in our development.

First, there's an example that's so obvious that we almost forget about it - muscle size. Genetics gives us a potential muscle size & strength, but our actual muscle size can be greatly affected by diet and lifestyle, particularly by being active or working out. This is a clear example of genetics and environment interacting to produce a trait.

Here's an article on height (since that was one of the traits my coworkers and I discussed specifically). Based on studies between twins and other relatives, it looks like genetics is 60 to 80% responsible for height, and environmental factors, particularly nutrition, are responsible for the remaining 20 to 40%.
http://www.scientificamerican.com/article.cfm?id=how-much-of-human-height

Here are a couple more links on height.
http://en.wikipedia.org/wiki/Human_height
http://www.newton.dep.anl.gov/askasci/mle00/mole00125.htm
http://jn.nutrition.org/cgi/content/full/135/9/2192

One important caveat on twins that doesn't get mentioned in many of these articles - identical twins don't look so similar solely because of their shared genetics (although that is the biggest reason). It is also due to the shared environment in the womb. That's why fraternal twins look more similar that siblings that didn't develop together. So, it's not enough to look at identical twins in these studies - you have to use fraternal twins as a control for early developmental factors.

Here's a really good site on the 'nature vs. nurture' debate that focuses on intelligence. I'm giving the link to the conclusion, but if you follow the links on the site, you can find the evidence they list. To quote part of that site:

Through the research we have done, it seems that heredity, as well as environment plays an important role in humans’ mentality; but these are not exactly equal in influence. A person’s entire environment seems to be more effectual in determining his mental ability than heredity is. The most fundamental way to explain our opinion is quite comprehensible. It is that heredity determines one’s potential, but environment determines how far one will reach that potential during his lifetime. In other words, every individual has a destined mental potential, but how much of that potential the individual will be able to gain solely depends on the environment that the individual grows in.

http://www.macalester.edu/psychology/whathap/ubnrp/intelligence05/Rconclusion.html

Here's another article that touches briefly on genetic determinism, mentioning an experiment where cloned plants (i.e. genetically identical) were grown in different environments, and the plants grew differently depending on the environment they were in.
http://scienceblogs.com/pharyngula/2009/10/richard_lewontingenetic_determ.php

Another point against genetic determinism is the fact that our cells aren't perfect machines, where given inputs give precise outputs. Cells are a cluttered stew of molecules inside a membrane. Depending on how molecules are dispersed throughout the cell, two genetically identical cells may have different reactions to the same conditions. Carl Zimmer's book, Microcosm, has a good explanation of this, if you ever get a chance to read it. A good example, one which made headlines, is the first cloned cat. Although it has identical nuclear DNA to its mother, it has a different color pattern, because the activation and inactivation of the responsible genes is more or less random.
http://www.accessexcellence.org/WN/SU/copycat.php

Here are two more links, dealing with related themes that we discussed. The first link is to an article on the Flynn Effect (the fact that IQ scores have been increasing). We also discussed abstract thinking, and whether or not it's a learned skill. The second link below includes a discussion of a study done in Uzbekistan which seems to confirm that abstract thinking is learned (though the article also mentions potential problems with the study).
http://www.americanscientist.org/bookshelf/pub/the-domestication-of-the-savage-mind
http://www.cscs.umich.edu/~crshalizi/slothblog/484.html

Okay, so what's my point in all this? Genetics plays a significant role in who we are, but so do environmental factors, and even random chance has a part. So, given the long complicated history that has led to the current conditions in the world, unless two people have had very similar upbringings, it would be nearly impossible to tell how much of the difference between them was due to genetics.

Posted by Jeff on Friday, Aug 6 | Permalink | Comments (0) | TrackBacks (0)

Well, I don't have anything really substantive for this week. I did leave two decent comments, though, in response to visitors. First is a discussion of why humans should be considered apes. Second is a bit of politics in response to a guy who didn't like my response to Gary Hubbell's anti-liberal article.

Posted by Jeff on Friday, Jul 9 | Permalink | Comments (0) | TrackBacks (0)

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

So ends Darwin's Origin of Species, giving the inspiration for the title of Carl Zimmer's latest book, The Tangled Bank: An Introduction to Evolution. It is described as a textbook on evolution for non-biology majors, and it is very good.

The term, 'evolution', is pretty broad. In general, when people talk of biological evolution, there are two broad categories they're referring to. The first is the concept of common descent with modification - that all life on this planet is related, and that populations of organisms change over time. The second is the theories describing how that works, with natural selection being the most famous. Pretty much every book that covers evolution will cover both areas to some extent, but often times they will focus on one area over the other. The Tangled Bank covers more of the latter subject. Of course, it uses examples, but it is more about how evolution works rather than a fossil by fossil account of the evidence for common descent (for that type of book, read Donald Prothero's Evolution: What the Fossils Say and Why It Matters - also, realize that there's much more evidence for evolution than just fossils).

Let me give an example of one of the concepts I learned about - Hardy-Weinberg Equilibrium. This term is probably familiar to biology majors, but it's not something us non-biologists generally read about in most popular books or magazine articles on evolution. The concept has to do with allele frequency. As a refresher, an allele is a variation of a gene. Think back to your high school biology class, and the genetic experiments of Gregor Mendel. For example, Mendel discovered a certain gene* that controlled pea color - one version would make them green, while the other would make them yellow. Each version is called an allele. Remember further, that us eukaryotes carry two copies of a gene (actualy, at least two - it can get a bit more complicated than this). So, individual plants in a population of all green peas might all carry two copies of the green allele - GG, and individual plants in a population of all yellow peas might all carry two copies of the yellow allele - YY. Now, if you were to bring those two populations together, the alleles woud start mixing, and you'd end up with three different combinations that the plants could have - GG, YY, and GY (GY and YG are the same thing). What Hardy-Weinberg equilibrium tells us, is that according to just random mating and chance distribution, these allele combinations should all be present in certain ratios. In this example, half of the plants would likely be GY, one quarter would be GG, and the remaining quarter would be YY. But what if you checked up on your pea population, and found that it didn't match the Hardy-Weinberg equilibrium? What if less than a quarter of the plants were GG, and more than a quarter were YY? Well, then we could conclude that something about the Y allele was advantageous to the plants, and that natural selection was pushing the population to have more plants with the Y allele.

This concept of Hardy Weingberg equilibrium can be applied to more complicated scenarios. It doesn't have to be just two alleles, and the initial distribution doesn't have to be 50/50. However, for any combination, the Hardy Weinberg equilibrium is the distribution you'd expect if there weren't any natural selection, and measuring how much the actual distribution varies from the Hardy Weingberg equilibrium is a measure of how strong the selection is.

To me, that's a pretty interesting concept, and it wasn't something I'd given much thought to before reading Zimmer's book. However, the book didn't go into much more detail than what I just gave in my summary. If you're not of a technical bent, that may be all you need. I realize that Zimmer's goal was to provide a book for non-biology majors, so maybe that's all the detail he felt was necessary. However, to someone like me, who may not be a biology major but wouldn't mind seeing a little light math, Zimmer's explanation was a little too superficial. I mean, if you follow that Wikipedia link I provided and read the explanation of Hardy Weinberg equilibrium, the math isn't all that hard. It's just a bit of algebra. Maybe as an engineer who works with equations all day long I'm a bit biased, but it's not as if you need to understand any calculus or differential equations to follow the basics of Hardy Weinberg equilibrium.

I can't discuss this book without mentioning the illustrations. Practically every page of the book has a figure or a graph. I'm sure that the printing cost associated with this contributed to the $50 price tag for the book, but it really makes it easy to understand certain concepts that would be difficult to get across with just words.

This book was published right around the same time as Richard Dawkins' The Greatest Show on Earth: The Evidence for Evolution, so there were inevitably comparisons. But the truth is that they're just not the same kinds of books. In my discussion above on the broad meanings of evolution, I said that Zimmer's book covered more the theories of evolution. Dawkins' book was more of a look at the evidence itself. Zimmer's book was a textbook with color illustrations on each page, while Dawkins' book was a popular book with few illustrations. Comparing the two is comparing apples to oranges.

If you'd like to get more of a taste of the book, I've found two excerpts available for download online. Chapter 1, Evolution: An Introduction is availabe from Carl Zimmer's own site. Chapter 10, Radiations and Extinctions is available from the National Center for Science Education. You can also read Zimmer's announcement of the book on his blog, to hear his intentions in his own words.

All in all, The Tangled Bank was very good. It was a nice broad introduction to many of the theories and mechanisms of evolution, but without getting too technical for those of us that don't plan to go into careers in biology. Unfortunately, being a textbook, it's a bit pricey. You may try going to your library to check it out, find it used, or maybe be lucky enough to be able to borrow it from a friend. However you manage to get your hands on a copy, I definitely recommend this book.

*Mendel's insight was that there were units of heredity, now known as genes, as opposed to the prevailing concept at the time of blending inheritance, but he didn't actually know the mechanism responsible. It wasn't until later that other scientists discovered that genes were contained on chromosomes, and later yet that scientists discovered that chromosomes were made of DNA.

Posted by Jeff on Thursday, Jun 17 | Permalink | Comments (2) | TrackBacks (0)

Guns, Germs, and Steel: The Fates of Human Societies is a Pulitzer Prize winning book by Jared Diamond. To quote from the book itself, it is "A short history about everyone for the last 13,000 years." Diamond has attempted to explain why world history has taken the course it has. But he's more interested in large scale trends and causes, as opposed to battle by battle or even war by war tracking of history. Or, to put it another way, he was taking a more scientific approach to history, as opposed to just stamp collecting. Wikipedia has a good overview of the book, so I'll only present a brief summary here.

To use an example, we all learned in school of the European conquest of the Americas, even though the Europeans were vastly outnumered. We've been taught many of the factors that lead to that result, most notably the superior weapons technology of the Europeans, horses, and the diseases that Europeans brought with them. Diamond noted all these proximate causes (and a few others), but then moved on to ask why the Europeans had developed those advantages, and not the other way around. Why hadn't Motecuhzoma sent ships to conquer Spain?

According to Diamond, much of the advantage of certain regions was a result of geography and the indigineous plants and animals. To help support his case, Diamond looked at native plant species around the world, how nutritious they were, and how easily they could be domesticated. Wheat, for example, is a very nutritious crop, with a fairly high protein content for a plant. It required only a single mutation in wild wheat, inhibiting the seeds from falling off the crop when ripe, to make it suitable for agriculture. Teosinte, by comparison, required many more mutations to become domestic corn (maize), which isn't as nutritious as wheat. As it turns out, Eurasia has a greater number of nutritious, easily domesticated plants than any other region.

