The Genetics of Convergent Evolution of Vocal Learning

Convergent evolution occurs when two unrelated species evolve similar results. The most famous example of convergent evolution is the eye of the octopus. The octopus, an invertebrate, has a “camera” eye, just like vertebrates do. A “camera eye” has a light-excluding orb like the box of a camera. It has, a lens to  focus light, like the lens of a camera. The iris  controls the amount of light entering like the iris of a camera controls the aperture. The retina on the far side of the orb from the lens and iris reacts to the light, like film or an image sensor. Shrimp, insects, and other creatures have different eyes that work in different ways. There are many ways to evolve an eye, but two widely separated groups reached similar results.

In “Convergent transcriptional specializations in the brains of humans and song learning birds1,” Pfenning et. al. took the full genetic sequences of several hominids, parrots, songbirds, hummingbirds and non-vocal learning birds and compared them using powerful and complex data analysis on computers. The researchers demonstrate that the area of the brain devoted to learning vocalizations evolved separately in primates and in birds. Among the birds (hummingbirds, songbirds, and parrots), the area for vocal learning evolved two or three separate times. That the same ability—the ability to learn and replicate vocalizations—evolved separately several times was to be expected. The ability to learn new patterns of vocalizations has many evolutionary advantages. But what the researchers found was the 50 or so genes used to control the development in this area were similar across the three groups of birds and primates. The last common ancestor of birds and humans was 310 million years ago. That’s a long time. Dinosaurs evolved about 230 million years ago, so the last common ancestor predates the dinosaurs by about 80 million years.

How did the different groups reach the same biochemical result?

Imagine you purchase a lot in a city. What you can build is determined by the size of the land, the geology, the surroundings, and any applicable zoning regulations. If the lot already has a foundation on it, your choices are more limited. You can destroy the foundation (expensive and time-consuming) or you can build based on the restrictions caused by the foundation. If the first floor has also been built, what you can build is much more limited unless you remove the additional work and start over.

In the same way, the structure of the brain of the last common ancestor of birds and primates imposed limits on how the brain could evolve.

Remember that evolution does not progress from simpler to more complicated or even from less fit to more fit. Evolution is random; it’s stupid, it doesn’t think and it doesn’t plan. The genes of the next generation are determined by chance: chance of mutations, chance in mating, and chance of survival. Even biologists have difficulty understanding this. We think of the first cells and then think of humans and mistakenly conclude evolution had a goal of creating intelligent creatures like us, but that isn’t a correct view of evolution. I find myself having to fight the incorrect urge to speak as if evolution had a goal. Anthropomorphizing evolution is an easy mistake to make, but very, very wrong.

If a bunch of organisms with a brain happen to evolve into creatures that can learn vocalizations, what’s the most likely way it can happen? Is it more probable that structures already in place will be used by chance, or is it more likely that those structures will be lost and then a new structure will happen to evolve? Now, actually calculating the odds on those possibilities is impossible, but you don’t have to run a Monte Carlo simulation to realize that more times than not, the existing brain structures will be used.

In the case of the vocal learning areas of the brains, apparently using certain genes is the most probable way to do it.

The finding that convergent neural circuits for vocal learning are accompanied by convergent molecular changes of multiple genes in species separated by millions of years from a common ancestor indicates that brain circuits for complex traits may have limited ways in which they could have evolved from that ancestor.2

Is it the only way to produce vocal learning? No one knows, but I doubt it. There could be some creature out there that evolved vocal learning a different way. If different gene patterns for vocal learning exist, one of the four groups examined (mammals, parrots, hummingbirds and songbirds) might have used it instead.  That the four groups all used a similar genes to perform the same function shows that alternate methods are likely rare.

Going back to the octopus, some species are capable of learning to mimic other creatures or their surroundings visually. Is this “display learning” a similar form of data analysis to vocal learning or is it hardwired mimicry? Do both systems use similar genes? The last common ancestor between vertebrates and invertebrates date back at least to the Cambrian. so that’s a very long time ago and in a totally different system in the brain. If the genes for display learning and vocal learning have similar properties (let alone similar genetic sequences), it would tell us there are severe restrictions on how brains learn.