Eurasia also had a higher number of potential livestock candidates. In many regions of the world, the Pleistocene extinction event killed off most large mammals at the end of the last ice age (there is debate over the cause of this extinction, but that's largely irrelevant to Diamond's hypothesis). If you don't have large wild mammals, you can't domesticate them into livestock. But you can't just domesticate any large animal. In this section of the book, Diamond quoted Tolstoy, "Happy families are all alike; every unhappy family is unhappy in its own way." There are many traits an animal has to have to make it suitable for domestication (diet, behavior, lack of aggression, social structure, etc.), but missing any one of them would make an animal unfit for domestication. Diamond used this reasoning to show why, for example, zebras weren't domesticated in Africa like horses were in Eurasia, or why bears or rhinos weren't suitable to domesticate for food or as draft animals.

Diamond went on to argue how differences in geography allowed agriculture and domestic animals (referred to collectively as food production) to spread more easily in some regions than others once they had been developed. Eurasia, without any great barriers such as deserts, and with an east-west axis that meant the climate was more similar along its breadth, facilitated this spread more so than other regions.

Once regions had developed food production, they could maintain higher population densities. Initially this gave them a military advantage just through shear numbers. But eventually, by providing for an artisan class that didn't have to grow its own food, it led to technological advantages, as well. The high population densities, along with domestic animals, also contributed to those regions having endemic diseases that didn't exist elsewhere.

As an example of how Diamond was attempting to explain the grand patterns in history over tens of thousands of years, he pointed out that someone could ask why, out of all the areas of Eurasia, Western Europe currently dominates the world stage, and not Eastern Asia. He stated that this simply might be a short term 'blip', and not part of the long term trend (just look at the resurgence of modern China).

As I said, this is only a brief summary of the book. Diamond had many more reasons and examples that he used to support his hypothesis.

Some parts were more convincing than others. It also didn't help that in a few examples he brought up that I already knew a bit about, I saw some mistakes. For example, when discussing ancient human history, he compared the Out of Africa hypothesis to the multiregional hypothesis. The weight of evidence strongly favors the 'Out of Africa' hypothesis, but Diamond seemed a little more ambiguous in the book. In another section, discussing why cultures might be resistant to adopting certain technologies, he brought up the old QWERTY/DVORAK controversy, claiming that DVORAK is clearly superior to QWERTY, but market forces have kept it from being adopted. This is an old urban myth that isn't true. There haven't been many actual studies comparing the two keyboard layouts, and the studies that have been done don't show a very big advantage of one design over the other (certain advantages of each layout are offset by different advantages of the other layout).

Overall, I thought the book was very interesting, and that Diamond did a good job of presenting his case. I'd definitely recommend it.

Update 2010-03-29 - Slightly revised wording in 4th from last paragraph.

Posted by Jeff on Friday, Mar 26 | Permalink | Comments (0) | TrackBacks (0)

As evidenced by one of my recent blog entries, I tend to place a lot of value in science. I think it's the best method we have for answering questions with objectively true answers, and I think we can have a pretty high confidence in the answers it gives us. But, as a few people have recently asked me, where does that confidence come from? Throughout the past, people have had explanations for aspects of the universe that they believed were correct, but have since turned out to be wrong (e.g. the Sun orbiting the Earth). Given humanity's history of failed explanations, shouldn't we expect that many of our current explanations are also wrong, and be a little more cautious in our certainty?

The simplest reason to be confident in science is a pragmatic one - just look at the results. Science as the formalized discipline that we're used to is a fairly recent development. It's only been around a few hundred years, getting started in the Renaissance, but not really coming into its own until after the Enlightenment. But look at how fast our technology has progressed in that short time compared to the previous millenia of human existence. We've invented telescopes, steam engines, automobiles, semiconductors, airplanes, computers, TVs, radio, lasers, vaccines, antibiotics, cures for some cancers. We've sent people to the moon. These accomplishments are all based on knowledge that we've learned through science. It seems very unlikely that we would have been able to accomplish all of that if we didn't have a pretty accurate understanding of reality. Granted, there are other fields of science that haven't yielded practical applications, and possibly never will. For example, understanding the Big Bang may not ever give us any new technologies. However, given the technologies we have developed from other fields, we know that the methods produce reliable results.

Moving away from pragmatism, let's look at how science works. Richard Feynman once said, "Science is a way of trying not to fool yourself. The first principle is that you must not fool yourself, and you are the easiest person to fool." There are all types of ways that we can make mistakes in our reasoning. There's a great article I've linked to before from this site, which does a fantastic job of discussing this: The double-blind gaze: how the double-blind experimental protocol changed science. The article is focused on medicine, but it's applicable to science in general. The article mentions a few of the confounding factors that can affect our reasoning, including the placebo effect, the re-interpretation effect, and observer bias. Wikipedia has a whole list of cognitive biases. A big part of science is recognizing and accounting for all these potential mistakes. Along similar lines, science is not just a search for evidence that confirms your ideas. It's a search for evidence that would disprove your ideas. A big part of science is recognizing when you're wrong.

Science also trains us to think less in terms of absolute certainty, and more in terms of degrees of certainty. If you're being honest with yourself, there's no way to be absolutely certain of anything. It's possible that we're living in The Matrix, or hallucinating, and nothing is as it seems (if this sounds familiar, I've discussed it before). In normal everday conversation however, we tend to ignore those types of outlandish possibilities, and say that we're positive of something, even if technically we mean nearly positive. There are many things we've learned through science that we can say that we're positive are true. The roughly spherical shape of the Earth, the Earth orbiting the Sun, common descent (if not all the exact lineages and mechanisms), are examples of a few of those facts. We should no sooner expect those facts to be overturned than we should expect to wake up on the Nebuchadnezzar fighting alongside Neo. Other things we've learned through science don't have quite as much evidence. Antrhopogenic global warming is an example of this. We can say that we're really darned sure that climate change is happening and that we're responsible, but it's not quite so certain. It would still be really surprising to see AGW turn out to be false, but not earth shattering. You can keep moving down through levels of certainty through things like String Theory, which doesn't really have any evidence confirming it specificaly over other theories, but which is at least consistent with known evidence. If string theory turned out to be false, I wouldn't be all that surprised. You can go even further, and find theories inconsistent with known evidence, such as the supposed link between vaccines and autism, or the aether theory of light. We can be pretty sure that those ideas are false.

In addition to making us think in terms of degree of certainty, science also makes us think in terms of degree of accuracy. Isaac Asimov wrote a good essay titled, The Relativity of Wrong. You should read the whole thing, but here's a great quote from that essay, "When people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together." An example I've used before is the atom. The current model is the valence shell model, where electrons have a probability of being in particular positions relative to the nucleus. This is an improvement over the Bohr model, where electrons travel in circular orbits around the nucleus and where the orbit radii are defined by quantum mechanics. The Bohr model was an improvement over the Rutherford model (or Solar System model), where the electrons orbited the nucleus, but quantum mechanics wasn't incorporated to predict the orbit radii. The Rutherford model was an improvement over the plum pudding model. And the plum pudding model was at least more accurate than not knowing of the existence of electrons. So, you can see how our explanations have gotten more and more accurate concerning the structure of an atom. Our current model may also be supplanted, but at least we're zeroing in on the truth.

Those are the reasons why we can have confidence in what we learn through science. It's produced results that just wouldn't be possible if the methods didn't work. But it's not simply a matter of thinking that everything science reveals is absolutely right - it's recognizing how science works, what explanations are most likely to be true, and how close we should expect those explanations to be to the actual truth.

Posted by Jeff on Friday, Feb 19 | Permalink | Comments (0) | TrackBacks (0)

Sometimes, a term that you've heard your whole life suddenly seems strange, That's how it is for me and 'scientific facts'. When you think about it, that phrase seems a bit redundant. If something is true, it's a fact. It's that simple. It doesn't matter how you came to know it. If a statement lines up with objective reality, it's a fact.

What does it add to describe a fact as 'scientific'? I guess the first thing is to understand is what's meant by science. Generally, there are two related meanings to the word. The first is that it's a method. We should all know this method from grade school - come up with an explanation, gather evidence to test the explanation, refine your explanation, and repeat. The second is the body of knowledge we've learned through that method. But the thing is, everything that has an objective answer can be examined through science.

Consider an example. Some would consider the Earth orbiting the sun a 'scientific' fact. We as humanity may have learned about it through science, and we as individuals may have learned it in science class, but it doesn't change the fact that it's true. It's not as if the Sun used to orbit the Earth until Galileo came along. Can't we just call it a plain old fact?

There are a couple reasons I bring this up. One is for the people who like to point out that science can't tell us anything with absolute certainty, and therefore science doesn't deal in facts (like this exchange I had). When you consider things like solipsism and Last Thursdayism, you have to grant that for fact to have any meaning, it must mean very high level of certainty, and not 100% absolute certainty. Going by that definition, science certainly does deal in facts.

The other is for the people who think of science as something separate, as not really describing things as part of their world. To them, it may be a 'scientific' fact that evolution occurs, but but in their world, science is wrong, so describing evolution as 'scientific' means it may not have actually occurred.

Oh well, I'm not be expressing myself as clearly as I'd like, but it's late on a Friday, and I'm about ready for some supper and a beer. I guess the main point I'm trying to get across is something I already said in the first paragraph. Calling something a 'scientific' fact is redundant. Statements are either true or not, and if they're true, then they're facts. Since we can study everything with an objective answer through science, it really doesn't add anything to describe any facts as scientific. If they're not scientific, they're not really facts to begin with.

Added 2010-02-01 I thought about this a bit over the weekend, and realized that that last sentence might come off as a bit smug. So, I thought that maybe I should list a couple examples.

As the first example, consider the claim that Hawaii is the 50th state of the U.S. To look at this scientifically, we need to gather evidence to support that claim. We could start off by looking at current legal documents, which show that Hawaii is definitely a state. We could move on to archived documents, and find the Hawaii Admission Act, which shows when Hawaii became a state. We could move on to find documents of when each of the previous 49 states became states. We could study newspaper articles from each of those periods for additional confirmation. After studying all that evidence, then we could say that it is a 'scientific' fact that Hawaii is the 50th state of the U.S.

Next, let's move on to something that some would think was a bit more subjective. Consider the claim that I love my wife and daughter. To test this, people could observe my behavior around my family, and the actions I commit in relation to my wife and daughter. They could study my involuntary facial expressions, to see how I react around them. They could observe my behavior when they're not around, looking for signs of loneliness, or observing how I talk about them. So, even the claim that I love my wife and daughter can be considered to be a 'scientific' fact, since we can use the scientific method to investigate it.

That's what I mean when I say that all facts worth talking about are scientific. Sometimes, we only practice rudimentary forms of the scientific method to determine their veracity, but, at least in principle, the scientific method can be applied to them.

Posted by Jeff on Friday, Jan 29 | Permalink | Comments (1) | TrackBacks (0)

Wow. Just, wow. I know I've talked about Ray Comfort more times on this blog than is healthy (for example - here, here, here, here, here, and here), but now, not just is he publishing his drivel on his own, making scam websites, or getting followers to put the equivalent of junk mail into books at the book store. Now, he's been published in a blog on the U.S. News and World Report website, and boy is it ignorant.

The background of this article is this. Ray Comfort is publishing two versions of a reprint of Darwin's Origin of Species, along with an introduction in each version. The first version was abridged, and the introduction was made publicly available on the web. After the negative publicity it received, Comfort made his second version unabridged, and supposedly with a modified introduction. To give an idea of the introduction, here's how Comfort himself described it (be forewarned - there are many falsehoods and examples of bad logic in just these two paragraphs*).

This introduction gives the history of evolution, a timeline of Darwin's life, Hitler's undeniable connections to the theory, Darwin's racism, his disdain for women, and his thoughts on the existence of God. It lists the theory's many hoaxes, exposes the unscientific belief that nothing created everything, points to the incredible structure of DNA, and the absence of any species-to-species transitional forms.

It presents a balanced view of Creationism with information on scientists who believed that God created the universe—scientists such as Albert Einstein, Isaac Newton, Nicholas Copernicus, Francis Bacon, Michael Faraday, Louis Pasteur and Johannes Kepler. It uses many original graphics and "is for use in schools, colleges, and prestigious learning institutions." The introduction also contains the entire contents of the popular booklet, "Why Christianity?"

Towards the end of September, Dan Gilgoff posted an entry in his God & Country blog on U.S. News & World Report describing Comfort's book (the first version). After all the feedback Gilgoff got for that entry, he decided to revisit the issue. He set up an online debate between Ray Comfort and Eugenie Scott, the executive director of the National Center for Science Education. The debate consisted of four posts in total - Comfort's original argument, Scott's original argument, Comfort's response to Scott, and finally, Scott's response to Comfort.

I guess there are several ways I could have addressed this in a blog post, but I've decided to focus on Comfort's second post. That one struck me as so out and out ignorant, that it seemed a ripe target. I encourage you to read Scott's response first, but I thought I could supplement what she already wrote.

Continue reading "Ray Comfort - Still Ignorant on Evolution" »

Posted by Jeff on Thursday, Nov 5 | Permalink | Comments (0) | TrackBacks (0)

A common misconception about evolution is that it has a goal, that organisms evolve from lower to higher forms. This is sometimes referred to as the Ladder or Progress, with primitive forms at the bottom and more advanced forms towards the top of the ladder (and commonly, being the self centered species that we are, with humans on the top rung). This isn't true. Evolution has no direction. Organisms adapt to fit their local environment in whatever way works best. But if evolution has no direction, why is it that life now is more complex* than life from billions of years ago?

This really is pretty easy to understand once you give it a little thought. Let's use distance as an analogy. There's an old saying, that the journey of a thousand miles begins with a single step. You can't walk from Los Angeles to New York instantly. It takes many, many small steps (literally in this example) to get there. If we consider Los Angeles to be simple, and New York to be complex, then at any point on your journey, as you've increased your distance from LA, you've increased your complexity. And it's obvious that you can't get to a certain point of complexity until you've already taken all the previous steps leading up to it. You can't just instantly go from simple to complex.

But a journey still implies direction, and I've said evolution doesn't work that way. Evolution is more like a drunkard's stagger. If you have a drunk that starts out in LA, and let him wander aimlessly with no particular destination in mind, he may eventually end up in New York, but it definitely wouldn't be a straight line. He may just as likely never make it to New York, and never even leave LA. To extend the analogy further, he may end up in Seattle. He'd still be a long way from LA, but in a completely different direction. Squids, for example, are remarkably complex, but they took a different path to their complexity than us vertebrates, and their resulting complexity is different from ours.

Below is a graph that roughly illustrates this in an evolutionary context. It starts off at zero, and for every step, it goes up or down by a random amount** between -0.5 and 0.5. After every 10 steps, it splits, and each new 'lineage' then varies in that same manner. This was carried on for 40 steps, resulting in 8 lineages by the end.

Remember, this is all random variation from a starting point at zero, going in small steps. After 40 steps, one lineage had varied to more than 3.4 away from zero, while other lineages didn't vary very much away from zero at all. If this was representing complexity, and if the steps were assumed to be thousands or millions of generations, it demonstrates how complexity can evolve slowly from simple beginnings, without any conscious aim toward increased complexity. (As I said, this is only a rough illustration of evolution. Evolution is driven by more than just random variation, and the divergence of lineages isn't as predictable as that.)

Evolution really does sometimes decrease complexity. For an intimate example, consider what you're sitting on - a nice smooth posterior. Some time millions of years ago, our ancestors lost their tails, a complex feature with muscles, bones, and tendons. Their lifestyles were probably such that a tail just didn't really do that much good, so there was no reason for natural selection to maintain it. And now, we have backsides that are less complex than our simian ancestors.

**Technically, a pseudo random number generator was used (Visual Basic). For this application, that's close enough to truly random.

Posted by Jeff on Wednesday, Sep 23 | Permalink | Comments (0) | TrackBacks (0)

I had an interesting experience at work last Friday. Some time in the early afternoon, we started noticing some bees around the entrance to a trailer. We hadn't seen any yet this summer, so I poked around to see where they were coming from. I saw a few going in and out of a hole in the liner under the floor, so I ran home to get some wasp poison, and sprayed around the hole. As the afternoon wore on, more and more bees kept showing up. I kept spraying for a while, but eventually gave up. By the time I left to go home, here's what it looked like (I gave two different resolution options to view these bigger):

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And here are a couple videos of it that I uploaded to YouTube. The first one's a bit long, but you don't have to watch the whole thing. At the end of the second one, I got scared when I felt something land on my arm, but I didn't get stung.

By Sunday, the bees were no longer on the step, but had taken up residence under the trailer. We had to call in a bee keeper to get rid of them. He came in after dark on Sunday (so that the bees would be in the hive) and worked until midnight. He said that there must have been at least 20,000 bees. He didn't think they'd been there very long, that they'd probably just arrived.

That is, by far, the most bees I've ever seen in my life.

Posted by Jeff on Wednesday, Jun 3 | Permalink | Comments (3) | TrackBacks (0)

This past weekend, I got into a discussion with a couple friends about global warming. This was a different group than the one that inspired this blog entry, Global Warming - It's Real, And We're Causing It. These two had several arguments against global warming, not just a general distrust of the science. Like I wrote in that other entry, I'm far from being an expert in climate science. I've kept up with it a bit, but I've mostly trusted that the actual experts know what they're talking about, and when they said that there's a very, very high probability that global warming is human caused, I believed them. Well, arguments from authority don't carry much weight when people are giving you specific reasons why they doubt a theory. So, I had to do a little deeper research into their claims.

Below is the response I sent to them via e-mail. Since it's so long, I'm not going to put it in blockquotes. Also, since I'm posting this on my blog, I'm not going to use their real names. But rather than calling them John Doe I and John Doe II, I'll go with the first names from Comedy Central's news hour, John and Stephen.

[start of e-mail]

John & Stephen,

John, I know you're used to these e-mails. Stephen, this is just what I do after discussing something controversial - backing up what I said with a few references and doing a little more research. It looks like you do about the same - [my wife] gave me the articles you found.

Okay, first I guess I'll try to cover a few of the things we discussed over the weekend. There were a few points brought up that stuck out to me: 1) CO2 is not a greenhouse gas, 2) 30 years ago climatologists were predicting an ice age, while now they're predicting global warming, so how can we trust what they're saying, 3) Current data indicates that we're actually headed into a cooling period, 4) Mars ice caps are melting, indicating that increased solar activity is responsible for the recent warming trend, and 5) Sensors used to take measurements of polar ice were flawed, so we can't trust those measurements. I probably got a few of those wrong, mixed up a few with claims I've read on the Internet, and there are probably a few that I forgot, but that's mostly what I remember. So, I tried looking up those claims and here's what I came up with.

1) CO2 is not a greenhouse gas.

I guess you already looked this up, Stephen, since you wrote on the printouts you gave [my wife] that CO2 actually is a greenhouse gas. Just to give a little information for John, though, here's some more info, mostly summarized from Wikipedia (http://en.wikipedia.org/wiki/Greenhouse_effect). Most of the electromagnetic radiation the sun emits is in the visible spectrum. Greenhouse gases, pretty much by definition, don't absorb light in the visible spectrum, so most of the radiation from the sun makes it all the way to the surface of the Earth. There, it does get absorbed by numerous objects. As these heat up, they will radiate some of that energy back out in the infrared spectrum. Now, greenhouse gases, again pretty much by definition, do absorb light in that spectrum. So, the gases absorb that infrared radiation and heat up. Some of that heat will be transferred to surrounding gases, with some of it eventually making it back down to the ground. Some of it will be radiated back out in all directions - some back towards the ground, and some out into space. So, the net result of having greenhouse gases in an atmosphere is that the temperature of the planet will be higher.

The main greenhouse gas in our atmosphere is water. It provides around 36% of the heating. Next comes carbon dioxide, at around 9%. It's a little difficult to calculate how much heating each gas provides, since they interact with each other. For example, if you remove all the CO2 and water from the atmosphere, we would lose more than 45% of the greenhouse heating.

Here's another link, showing the actual absorption spectrum of CO2, and giving a more detailed explanation of how the absorption works on a molecular level:
http://www.wag.caltech.edu/home/jang/genchem/infrared.htm

There are other greenhouse gases, as well. Some are more effective on a pound for pound basis (such as methane). However, because their concentrations are so much lower, their total effect isn't as great.

One argument I have heard, is that carbon dioxide may be a result of warming - that some mechanism causes more CO2 to enter the atmosphere as the temperature increases. This argument is usually in response to the historical trend of global temperature vs. CO2. However, we can be pretty darn sure that much of the reason CO2 levels are rising right now is because of people burning fossil fuels. All that carbon was sequestered underground, and we're releasing it faster than it can be sequestered again. So, knowing that CO2 is definitely a greenhouse gas, if there's a mechanism that causes CO2 levels to rise with temperature, it's a feedback that's going to make the current situation worse.

2) 30 years ago climatologists were predicting an ice age, while now they're predicting global warming, so how can we trust what they're saying.

I wasn't paying much attention to climate science 30 years ago, so I can't speak to this directly. I do know that the way the media currently presents science is pretty bad. Look how much the media hyped the recent announcement of finding methane on Mars and how it could be indicative of life. The reality is that the current scientific consensus is much more conservative - it may be life, but there are many other possibilities it could be, and we just won't know until we get more data. So, if science reporting 30 years ago was anything like it is today, I could easily see the media playing up reports far more than what was the actual scientific consensus.