  1. Pfenning, A. R. et al. “Convergent transcriptional specializations in the brains of humans and song learning birds.” Science 346 1256846 (2014) PDF downloaded 12 Dec. 2014. []
  2. Ibid []

What’s the Matter with an Aquarium

Note to the adult helper:

Please look over the following material. You might want to cut some things out. Remember, you want this to be a pleasant experience for the child. If the child asks questions, maybe you’ll think of some things to add on your own. In this series, I’m giving what I’m wishing I had been given when I was in grade school starting with aquariums, but 8 year old me is not the child you’re working with.

Major points:

  1. Matter has mass and, in a gravity field, weight.
  2. Mathematics has practical uses.
  3. The aquarium will be heavy. What are the consequences?
  4. Estimation allows us to think about and check the answer.

Lesson:

For this lesson, you will need your notebook and something with which to write.

If there’s a place on the cover, write “Aquarium Notebook #1.” Beneath it, write your proper name. This is your notebook. If there’s no place on the cover, there might be on the inside. If not, write it on the first page. On the next page, write the date.

There are many different types of aquariums. An aquarium can be a lush freshwater tank with plants and fish; it can be a crystal clear saltwater tank filled with animals. Some people keep aquariums with only plants. If a fish is ill, the “hospital tank” might only contain water, medicine, and the sick fish.

There are two things that all aquariums have: the tank and the water. You need both: without the water, it’s not an aquarium. Without the tank…it’s a mess!

Let’s look at the water first.

Write this question down in your notebook: “What is water?” What are the things you think of when you think of water? Write down as many as you can before you read my suggestions.

When I think of water, some of the things that I think of are that it’s wet, it’s heavy, it can be hot or cold, it’s transparent, and it’s necessary for life. You can freeze it into a solid, you can boil it into a gas, and when you have a leak in your house, it’s a mess to clean up. You can dissolve things in water—including air!

Many of those properties of water are what make an aquarium possible. Imagine water with no weight—the water would float away, which would make keeping an aquarium very difficult. Imagine water that you couldn’t see through. You might have fish in your aquarium, but it wouldn’t be any fun.

Water is a form of matter. In very advanced science, what matter “is” can get very strange, but for everyday use, you can think of matter as being something that has mass, volume and temperature.

What is mass?

Mass is how much an unattached object resists being moved. If something is just sitting there, you have to work to move it. Once something’s moving, you have to work to stop it from moving. How much you have to work is its mass.

On everyday Earth, we treat mass and weight as the same thing. Weight is the force of an object produced by gravity pulling on it. If you’re on Earth, you can get away with saying mass and weight are the same. But if you were on the International Space Station, where things are weightless, nothing has weight but it still has mass!

There have been aquariums on space stations, but I doubt you’re creating your aquarium on a space station or on the moon. So we’ll treat mass and weight as the same. But whenever someone treats mass and weight the same, I want you to think “Yeah, but they’re not the same!” Just don’t say it out loud, because people will look at you funny.

Water, being a form of matter, has mass—and on Earth, it has weight. Milk is mostly water, and if you pick up a gallon jug of milk, you’ll realize it’s pretty heavy. A gallon of milk weighs 8.6 lbs. Now, water, which doesn’t have all the extra things of milk dissolved in it, weights 8.3 lbs.

Estimation is when you want an answer that’s “good enough.” Everyone estimates, because it makes life easier. If you want to play catch with a friend, and you say “Go about 10 yards away,” your friend doesn’t take out a tape measure and measure 10 yards exactly. Your friend might go 9 yards away or 10.1 yards away or even 15 yards away. Your friend estimates the distance. The answer is “good enough.”

We said that water is 8.3 lbs. per gallon. If you have a 20 gallon aquarium, how much does the water weigh? Can you multiply 8.3 * 20 in your head? 20 is 10 * 2, so 8.3 * 20 is the same as 8.3 * 10 * 2, which is 83 *2. 2 *3 is 6, 80 * 2 is 160, so 8.3 * 20 is 166.

What if you’d estimated by saying water is 8 lbs. per gallon? 8 * 20 is 160 and you’re done. It’s not the correct answer, but it’s only wrong by 6 / 166 which is about .036. That’s pretty small. For what we’re doing, we can estimate by saying water is 8 lbs. per gallon.

When your teacher at school asks for an answer, assume she wants an exact answer. But when you’re trying to work things out for yourself to see about how much something is, you can estimate.