I found a fairly recent paper in the journal of the American Meteorological Society doing a literature search on climate research during the 60s and 70s. They found that a small minority of papers predicted global cooling, but that the majority actually were predicting global warming even then. So, it appears that the scientific consensus on global warming hasn't changed in the past 30 years, and has just gotten stronger. Here's a short blog entry describing the paper, which also has a link to the full paper:
http://www.realclimate.org/index.php/archives/2008/03/the-global-cooling-mole/

3) Current data indicates that we're actually headed into a cooling period.

For your reference, John, here's one of the articles Stephen printed out for me:
http://www.dailytech.com/Temperature+Monitors+Report+Widescale+Global+Cooling/article10866.htm

My main take of that article is that there's not enough information in it to predict that we've actually started a cooling trend. Average global temperature is influenced by quite a few factors, and thus fluctuates quite a bit from year to year. Global warming doesn't predict that every year will be warmer than the last, only that the trend is to higher temperatures. Just look closely at the graph they've provided. Several other periods show similar valleys, quickly rebounding to higher temperatures. Maybe this recent drop was the biggest, but not by a lot. Unless these temperatures stay low for a longer period than previous valleys, there's no reason to believe that this is a long term trend.

The only mechanism the article gives for why temperature might be decreasing is "reduced solar activity." Looking at the article linked to in the original article, the mechanism claimed seems to be the Sun's magnetosphere shielding Earth from cosmic rays, and the effect that has on cloud formation. The solar activity being described is not the solar irradiance. If solar irradiance were decreasing, I would fully expect that would decrease the Earth's temperature. How could it not? But actual measurements of solar irradiance show it to be pretty darn constant. It does vary slightly over an 11 year cycle (same as sun spots), but that variance is only ±0.65 W/m² about a 1366 W/m² average, or about 0.1% total variance.
http://en.wikipedia.org/wiki/Solar_variation

Hmm, I just found another record of solar irradiance in the NASA link a few paragraphs below. It looks like the current valley in solar irradiance is a little lower than the previous two valleys, but still not very far off from the average - maybe abut 0.15% total variation. It looks like we're right about at the minimum, and getting ready to start receiving more energy from the Sun again.

The links between other properties of the Sun and Earth's climate are more tenuous. I've seen a few studies claiming such links, but none that seem to hold up to scrutiny from other scientists. If either of you could send something showing a strong link, I'd be interested in reading it. That same Wikipedia article linked above discusses some of these proposed correlations:
http://en.wikipedia.org/wiki/Solar_variation#Global_warming

This article also addresses proposed correlations:
http://www.realclimate.org/index.php?p=180

As far as what could have caused the cooling, it looks like it my be due mainly to La Niña. NASA's Goddard Institute has a good discussion of this:
http://data.giss.nasa.gov/gistemp/2008/

I also found a report from June of last year that predicted this cooling. According to the link below, most climate models ignore short term effects such as El Niño and La Niña. For long term forecasts, they're not that important. For short term forecasts, however, they can have big impacts. The authors incorporated ocean currents into their model to give more short term predictions, and as I already said, they predicted the recent cooling.
http://www.ifm-geomar.de/index.php?id=4192&L=1

4) Mars ice caps are melting, indicating that increased solar radiation output is responsible for the recent warming trend.

The solar irradiance trends linked above show that the melting of Mars ice caps definitely isn't due to solar radiation, since solar irradiance hasn't changed by more than a fraction of a percent, and has actually been on the downward side of the cycle for the past few years. I'm not sure what other properties of the Sun would influence the ice caps on Mars.

A National Geographic news clip on this mentions that a Russian scientist, Habibullo Abdussamatov, thinks increased solar irradiance is heating both planets (again - see the actual measured solar irradiance in the Wikipedia link), but other scientists offer explanations for other factors that drive Mars' climate, including that the wobble of it's tilt axis is more pronounced than Earth's.
http://news.nationalgeographic.com/news/2007/02/070228-mars-warming.html

Wikipedia also has a section on this. The consensus seems to be that no one's exactly sure what's causing the Martian ice caps to melt, but it seems to be a local climate phenomenon, not a global one. With Mars' thin atmosphere and lack of oceans, it doesn't have the same thermal buffers as Earth, so smaller phenomena can have a larger effect. It mentions that dust storms could have darkened the ice caps, increasing the amount of solar energy they absorb, causing them to melt faster.
http://en.wikipedia.org/wiki/Climate_of_Mars#Evidence_for_recent_climatic_change

Here's another article discussing the southern Martian ice cap:
http://www.realclimate.org/index.php?p=192

I guess the short of it is, although people have hypotheses, no one's exactly sure what's causing Mars' ice caps to melt, because it's another planet that we haven't been able to study in enough detail to know the intricacies of what drives its climate. Although the solar irradiance argument put forth by Abdussamatov is almost certainly wrong.

5) Sensors used to take measurements of polar ice were flawed, so we can't trust those measurements.

To be honest, I'm not sure exactly which measurements you were talking about. I did see a mention of something in a recent entry on Carl Zimmer's blog (he happens to be one of my favorite science writers). Was this what you were referring to?
http://blogs.discovermagazine.com/loom/2009/02/22/a-wrinkle-in-ice-or-not/

I still don't know as much about global warming as I do about other fields, but the more research I do, the more confidence I have in the science. But, I could still be wrong. Keep sending me articles you think show global warming to be wrong. If it is, I'll change my view eventually. If the scientists are right, though, then the next thing to discuss is what to do about it. Do we even try to reduce our carbon output, or do we just adapt to any changes global warming causes? Personally, I think it will be somewhere in between. Trying to eliminate carbon output cold turkey would be more costly than adapting to the changes from global warming. But not doing anything about carbon output and focusing solely on adaptation would probably be more expensive than a little up front cost on energy research right now.

-Jeff

[end of e-mail]

If I get any responses from them that show anything I wrote to be wrong, I'll be sure to add it here. I also let both of them know that I was putting a copy of this here on my blog, so maybe they'll post their comments here.

Posted by Jeff on Friday, Feb 27 | Permalink | Comments (1) | TrackBacks (0)

In honor of Darwin Day, I figured that I'd post an entry related to evolution. Here is my review of Evolution: What the Fossils Say and Why It Matters, written by Donald Prothero, Ph.D. Let me say right at the beginning that the book was very good, and that I recommend it.

The title of the book is a bit misleading, in that it leaves out a major theme that was covered. A good portion in the beginning of the book is spent debunking creationism. Perhaps some readers are aware of Duane Gish's Evolution? the Fossils Say No!, and so notice the play on words and realize that Prothero's book was partly in response to Gish. For others (such as me before I read the book), the allusion isn't so obvious. In any case, Prothero devoted a good bit of space to pointing out the errors in many creationist arguments, including a detailed explanation on how the Grand Canyon was formed through slow geological processes and not through a catastrophic flood, along with the evidence on how we know this.

Also in the beginning of the book, Prothero spent some time explaining science & paleontology, which is what you'd expect for a book intended for a lay audience. His explanation of cladistics was very good.

Finally, on page 145, Prothero started Part II, which presented the evidence and explanations of the history of life on this planet. He started right from the beginning, with a few theories on abiogenesis. Consequently, his first chapter from Part II didn't really have any fossil evidence. As soon as he progressed in time to when organsims developed hard parts that could fossilize, the book finally lived up to its name. He tried to cover a little bit of everything, from pre-cambrian single celled organsims, on up to very recent mammalian evolution. Obviously, with a 400 page book trying to cover that much territory, he couldn't go in depth into any particular topic, but he did give a very good overview. He did tend to cover vertebrates in more detail than any other lineage, but I suppose that's because that's what most readers would be most interested in.

Since the book was about fossil evidence, it included a great deal of photos and drawings of fossils. To give a sense on what was in the book, below is one of my favorite figures, illustrating the transition from seal-like mammals to walruses. (I apologize for the poor quality of these images, especially along the edges, but I wasn't about to ruin the binding on my book just to make it lay flat in the scanner.)

Another good example of the way fossils were presented is the figure below, showing the homology between non-avian dinosaurs and birds.

As would be expected in a book about evolution, there were many cladograms (family trees). They were almost all well illustrated with representative members of each lineage, such as the one below.

The center of the book contained several pages of color plates. These included some nice color photos of fossils, as well as some artistic renderings of what the animals might have looked like in life.

I did have a few reservations. For one, I would have liked to have seen even more photos & illustrations of fossils. In some sections, Prothero mentioned fossils in the text, but had no illustrations to show the reader what they actually looked like. In several sections, Prothero made statements to the effect of, a highly trained paleontologist can see that... I realize that expertise is important, but Prothero came off as a bit condescending in several places. I would have preferred to have seen wording like careful observation shows that...

Overall, it was a very good book, and very informative. I'd already read a few books on evolution prior to this, but they had dealt with much more specific topics, such as the transition from sea to land, or human evolution. This was the first book I'd read that covered such a wide range of transitions, with so many photos and illustrations to support it. If you're already familiar with the creationist arguments, or have a good lay understanding of how evolution works, Part I can be a bit of a slog, although I can see how those chapters would be very informative to people without that background. But once you get to Part II, it's a very informative, fun to read book.

Posted by Jeff on Thursday, Feb 12 | Permalink | Comments (3) | TrackBacks (0)

Today is the 200th birthday of Charles Darwin, the man who presented evolution in such a way and with sufficient evidence that it became obvious that it was the explanation for how life developed on this planet. Others had ideas of transmutation before Darwin, and Alfred Russel Wallace even came up with a theory of natural selection very similar to Darwin's at around the same time, so it's apparent that humanity would have eventually recognized how evolution works. But Darwin's genius in presenting all the evidence for evolution in the way he did certainly gave the field a huge head start.

If you're looking for a way to celebrate Darwin Day, DarwinDay.org has a list of events from around the world. If you're in the DFW area, the Dallas Museum of Nature & Science is having Drinks with Darwin from 6:30 to 8:00. If I was just a little closer, or if this was the weekend, I'd probably go. However, I think I'm just going to have to content myself with watching the lineup of evolution documentaries on The Science Channel (and maybe the episode of Walking with Dinosaurs on Animal Planet).

Posted by Jeff on Thursday, Feb 12 | Permalink | Comments (1) | TrackBacks (0)

This news has already made it around practically all of the science blogosphere, and I even saw it mentioned in a special breaking news type segment on the Science Channel last night, but it's so cool that I can't resist commenting on it.