Here are some other estimating tricks. In English units, we use pounds (lbs.) for weight and gallons for volume. In the metric system, we use kilograms for mass (and we’re going to use mass as if it were weight, but we know that’s not quite right, right?). 1 liter is .264 gallons, which is a little bit more than 1/4th. There are .454 kilograms in a pound, which is almost ½.

So we can estimate the number of liters in a gallon by saying there are 4 liters in a gallon and ¼ a gallon is a liter. We can estimate number of kilograms by saying it’s a half a pound and half a pound is 2 kilograms.

So how many liters are in a 20 gallon aquarium? There’s about 80 liters. Now, the fun thing about the Metric system is, water weighs 1 kilogram per liter. So how much does an 80 liter aquarium weigh? It weighs 80 kilograms.

Your friend bought a 5 gallon aquarium. What does it weigh in lbs? How many liters is it? How much does it mass in kilograms? Write down in your notebook “A 5 gallon aquarium is approximately”. Below that, write down approximately how many pounds it is, how many liters and how many kilograms. Try to do the calculations in your head. Don’t move on until you do.

What did you get for the answers? Did you write “40 lbs, 20 liters and 20 kilograms”?

Now, write down A 5 gallon aquarium is exactly”. Below that, multiply 5 by 8.3 to get the exact number of pounds. Divide the number of gallons by .264 to get the exact number of liters. Once you have the number of liters, you’ll know how many kilograms it is. You can do these calculations with a calculator, or, if you’re feeling adventurous, do it using a pencil and paper. Write those answers down.

Again, what were your answers? Did you get 41.5 lbs? 18.9 liters and 18.9 kilograms?

Which way was easier to solve the problem?

Let’s say another friend bought a 55 gallon aquarium. Write down “A 55 gallon aquarium is approximately” and below it write down how many lbs., liters and kilograms. See if you can do the calculations in your head. Then write down “A 55 gallon aquarium is exactly” and below it write down how many lbs., liters and kilograms.

Did you get 440 lbs, 220 liters and 220 kilograms for the approximation? Did you get 456 lbs., 208 liters and 208 kilograms?

Now, let’s think about our results a little bit. Is 160 lbs and 80 kilograms—the weight of the water in a 20 gallon aquarium—a lot? Scientists estimate the mass of an adult man at 75 kilograms. 80 is a bit more than 75 kilograms. 80 kilograms not a tremendous amount, but it’s more than a gallon of milk. What do you think would happen if you put a 160 lb. aquarium on one end of a table? Have you ever seen someone sit on a table and the table move or even get tipped over? Would you put an 80 liter aquarium on top of a cardboard box? It might be possible to make a stand out of cardboard that would safely hold 80 kilograms. But what happens to cardboard when it gets wet? Do you think working on an aquarium might get the cardboard wet? Even if you were careful, the aquarium could leak. A leak would be a problem by itself, but imagine what would happen if the cardboard stand got soggy!

You have to put your aquarium on a piece of furniture so you can see it easily. What do you think that piece of furniture should be like?

With permission of an adult, jump up and down in the middle of a room. Does it make a lot of noise and do things vibrate a bit? Now, go jump near a wall. What kind of noise does it make and how do things vibrate? Finally, go jump up and down in a corner. What happens? Write down in your notebook what you did and what you observed.

Next, stand in the middle of the room on one foot. How easy is it to stand on one foot? Go over to the wall, lean slightly on it, and see if you can stand longer on one foot than you could in the middle of a room. Finally, lean in the corner and stand on one foot. Where is it easiest to stand? Write down in your notebook what you did and what you observed.

You want the aquarium to be stable. You don’t want it to vibrate, you don’t want it to fall over, and you don’t want it to fall through the floor. There’s not much danger of a 20 gallon aquarium falling through the floor, but what if you had a 100 gallon aquarium? About how much would that weigh? Could it cause problems in the middle of a room?

Where do you think the best place to put an aquarium is based on your jumping up and down and trying to stand on one leg? Write down in your notebook how you would rank places to put your aquarium.