NASA just announced that they've definitively found methane on Mars. This is the first time they've been positive - previous announcements of methane were tentative, requiring more examination of the evidence. Since methane gets broken down very quickly in the Martian atmosphere (through as yet unknown mechanisms), finding methane means it must have been released into the atmosphere fairly recently. From what I've been able to gather, there are three likely sources for this methane:

1. Biology This is most exciting possibility, that living organisms beneath the Martian permafrost are creating the methane as waste.
2. Geochemical While I don't find this quite as exciting as life, it would mean that Mars is still geologically active. There are several processes that this could be.
3. Reservoir In other words, there's no current process producing new methane. It was previously generated either biologically or geochemically (or both), and became trapped, and all we're witnessing now are periodic leaks.

I'm trying to be reserved about this, since NASA got my hopes up before with the announcement of probable fossil microbes in a Martian meteorite, which turned out to be not as probable as they'd initially thought. It still could be microbe fossils, but it could also be from non-biological sources along with Earthly contamination. So, I'm trying not to get too excited about this announcement.

But, if the methane does turn out to be from biological origin, it means we've found aliens! Granted, life on Mars may be little green slime instead of little green men, but it would still be extraterrestrial life. From Carl Zimmer's blog coverage of the news conference, there were a few statements that do seem to indicate that biology is the most likely source of this methane.

2:18 Mumma points out that if volcanoes were making the methane, you’d expect other gases too, which they don’t see. NASA will look for other things that would be consistent with biology.

2:21 Mumma is explaining some of the backstory–first reports of observations were in 2003. We knew we had methane since late 2003, he says. But they’ve been working to make the data “unassailable.” We’ll see…

2:35 Back to the science: Lisa Pratt says methane from rock (serpentinization) is rare on Earth and actually plugs up active sites. This is why she takes biology seriously as “slightly more plausible.”

There are two possibilities I can think of for this life (if it does indeed turn out to be life):

1. uses DNA or RNA
2. uses something else

If the microbes use DNA or RNA, then it would seem extremely likely that they have a common ancestor with life here on Earth. From what I've read, scientists think it's more likely that life would have originated here on Earth, and then got transferred somehow to Mars. Though it's still possible that it went in the other direction - life originating on Mars and then seeding Earth.

If the microbes don't use DNA or RNA, then it would seem most likely that they originated independently from the life here on Earth. Now that would be super exciting. For one, it would mean that life probably is fairly common in the universe, and that we're not all alone. Heck, if so many solar systems have life, then other multicellular and intelligent life out there seems much more likely, maybe even other technologically inclined organisms capable of producing civilizations. However, it will be a long time before we can look into those possibilities. But, the possibility of independent life on Mars is exciting for another reason - it would show us another strategy for life to take. It would start to show what types of things common to life on Earth are that way because they're needed for life, or simply because of historical contingency.

This really is some of the most exciting news I've heard in a while. Now we just have to wait to see what the actual source turns out to be.

Further Reading:

• Article on Aerospace & Defense Network - gives a really good synopsis of the whole thing
• Carl Zimmer's Live Blogged Coverage of the Press Conference
• Abstract of the Paper in the journal, Science
• Blog Entry on Pharyngula - The comment thread contains some good discussion from some knowledgeable people, as long as you ignore the comments on religion

Added 2009-01-19 Phil Plait of the Bad Astronomy Blog has finally weighed in on this topic. He's very reserved about the whole thing, stressing that we don't know exactly what's creating the methane, and that we just need to wait for more data. He also criticizes much of the media for over hyping the biology aspect of the story.

Revised 2009-02-13 to added the statement "(if it does indeed turn out to be life)." That section's been bugging me ever since I first posted this - I should have edited that a while ago.

Posted by Jeff on Friday, Jan 16 | Permalink | Comments (0) | TrackBacks (0)

I wrote an e-mail to the Dallas Museum of Nature & Science asking them about Darwin Year events. Since the events don't seem to be advertised very prominently on the museum's site, I'll post their response here:

Hi Jeff. We are going to host two events. Cocktails with Charles on his actual birthday 2/12 and cupcakes with Charles on Saturday 2/14. The Thursday event is for adults only and the Saturday event is for families.

I don't think I'll make the two hour drive to to Dallas just for cocktails or cupcakes, but if I just happen to be visiting my wife's family that weekend...

Posted by Jeff on Thursday, Jan 15 | Permalink | Comments (3) | TrackBacks (0)

Since 2009 marks the bicentennial of Charles Darwin's birth, as well as the 150th anniversary (sesquicentennial) of the publication of On the Origin of Species, many groups have decided that 2009 should be Darwin Year. So, to kick off the year, here are a couple links to good sites dealing with Darwin.

• Nature's Darwin 200 The prestigious journal has put together a collection of articles, editorials, news stories, and various other essays and features that have to do with evolution in general or Darwin in particular.
• The Darwin 200 Consortium Hosted by London's Natural History Museum, this site also has a collection of info on evolution, as well as info about upcoming events to celebrate Darwin Year.
• DarwinDay.org Another good site with evolutionary info. The events on this site are mostly on or around Darwin Day, February 12th.
• American Museum of Natural History's Darwin page Yet another good collection of information. This is from the exhibit that ran in the museum from 2005 to 2006.

To give a short taste of the Nature site, they've made freely available, and even encouraged dissemination of (so sharing it here is perfectly legal), an article on 15 Evolutionary Gems, collecting information from articles published in the journal "over the past decade or so to illustrate the breadth, depth and power of evolutionary thinking."

Don't forget to check with your own local museums. Even if they don't have any special events scheduled for Darwin Year, they're always fun to visit, anyway.

Added 2009-01-02 Well, I figure that for the kick off to Darwin Year I might as well post links to the previous posts I've made on evolution or Darwin. If I happen to post anything else on the subject during this year, I'll try to remember to update this list.

• Book Review - Voyage of the Beagle
• Book Review - Origin of Species
• A (Somewhat) Brief Introduction to Evolution
• Book Review - At the Water's Edge
• Book Review - Smithsonian Intimate Guide to Human Origins
• Review of the Lucy's Legacy Exhibit at the Houston Museum of Natural Science

Posted by Jeff on Friday, Jan 2 | Permalink | Comments (1) | TrackBacks (0)

Speaking of space, my daughter and I broke out the telescope tonight, and I figured that just for the hell of it, I'd try to take a picture of the moon. No fancy equipment - just sticking the camera up against the eyepiece, and doing my best to get it in focus.

(click image to enlarge)

If anyone's interested, it was an Astroscan telescope, and the box the eyepiece was in said "Plossl F15." The camera was a 7.2 MP Sony DSC-W80. I probably could have gotten a little better picture if I'd messed around a bit more, but I thought this one still turned out decent.

Posted by Jeff on Friday, Nov 14 | Permalink | Comments (0) | TrackBacks (0)

Douglas Adams once wrote,

Space is big. Really big. You just won't believe how vastly hugely mind-bogglingly big it is. I mean, you may think it's a long way down the road to the chemist, but that's just peanuts to space.

Phil Plait from the Bad Astronomy Blog recently posted about "the deepest ground-based look into the universe ever undertaken." I've put a compressed image below, but I would highly recommend downloading the 32MB full resolution image (The ESO reorganized their site. The image can now be found here. It's offered in several resolutions, including a gigantic 78.6 MB tiff. You could also use this flickr link instead, for a slightly lower res version). Don't be fooled - most of those smudges of light aren't individual stars; they're galaxies.

Okay, to give an idea of scale, I've superimposed that image onto the moon, to show how much of our field of view it takes up (If you make a thumbs up sign and hold it at arm's length, the full moon's about the size of your thumb nail). Not just that, but notice that little white square in the top left corner of the superimposed image? Well, I put the full size of that portion on the right. Note that in the image above that that region appears to be pretty empty, but once you zoom in on it, you can see there's still a lot there. And remember, those are galaxies, not individual stars. That's why it's so impresive to download the full size image and just scroll around it.

Okay, to put this into a little more perspective, I did a rough calculation. It seems like people like comparing stars to grains of sand. Well, it's been estimated that our galaxy contains around 100 billion (1 x 10¹¹) stars. For a rough calculation, let's assume we have spherical grains of sand around 0.5mm in diameter (source), or about .02 inches in diameter. I won't bore you with the calculations, but 100 billion grains of sand would have a combined volume of 231 cubic feet. Assuming a 64% packing ratio (because there're going to be air spaces in between the grains), you'd actually need a container of around 361 cubic feet to hold all that sand, which works out to a cube of around 7 ft. per side.

So, the point of all that calculation - if you had a 7'x7'x7' container full of sand, that's about how many stars there are in our galaxy. Assuming we have an average size galaxy (some are bigger, some are smaller), just about every smudge of light in the image above represents around that many stars. I really can't even begin to comprehend that - all I can do is describe it. Scrolling around that full size image gives me butterflies in my stomach thinking about just how big this universe is.

Added 2008-11-14 Okay, that assumption about our galaxy being typical has been bugging me a bit. I still haven't been able to find a good source showing the distribution of sizes of galaxies (admittedly, I haven't looked very hard), but Wikipedia says that most galaxies range in size from 10 million to 1 trillion stars. So, repeating the calculations I did earlier with that star count, it would take a 15x15x15 ft cube to hold a trillion grains of sand, and a 4x4x4 inch cube to hold 10 million. Now, a 4" cube may not be all that big compared to the 15' one, but that's still a lot of grains of sand.

Now, just to add one more bit of comparison, if you're in a dark area on a clear night, you could probably see around 2000 individual stars with your naked eye (since you can't resolve individual stars in the Milky Way or 3 three galaxies you can see with the naked eye, the Andromeda Galaxy, The Large Magellanic Cloud and the Small Magellanic Cloud - source1, source 2). It would only take a 1/4 inch cube to hold that many grains of sand.

So now, when you look at the picture, you'll have a slightly more accurate guess of how many stars each one of those smudges of light represents.

I'll also add that after working on this entry yesterday, and then staring up at the night sky with a near full moon for comparison, it made me feel tiny.

Posted by Jeff on Thursday, Nov 13 | Permalink | Comments (0) | TrackBacks (0)

I was with a group of people yesterday, and one of them brought up the recent news of the U.S. listing polar bears as a threatened species under the Endangered Species Act, due to their expected decline as global warming melts the arctic sea ice they depend upon for survival. And of course, this got the conversation going on global warming. Out of the six of us, one guy thought that scientists just didn't know what the hell was going on with the climate, that there wasn't any real consensus on global warming at all, and that even if global warming were real, which he doubted, polar bears would find a way to survive, anyway. Another guy seemed more open to the idea that global warming could be happening, and could be human caused, but wasn't entirely convinced. I tried my best to defend the science, while the other three people stayed pretty quiet on the subject (although from a previous conversation, I think that one of them at least accepts that global warming is happening). Later on, when I told another guy about this conversation, he seemed to think that the current global warming might just be a natual cycle, and that it's not human caused. So, out of 7 people, I was the only one to strongly accept that current global warming is human caused.

Now, I'll admit I'm no expert on global climate. Not only am I not involved with the field at all, but I haven't really studied it in depth on a lay level, either, like I have other fields such as evolution. So, I guess I need to ask myself, how can I go on accepting that humans are causing global warming, and that it is a major problem?

First, I'll defer to the experts. I realize this isn't exactly a sound logical approach - after all, evidence is evidence no matter who discovers it. But, in the same way that I'll take my doctor's advice on what effects different medicines and procedures have, I'll put a fair amount of weight on the statements of the people who devote their careers to studying climate.

Continue reading "Global Warming - It's Real, And We're Causing It" »

Posted by Jeff on Friday, May 16 | Permalink | Comments (8) | TrackBacks (0)

The other night, we went out to eat with some friends. I forget why, but for whatever reason my daughter was going through, with our help, trying to think up a mammal for every letter of the alphabet (aardvark, bear, cat...) Well, for P she picked platypus, so when the game was all over, it got us to talking about them. And I foget exactly how the next part came up, but the guy I was talking to brought up that he couldn't see how they were related to other mammals, and that he really doubted the whole theory of evolution. I tell ya what - get a couple beers in me and then tell me you don't accept evolution, and just see what type of conversation gets going. Boy, was it fun. Unfortunately, I don't think I did much convincing. It had nothing to do with the beer, but a whole lot to do with the fact that discussions like that are basically my word vs. your word. Considering that I'm not a biologist or in any related field, and it makes my word worth that much less. So, I decided to write up an e-mail to send him, along with links to lots of sources backing it up. Once I got through with typing it, I figured that it made for a decent general introduction to evolution. Maybe at some point I'll clean it up and make a good essay out of it, but even in its rough e-mail form, I figure it makes for a decent blog entry. So, if you want to read it, go head below the fold.

Continue reading "A (Somewhat) Brief Introduction to Evolution" »

Posted by Jeff on Friday, Mar 28 | Permalink | Comments (2) | TrackBacks (0)

The full title of this book is At the Water's Edge : Fish with Fingers, Whales with Legs, and How Life Came Ashore but Then Went Back to Sea. It was written by Carl Zimmer, and as the long title suggests, is all about those two dramatic transitions of life evolving into such distinct environments. This book was great - one of the best non-fiction books I've read in a while. It was just the right blend of story telling, concepts, and evidence, and made for a very compelling read. In fact, I think I finished it in less than a week.

When I reviewed another book by Zimmer, the Smithsonian Intimate Guide to Human Origins, I commented that it wasn't very in depth. At only 176 pages, much of them filled with photos and illustrations, it was a little light on commentary. At the Water's Edge is very different in this regard. It's 304 pages, filled with small print, with only enough diagrams as are needed to illustrate a few key points. It's not a tome, by any means, but it certainly provides Zimmer with enough space to do this subject justice.

The book is divided into basically two halves - the first dealing with the transition from lobe finned fish to early tetrapods, and the second half dealing with the transition from mesonychids to dolphins and whales. As would be expected, both halves deal with the specifics of each of those cases - transitional forms that have been discovered, environmental pressures that would drive the transition, etc. However, mixed throughout the entire book are also sections on general theory. There's a nice section on development in the beginning, covering such topics as Hox genes and non-genetic factors; he describes exaptation; there's another section on cladistics; as well as sections on many other concepts related to evolution.

I learned quite a bit by reading this book. Even though I was already familiar with much of the general theory, Zimmer presented it in ways that made me think of things differently. He also introduced a few concepts, such as the evolutionary "quit point," that I hadn't thought of much before. Still, where I learned the most was in those specifics of the transitional forms between fish and tetrapods, and land mammals and whales.

I'll give one example of something very interesting I learned from this book. (In fact, this was the very first passage of the book that I read, when I first got it and was just thumbing through to see what it was like.) At some point, our ancestors must have developed lungs to breathe air, obviously. When we look at the world around us, most fish today cannot breathe atmospheric air - they rely on their gills to get oxygen from water, but also have organs similar to lungs called swim bladders, which they use to regulate their buoyancy. From that observation, you may be tempted to think that lungs are a modified swim bladder, which perhaps evolved to allow fish to survive in swamps or other oxygen poor environments. After all, what need would an ocean going fish have of lungs? I know that's what I had thought, but as it turns out, it's almost certainly wrong.

Continue reading "Book Review - At the Water's Edge" »

Posted by Jeff on Friday, Mar 7 | Permalink | Comments (0) | TrackBacks (0)

I already posted a brief review of this book in my review of the Lucy's Legacy Exhibit at the Houston Museum of Natural Science. I don't really have much to add, but I thought I ought to at least give that review some closure, since I'd only read 2/3 of the book when I wrote it. I also figured this would give me a good chance to get the review into my Books section.

The book is the Smithsonian Intimate Guide to Human Origins, by Carl Zimmer. I liked it. It's not very in depth - it only took me about one weekend to read the whole thing - so if you follow science news, you probably won't learn a whole lot from it. That's not to say you won't learn anything - I certainly did learn a few things from this book, but most of the information was a review of what I alread knew.

But, it does have lots of pretty pictures that make it worth the price. And I mean that in the best possible way - paragraphs are all well and good, and it would be impossible to teach evolution with nothing but glossy pictures, but it can be nice to have a page full of pictures of fossil skulls, to see with your own eyes the similarities and differences. Sometimes pictures do show things more clearly than words ever could. Plus, if you don't follow science news as much as I do, or happen to know a person who doesn't know much about human evolution, it makes for a very good overview. If someone doesn't want to read the whole thing, but they're willing to listen to you explain something to them, you can still use the book, and open it up to some of those pretty pictures to help illustrate your point.

Posted by Jeff on Friday, Feb 22 | Permalink | Comments (0) | TrackBacks (0)

In honor of Darwin Day, I figured I'd post a review of The Voyage of the Beagle, which I just recently finished reading. The edition I read was actually the one from The Folio Society, given to me as a gift, and not the one pictured at right from Amazon. The book is also available as a free download from Project Gutenberg as a text only version, or as html with pictures, or from The Complete Works of Charles Darwin Online.

There are many reasons to like this book. One can't ignore the historical importance, since this expedition gave Darwin much of the insight that would lead to developing the theory of evolution, but this book would still be interesting even if Darwin had gone on to do nothing after sailing on the Beagle. The book is basically the journal of a young man on a round the world voyage, visiting much of South America, Tahiti, Australia, and a few other places, describing all the different cultures, geographies, and animals that he encountered.

For this review, I'll quote heavily from The Voyage of the Beagle, letting Darwin speak for himself, to give the reader a better idea of the language of the book. But first, let's get the somewhat confusing background out of the way. Darwin went along on the second survey expedition of the HMS Beagle. The first expedition, begun in 1826, consisted of two ships, the larger HMS Adventure, captained by Phillip Parker King, and the smaller HMS Beagle, captained by Pringle Stokes. Stokes committed suicide near the end of the first expedition, and 23 year old Flag Lieutenant Robert FitzRoy was named as temporary captain of the Beagle. On the second expedition, begun in 1831, only the Beagle returned, and as FitzRoy had proven himself well enough as temporary captain on the first expedition, he was given command of the ship for this second expedition. Worried about becoming depressed and suffering the same fate as Stokes, FitzRoy invited Darwin along for the journey so that he could have someone to talk to. As survey expeditions, the main purpose was acquiring data to produce nautical charts. Darwin had a slightly different agenda, as a naturalist, collecting many samples of the flora & fauna and taking many notes along the way. After the expeditions' completion, a four volume account was published, titled, Narrative of the Surveying Voyages of His Majesty's Ships Adventure and Beagle. The third volume of this narrative was written by Darwin, and titled, Journal and Remarks, 1832—1835. Darwin's volume proved to be so popular that the publisher, Henry Colburn of London, decided to publish it as a stand alone book, renamed, Journal of Researches into the Geology and Natural History of the various countries visited by H.M.S. Beagle. The book was published several more times under several different titles, but is most commonly referred to today as The Voyage of the Beagle.

Continue reading "Book Review - Voyage of the Beagle" »

Posted by Jeff on Tuesday, Feb 12 | Permalink | Comments (1) | TrackBacks (0)

Well, I just announced that I was starting a new Books section, so I figure I ought to post a book review. But, I'm going to cheat a little on this first one - I'm going to combine two previous posts, with a little bit of editing, and adding only a paragraph's worth of new content.

The book is the classic, Darwin's The Origin of Species. Long before I picked up the book, I already had a pretty good understanding of evolution - better than most laymen, I'd wager. So I didn't start reading Origin of Species to try to learn anything about the theory. Rather, it was more to do with my interest in history, particularly my interest in the history of science and technology. And it doesn't disappoint.

Continue reading "Book Review - Origin of Species" »

Posted by Jeff on Thursday, Oct 18 | Permalink | Comments (0) | TrackBacks (0)

This exhibit is now at the Pacific Science Center in Seattle, Washington. I haven't seen the exhibit there, but I'm guessing that it's pretty similar to what was in Houston. If anybody who's seen Lucy in Seattle happens to come across this review, please leave a note in the comments section to let me know if they've changed the exhibit at all.

This past weekend, my family and I went down to the Houston Museum of Natural Science to see the Lucy's Legacy exhibit. For anyone unfamiliar with this topic, Lucy is the nickname given to an Australopithecus afarensis fossil found in 1974 in Ethiopia (her nickname in Amharic is dinqineš, "you are wonderful"). At the time, she was one of the oldest, most complete hominid fossils found, and helped clarify a long standing question in human evolution of which came first - big brains or bipedalism. (Thanks to Lucy, and confirmed by other fossils, we now know it's bipedalism.) She is still one of the most complete early hominid fossils, and still very important to science (more info - article on Slate).

I'm going to do this review a little backwards. Lucy was the very last part of the exhibit, but since she was the main reason we drove 6 hours to go to Houston, she's what I'm going to discuss first. If you study human evolution at all, there's really not much to be said. You already know what the bones look like. Seeing them in person doesn't teach you much, but there's just something magical about it. I stood and stared at her for as long as my family would let me, and had butterflies in my stomach the whole time. To look down at that little 3'-8" skeleton, knowing how long ago she lived and how closely related we are to her - no words can do justice to the feeling you get.