Next, what if you had to put the aquarium in the worst place in the room? What can you think of doing to give your aquarium the best chance to survive if you put it there. Write that down in the notebook. Drawing pictures will help explain what you’re saying. You can also talk to the person helping you. Can they think of other things that could be done to make the aquarium safe? If you don’t have to, would you want to do these things? Do you think they would be more or less expensive?
By estimating, you were able to figure out how much different size aquariums would weigh (or mass). Estimation lets you think about things without investing effort you don’t need to make. If you had done the exact calculations, would it have made any difference in the answer as to where you’d put an aquarium? If you had a 5 gallon aquarium, do you think you could get away with putting the aquarium in the worst possible place? What if it were a 55 gallon aquarium? Would you be worried if you had to put it in the worst possible place?

Estimation lets you know if it’s worth doing the full calculations!

When I was writing this, I did the multiplication in my head and got an answer for the weight of a 20 gallon aquarium of 8.3 * 20 as “246 lbs.” I multiplied the 8 by 30, not 20. Because I estimated the weight at 160 lbs., I knew something was wrong. Now, I didn’t know whether my estimation was wrong or my full calculation was wrong, so I pulled out a piece of paper and did the calculation carefully. I got the correct answer of 166. Because I had estimated, I avoided a significant mistake.

When you’re done with a test, go back through and look to see if your answers are reasonable. Where appropriate, estimate the answer—does the estimate match the answer you put? Estimating is a way to check your work!

Finally, draw a line under the last thing you wrote in your notebook. That’s all for today, and the line lets you know where that day’s data ends!

Before You Start (2)

How big will your aquarium be?

You will have your child work out how big an aquarium to get, but you will want to direct the conversation. There are several considerations.

  1. The larger the aquarium, the easier it is to care for—up to a point. The smaller the tank, the easier it is for something to go wrong. Things can go wrong quickly with a 5 gallon tank that will take longer to develop for a 55 gallon tank. But there are maintenance issues. A 20% water change on a 20 gallon tank is 4 gallons. A 20% water change on a 150 gallon tank is 30 gallons.
  2. Where the aquarium will go will be an issue. Aquariums are heavy. A liter of water is a kilogram. A liter is about a quart, so a gallon is about 4 kilograms, or about 8 lbs. A 20 gallon aquarium is 80 kg. Or 160 lbs., and that’s not including the weight of the aquarium itself. Generally, aquariums go away from direct light to control temperature and algae, away from drafts to control temperature, and along a wall (to prevent problems with the floor). You want the aquarium away from fumes that be absorbed into the water and kill the fish, so the kitchen is probably out.The result is usually either the child’s room or the family room, which may limit the size.
  3. Finally, there’s the cost of the aquarium. I put together a spreadsheet and listed everything I purchased for my 20 gallon aquarium. I’m up to $525 dollars as I write this. Please realize that I went with the best available equipment and supplies, and I probably won’t need to buy anything for a year.There are ways to cut the costs. I purchased from a local store that charges more but can give me advice when I need it. The costs in the graph below are from online, and are cheaper than what I paid. I’ve seen aquariums for sale at estate sales, Craigslist, and at aquarium club meetings. Making friends with someone who has aquariums may be a way to get a deal on someone’s spare tank! There are a number of ways to get less expensive aquariums, but you must also ask what happens if the tank leaks. Stores have sales. If you wait a couple months, you may find a deal on an aquarium kit.Aquarium Kit Cost

I hope this post helps you think about the important points before you begin this project.

I named this series “Science in 80 Liters” because an 80 liter (20 gallon) aquarium is a nice compromise between size, ease of maintenance and cost.

You may wish to go smaller or larger, depending upon your situation. You may guide your child or children through the decision, or you may simply choose a size and go on from there.

Before You Start (1)

Some advances in science happen accidentally. We all know the stories of radioactive samples left on top of photographic plates, mold getting into your bacterial colonies, etc. It’s great when it happens. And you should take advantage of random opportunities to present science, technology, engineering and/or mathematics (STEM) to your child.

But that’s not how most science happens, and that’s not how an aquarium should happen.

Most science happens while going through a set of steps. Now, most people don’t think of these steps as steps, and they may rearrange the steps, combine them, or just do it subconsciously. But the steps look approximately like this:

  1. Thinking
  2. Planning
  3. Calculating costs
  4. Purchasing
  5. Assembling
  6. Performing experiments & taking data

At this point, I’m supposed to put “Evaluating “ as #7. In real life, evaluating happens all the time. During the “thinking” phase, evaluation happens naturally. That’s part of thinking. The same goes for planning. Unlike comic books where Reed Richards (Mr. Fantastic) and Tony Stark (Iron Man) have unlimited funds, a lot of evaluating can happen during the “Calculating costs” and “Purchasing” parts of the experiment. A researcher might ask herself questions like these:

  • Can we afford this?
  • Is there a cheaper way to do this?
  • Does someone else have this piece of equipment that I can borrow?
  • Do I want to look for another topic to research?