Lucy's skeleton was in a case in the middle of the room, with all the bones laid out flat. There's was thick glass or plexiglass protecting the bones (or some other material - I didn't want to touch it and put my fingerprints on it). A few feet away on one side, cast replicas of the fossils were arranged in an upright position, in the way they would have been in life (similar to the picture of Lucy on Wikipedia). A few feet away on the other side is a fleshed out, full size reconstruction of what Lucy might have looked like (this article on Bloomberg has a photo of the head of the reconstruction). It was nice to see those three things together to put the bones into perspective. On the circular outside wall of the room was a 78 foot long, 10 foot high mural by Viktor Deak, artistically representing 6 million years of hominid evolution (if you subscribe to Natural History, the cover of the October 2007 issue shows a portion of that mural, and for the time being, their website does as well). I think the mural was my wife and daughter's favorite part of the exhibit.

I have to bring up one negative point about the exhibit. Just before you go into the room with Lucy, they show a short film about how she was found and the fossils' significance. And it was during this film that something jumped out at me as being wrong. I forget the exact wording, but the film said something to the effect that some scientists believe Australopithecus might have split into two groups - one giving rise to chimps and the other to humans. However, my understanding is that the chimp/bonobo and human split was around 6 million years ago (more info), and that australopithecines are on the hominid side of that split. And with Lucy being a member of the species A. afarensis, and living around 3.2 million years ago, she almost certainly was not an ancestor of chimps or bonobos, as that film seemed to imply (or at least what a laymen ignorant of human evolution might have taken away from the film, giving the film makers the benefit of the doubt and assuming they were referring to an earlier species of Australopithecus).

As far as I could tell, Lucy was the only actual fossil in the exhibit. Maybe I missed them, but all the other "fossils" I saw were cast replicas. They were still interesting, and still helped tell the story of hominid evolution, but didn't inspire the same awe you get looking at the real thing. There were, however, several stone tools in the exhibit, that actually were ancient.

Even though hominid evolution, and Lucy in particular, were the main points of the exhibit, they were really only a small part of it. Most of the exhibit was dedicated to more recent Ethiopian history, from a few thousand years ago on. As the Houston Museum of Natural Science puts it on their website, "In addition to the fossil of Lucy, over 100 artifacts such as ancient manuscripts and royal artifacts from a dynasty Ethiopians believe stretches back to the son of the biblical King Solomon and the Queen of Sheba will be on display." Most of those artifacts besides the manuscripts were painted diptychs and processional crosses. There were also a handful of weapons, baskets, and other miscellaneous artifacts. Afterwards, my wife told me that she enjoyed those paintings much more than the Lucy fossils.

After we got done with Lucy's Legacy, there was still the rest of the museum to explore, and the permanent exhibits were very interesting. I do have one gripe, though, and maybe it comes from living so many years in D.C. with the Smithsonian museums, where admission was free. But there were three other temporary exhibits besides Lucy - Lizards & Snakes Alive, Treasures from Shanghai, and Frogs! - that you had to pay an additional fee to enter, along with another permanent exhibit, a greenhouse filled with butterflies, that also cost extra. When you've got even a small family of three, those extra prices add up pretty quickly. So, we didn't go to any of those other exhibits, even though my wife really wanted to see the Chinese art, and my daughter really wanted to see the snakes and lizards. Even for members, the discounted prices are still 1/2 to 2/3 of the non-member prices, and since we don't live very close to Houston, becoming members doesn't make much sense. I suppose they have to pay for the exhibits somehow. It's just a little disappointing, when I've been to other museums, like the Carnegie Museum of Natural History in Pittsburgh, where the regular admission price lets you see so much.

One final note - I really wanted to get some type of coffee cup or shot glass as a souvenir, but just about everything in the gift shop that had to do with Lucy had the same logo on it. And to be honest, I don't particularly like the logo, especially the way it looked printed out small on a mug. If they had just had a picture of the fossil itself, I would have bought one. So instead, I bought a copy of Carl Zimmer's book, Smithsonian Intimate Guide to Human Origins*.

I know I did a little bit of complaining there at the end of this review, but that's only so the reader knows what to expect when going to the museum. As I said, seeing the actual fossils of Lucy in person really was awe-inspiring. It was worth the 6 hour drive to get there, and I'd do it again in a heart beat.

Posted by Jeff on Monday, Oct 1 | Permalink | Comments (2) | TrackBacks (0)

This past weekend, my family and I went down to Dallas to see BodyWorlds, the traveling museum exhibit that shows preserved human bodies in various poses and various states of dissection. After reading PZ Myers' review on Pharyngula, I was a little worried that it was going to be too artsy. But I have to say, it was great. After reading a few reviews from other locations, it seems like certain locations may not get the full exhibit, either because the venue isn't large enough for all the exhibits, or political pressure keeps the museum from displaying all of the specimens, but it seemed like Dallas had quite a bit.

If you haven't heard of this exhibit, yet, like I said above, it's made up of many specimens of preserved humans. The preservation process is called plastination, which, to quote the Dallas Museum of Nature and Science, "Plastination, invented by German anatomist Dr. Gunther von Hagens in 1977, is a process whereby all bodily fluids and soluble fats are replaced with reactive plastics that harden after curing with light, heat or gas. All tissue structures are retained." To make things even more interesting, the bodies have been dissected in various ways to show off different aspects of human anatomy (and a handful of other animals, as well). For example, there are some specimens that show all of the muscles, others that show the circulatory system, others that show the nerves, and yet others that show different combinations of systems, so that you can see how it all works together. Yes, a few of the specimens may have been overly artistic, but those were the exception, and not the rule. Aside from the "whole body plastinates" in poses, there were several specimens of whole bodies that were sliced into ~1/4" sections. These were another, very interesting, and very informative way to show how the body fits together. On top of that, there were many, many more specimens that were of individual organs, or smaller groups of organs (such as the digestive system), also disected in various ways. These included not just healthy, but also abnormal and diseased tissues, so you could see what they looked like. It also showed how much variation there is from person to person.

One of the other complaints from Myers' review that had me a little worried was this, "I like my biology wet. It's supposed to be vital and dynamic and messy and complicated, but it all ties together into a lovely integrated whole. A collection of plastinated cadavers is precisely the opposite of what I enjoy about the science: it's dead and static and distressingly dry." So here's my response to that. In our trips to Guatemala (2005 & 2006), I've been lucky enough to help out in a few of the operations and get a peek inside of a living body. My wife's a nurse, so she's gotten to see much more than I have, and she had to go through all of those anatomy classes to get her degree. And both of us thoroughly enjoyed BodyWorlds. It gives you the type of overall view that you just can't get unless you actually perform your own dissection, and that's certainly not something that's going to be available to most people. The closest most of us will ever get to that is dissecting non-human animals, which although informative, just isn't the same as seeing the inside of your own species.

One more positive review is the fact that my 7 year old daughter was interested enough in the whole thing to spend an hour and a half looking at it, up until the time they closed the exhibit and kicked us out. She probably would have spent a little more time there if we'd had it.

I guess I ought to make note of the general mood. It was, after all, an exhibit full of dead people. The atmosphere was respectful, almost like a cemetary, with everybody talking in hushed tones. For the most part, I wasn't too bothered by it, since these were mostly adults who had lived (hopefully) full lives, and who had willed their bodies to this exhibit. There's still the sense that these were once living, feeling people who were now gone, but the presentation, and the knowledge that this was how these people wanted to be remembered, kept it from being sad. That is, all the exhibits except for the babies. I must admit, those were very moving. If you think that would bother you too much, the way the exhibit was laid out in Dallas, you could bypass that section if you wanted to. But even though it was sad, I think it was still worth seeing.

So, if you're reading this and planning on going to see BodyWorlds, my advice is to buy your tickets a few days in advance. The exhibit is so popular that the Dallas museum has expanded their hours to 9 am till 9 pm. And even at that, they're selling out. We waited until the night before to buy our tickets, and they were all sold out until the 7:15 pm entry time - 7:30 was the last slot they sold tickets for (and because they were running late, we didn't get in until 7:30 - so we ended up having to rush a bit at the end just to see everything). Buy your tickets well ahead of time so you can go in the morning and look at your own pace, and then have plenty of time to go look at the rest of the Museum of Nature and Science.

Posted by Jeff on Monday, Mar 19 | Permalink | Comments (0) | TrackBacks (0)

This is a follow-up to a previous entry. However, both of thses entries have been supplanted by a newer post, which combines the two, with a little editing, and a paragraph's worth of new content.

Well, I finally finished reading Origin of Species (actually, I finished it a couple weeks ago, and I'm just now getting a chance to write about it). My impressions that I wrote about in a previous entry haven't really changed, but there were two other things that struck me that I wanted to write about.

First, and maybe this is just my fault for my own ignorance, but it's changed my perception of Darwin (kind of like as an aviation buff, I always get upset when people think of the Wright brothers as just tinkerers, and don't give them their proper due as engineers). The story you're always presented with about Darwin is this naturalist who went on a voyage on the Beagle to observe plants and animals, had an epiphany at the Galapagos islands, and came up with this theory of evolution. While this is true to a certain extent, and Darwin was a very keen observer, Origin of Species had more than just his observations from the Beagle and some interesting ideas to explain it. Let me give a couple examples. In one of the chapters on geographical distribution, Darwin discusses how certain plants might spread from one pond to the other. In addition to trying to think up plausible means, he then goes on to test how plausible they might be. Consider this passage, discussing the possibility of seeds sticking to water fowl and being transported from pond to pond in that way:

I do not believe that botanists are aware how charged the mud of ponds is with seeds: I have tried several little experiments, but will here give only the most striking case: I took in February three table-spoonfuls of mud from three different points, beneath water, on the edge of a little pond; this mud when dry weighed only 6 3/4 ounces; I kept it covered up in my study for six months, pulling up and counting each plant as it grew; the plants were of many kinds, and were altogether 537 in number; and yet the viscid mud was all contained in a breakfast cup!

Later in the same chapter, Darwin discusses inhabitants of oceanic islands, and the problem of how certain animals could have come to live on them. I'll just let Darwin speak for himself on this one:

Almost all oceanic islands, even the most isolated and smallest, are inhabited by land-shells, generally by endemic species, but sometimes by species found elsewhere. Dr. Aug. A. Gould has given several interesting cases in regard to the land-shells of the islands of the Pacific. Now it is notorious that land-shells are very easily killed by salt; their eggs, at least such as I have tried, sink in sea-water and are killed by it. Yet there must be, on my view, some unknown, but highly efficient means for their transportal. Would the just-hatched young occasionally crawl on and adhere to the feet of birds roosting on the ground, and thus get transported? It occurred to me that land-shells, when hybernating and having a membranous diaphragm over the mouth of the shell, might be floated in chinks of drifted timber across moderately wide arms of the sea. And I found that several species did in this state withstand uninjured an immersion in sea-water during seven days: one of these shells was the Helix pomatia, and after it had again hybernated I put it in sea-water for twenty days, and it perfectly recovered. As this species has a thick calcareous operculum, I removed it, and when it had formed a new membranous one, I immersed it for fourteen days in sea-water, and it recovered and crawled away: but more experiments are wanted on this head.

It's this practical approach from Darwin that impressed me. He didn't just sit around trying to come up with just-so stories - when he came to a question, he'd go and get his hands dirty doing real experiments.

The other thing I wanted to discuss from Origin of Species is how it made me appreciate how much we know now. Let me explain this a bit - right now, there's a lot we don't know about a lot of things in the universe, and it kind of fills you with a longing to know the answers, even though you know you won't survive long enough to learn them. Like life on other planets - I would love to travel to other solar systems and see how complex life has developed on them, what strategies and structures have evolved in an environment completely isolated from our own, but I know that that's something I'll never know. Now, consider Darwin's condition in relation to his theory, having the limited evidence that he did. In the final chapter of Origin, Darwin wrote, "Numerous existing doubtful forms could be named which are probably varieties; but who will pretend that in future ages so many fossil links will be discovered, that naturalists will be able to decide, on the common view, whether or not these doubtful forms are varieties?" We are those "future ages!" Granted, our knowledge of the fossil record is still far from perfect, but we've discovered so many things since Darwin's time. For example, we now have a pretty good idea how whales evolved, how the first tetrapods went from water to land, how birds evolved from dinosaurs, and so many other things that Darwin could only dream of. So, while I'll still long to know the things I can't, I can at least be grateful for the things we know now, that were the longings of people in the past.

Posted by Jeff on Friday, Mar 9 | Permalink | Comments (0) | TrackBacks (0)

There is a follow-up to this review, written after I finished reading the book. However, both of thses entries have been supplanted by a newer post, which combines the two, with a little editing, and a paragraph's worth of new content.

Since today is Darwin Day, I figured I ought to post something. As it turns out, I'm currently reading The Origin of Species. I'm not quite done with it, yet - only about 2/3 of the way through - but I wasn't intending to write an in-depth review, anyway; I was only going to cover my general impressions of the book. So, with today being the day it is, I figured this would be a good time to do it, as I doubt my opinion will be changed much with the last third of the book.

Long before I picked up the book, I already had a pretty good understanding of evolution - better than most laymen, I'd wager. So I didn't start reading Origin of Species to try to learn anything about the theory. Rather, it was more to do with my interest in history, particularly for this case my interest in the history of science and technology, that was the reason I wanted to read this. And it doesn't disappoint.

Okay, let's get the background out of the way, first. Origin of Species was published in 1859, with the full title, On the Origin of Species By Means of Natural Selection, or, the Preservation of Favoured Races in the Struggle for Life. It's not that Darwin was the first to propose some type of evolution and common descent, but Origin of Species really was the book that presented the evidence in such a way, and proposed a plausible mechanism, that the theory really came to be accepted.

Part of what I find just so fascinating is how Darwin came up with all this without any knowledge of genetics. Even though Gregor Mendel was performing his pea plant experiments around the same time that Darwin wrote Origin of Species, it appears that Darwin wasn't really aware of Mendel's work. In fact, it wasn't until the early 1900's that the scientific community recognized the importance of Mendel's experiments. And it wasn't until the 1940's and 50's that people finally understood what DNA was and how it controlled heredity. Obviously, people in the 1800's knew that offspring bore some resemblance to their parents, but nobody knew how exactly this happened, or what it was that caused offspring to have variations. So Darwin was kind of left groping around in the dark, and all throughout the book, he's reduced to explaining concepts while admitting that he doesn't truly understand the mechanisms responible. From a modern viewpoint, understanding genetics, it almost makes you wish you could travel back and explain it to Darwin. It would have made things so much easier for him.

So knowing that Darwin was ignorant of genetics, and knowing that our knowledge of the geologic record was even less complete then than it is now, it's interesting to see the insights Darwin had that lead him to formulate the theory. For me, when I think of evolution, I think of fossils. Yeah, I know there are multiple other lines of evidence, but growing up, that was the main line of evidence that convinced me that evolution actually happened. But Darwin only briefly discusses fossils in two chapters of the book. The rest of Origin of Species is about what he observed in the world around him - how there seem to be clusters of similar species, the difficulties of distinguishing between true species and merely varieties of the same species, the geographical distribution of species, etc.

It's also interesting how Darwin determined that variation and natural selection were the mechanisms responsible for evolution. Consider one of Darwin's contemporaries, Jean-Baptiste Lamarck. Lamarck came up with the idea of "Use and Disuse," that animals could affect their own bodies through their actions, and that they could then pass on these acquired traits to their offspring. The classic example of this is a giraffe stretching its neck to reach higher leaves, and it's offspring thus having a longer neck because of it. Thanks to genetics, we now know this is a false view. To be fair, Darwin didn't rule this out entirely in Origin of Species, but he concluded that it must have been secondary to variation and natural selection. And one of the best examples he used to demonstrate this was ants - all the variation evident in workers, even though it's the queen that lays eggs.

I also find it fascinating to read Darwin comparing evolution to special creation, to think that creationism was the dominant scientific theory of the time. What I find especially fascinating, is to think how people integrated this into the knowledge of an ancient earth. Darwin fequently cited Charles Lyell in Orign of Species (Charles Lyell was one of the early popularisers of uniformitarianism, and helped promote the idea of the Earth being truly ancient), and in his chapters on the geological record, Darwin discussed some of the different geological periods. And concerning fossils appearing in the geological record, Darwin tells of how people proposed that those species were created during those periods. Just imagine that - seeing all the evidence for an ancient earth, and thinking that different species had been specially created throughout the history of the earth. I suppose without a better explanation, that's all the people could come up with then, but it certainly does seem an odd idea now.

I've read other places that evolution, through Origin of Species, was one of the last major scientific theories that was first presented to the world in a book intended for a lay audience. It wasn't presented in a peer reviewed journal; it wasn't full of technical jargon or equations; it was a book published by a regular publisher and sold through normal venues. It was easy to understand, and became a best seller. Now we need science writers to translate for us lay people, so we're always a few steps removed from the real science. It's hard to imagine any new major theories being presented the same way evolution was in Origin of Species.

I'd recommend this book to anyone with a good understanding of evolution who's interested in the history of the theory, but not necessarily to those people who don't undertand evolution, yet. For one thing, Darwin gets a few things wrong. For another, being written in a style 150 years old, it's not the easiest thing for a modern reader to understand. And finally, genetics is such a huge component of evolution, that a good introduction to evolution should include genetics in its explanation.

Anyway, despite any mistakes he may have made, Darwin certainly made a huge contribution to our understanding of the world. Happy Darwin Day, everybody.

Posted by Jeff on Monday, Feb 12 | Permalink | Comments (1) | TrackBacks (0)

While reading the latest entry on The Loom, I found out that there's actually a holiday called Darwin Day. Following the link that Zimmer provided, I found that there's even an event going on right here in my own hometown of Wichita Falls. Whoda thunk it? I doubt I'll go, but it's nice to see things like that here in this part of Texas.

(Yeah, I stole that picture from Zimmer, but I figured that a caricature from the 1800's was probably in the public domain by now.)

Posted by Jeff on Tuesday, Feb 6 | Permalink | Comments (3) | TrackBacks (0)

This is something I wrote the other day in the comments of a TerrapinTables thread. It's short, but I like it enough that I wanted to post it here on my own blog. It was in response to the following question posed in relation to studying dark matter (prompted by this article), "But tell me this: first, I mean, seriously, aside from knowledge for knowldege's sake, why do we need to know what comprises a galaxy cluster infinity-miles away?" Here is my reply:

First off - I think knowledge for knowledge's sake is a good enough reason to do research. In the same way that some people may find beauty in a painting, others can find beauty in a deeper understanding of the mysteries of our universe. If you're going to question why we need to know about a substance that composes 1/4 of the universe, I could just as easily ask why we have an entire profession dedicated to smearing paint on canvas, or another profession dedicated to plucking guitar strings and beating on drums. (Don't take me the wrong way - I'm not saying the arts aren't worthwhile; I'm saying that I think pure knowledge with no practical applications is just as important.)

But aside from that, who knows where knowledge will lead? Like in the 19th century, when physicists were trying to measure the ether that light travels in, could they have known that it would eventually lead to such practical applications as lasers, CDs and DVDs? Or the geologists of that era, did they really start off thinking that their theories would lead to the abandonment of a literal interpretation of the bible (at least in most of the developed world, not counting the U.S.)?

So there you go - one example of knowledge that led to practical technical applications, and another that had huge societal & cultural implications. I'm sure I could go on listing more, but you get the point.

Posted by Jeff on Thursday, Aug 24 | Permalink | Comments (0) | TrackBacks (0)

Not too long ago, I made a blog entry, Request for Information - Physical Comparison of Humans to Animals I actually did receive some feedback in the form of e-mail, which inspired me to do more research. In the course of which, I found the paper, Differential scaling of locomotor performance in small and large terrestrial mammals, written by Jose (Pepe) Iriarte-Diaz, which was published in the JOURNAL OF EXPERIMENTAL BIOLOGY, 205 (18): 2897-2908 SEP 2002. Anyway, as part of his research into animal locomotion, he had compiled a large set of data of mammal max running speeds along with their body mass and length. This was exactly the type of thing I was looking for in order to characterize how humans compare to other animals.

Continue reading "Physical Comparison of Humans to Other Animals" »

Posted by Jeff on Friday, Jul 14 | Permalink | Comments (0) | TrackBacks (0)

I'm throwing out a request for information for how humans fare physically in the animal kingdom. If anyone can supply me with links or recommend books on this topic, please do so in the comments. (I don't know how many people will even read this entry, but throwing it out there doesn't hurt.)

Here's where I'm coming from on this. I grew up as a kid who loved watching PBS, and then the Discovery Channel once we got cable. The types of animals that get all the attention are the fastest, the biggest, the strongest, etc.. And these animals are always compared to people, to try to put their skills into perspective. Growing up, I got the impression that humans were pathetic physically, and it was mainly our cleverness that allowed us to be so successful (along with our bipedalism and opposable thumbs). Now, my daughter watches The Most Extreme on Animal Planet, which seems to emphasize this even more.

Recently, there was an article in the 18 November 2004 issue of Nature, titled "Endurance running and the evolution of Homo." There is a very good summary and discussion of this article at the old Pharyngula site. Whether or not endurance running was a major driver of human evolution, I find it very interesting that humans are so good at long distance running, especially after all those years of documentaries telling me how pathetic of runners we are.

Hence, the request for information. Are there any places out there with comparisons similar to the above article, that show how humans fare in the animal kingdom, and not just compared to the biggest/fastest/strongest? If not, where would I go about finding this type of information, so that I could start making my own comparisons.

Posted by Jeff on Wednesday, May 31 | Permalink | Comments (0) | TrackBacks (0)