Evaluation can occur during “Assembling,” especially when the researcher finds out things don’t go together like the instructions say. Think “Ikea furniture.” I know of one case where it really was Ikea furniture that didn’t go together like the drawings showed and changed the experiment.

Some of the most important evaluation occurs during the first couple runs of the experiment. Even when doing a double blind study, a researcher will check to make sure things are running smoothly. Most of the time, they don’t. The researcher may not have ever done this particular experiment before. Perhaps no one has done it. The first couple times, researchers check to make sure everything works as planned. Often it doesn’t, and the researcher goes back to the beginning and work through the steps again with the new knowledge.

Sometimes things don’t work as planned. And, if you look at all those serendipitous discoveries, you’ll find that those wonderful accidents were found during the evaluation phase of going through these steps.

What’s the one thing common to all of these steps?

Taking notes.

Seriously. Everyone knows that scientists record data. there are even cute aphorisms about data collection like “Document or it didn’t happen” and “Collect data; it makes it look like you’ve been doing something.”

But think about it even in your own life. Ever come up with a great idea and forget it during lunch? If you’d kept notes, that wouldn’t have happened. Think of something when planning a party but forget about it until the first guest knocks at the door?

So your first homework assignment is to go out and buy lab notebooks: one for you and one for each child with whom you’re working.1

You don’t need to get the big expensive professional lab books. Composition notebooks are wonderful, especially if they happen to have the numbered pages. Everyone keeps their own data. The adult will keep the adult version, but each child should keep his or her own. Yes, there should be words and numbers in the book, but there should also be drawings of things observed. If you take a picture of the aquarium or the supplies, printing out the picture and taping or gluing it in the book is wonderful. Scientists use drawings, photographs and more to record things–as well as words and numbers.

By keeping a notebook yourself, you’re modelling the behavior for your child or children. The children are practicing important skills like writing and drawing.

Also, when something goes wrong, that notebook might help you figure out what it was or keep you from making that mistake again!

  1. I’m keeping my notebook on a computer. The first time the data files get corrupted, you can laugh at me. Lab notebooks are things the child can touch and hold and look back on years from now. It’s a simple thing, but your child will benefit. []

Science in 80 Liters (20 Gallons)

In 1967, I was in third grade and got a book by Beverly Cleary titled “Henry Huggins.” In the book, Henry goes to a pet store and buys a pair of guppies. The two guppies had babies. Soon Henry’s room and life are over-run with jars of fish. This story disaster inspired me to ask my parents to let me have an aquarium. My parents agreed, and soon there were three aquariums in our new house.
Recently, I looked back on those experiences with tropical fish and realized just how much science I learned from them. Making the water safe for the fish taught me a lot of chemistry. Learning about the fish, keeping a balanced tank the fish could live in, and breeding them introduced me to topics in biology long before I had them in my classes. Even mathematics, physics and a touch of engineering came into play.

Today, scientists and educators are making a deliberate attempt to interest children in science, technology, engineering and mathematics—it’s abreviated STEM. In the past, such activities tended to be aimed mostly at boys. Now, the goal is to interest everyone, no matter their gender.

I learned through books. My first book on aquariums taught me how to set up a small 5 gallon tank. As I got bigger books, I got bigger tanks. My Dad was an engineer, but for the most part, he stuck to lifting heavy objects, curbing some of my excesses, and suggesting how to look up an answer. It worked for me.

Part of me would love to write a book for third through fifth graders explaining the science as they set up a modern aquarium. Unfortunately, my wife and I weren’t blessed with children. I’m not sure if I’d know how to write for third to fifth graders.

As I thought about it, I realized I don’t want to write for those third to fifth graders. I want to write for their parents. The parents can guide their children, pick and choose the topics that are appropriate, and interpret the lessons for their children’s level of understanding. With any luck, the parents and children have fun together with the tank.

And who knows? Maybe the parents will gain a little more understanding and appreciation for science.

As I see it now, I’ll write a lesson about once a week, focusing on the particular topic involved with that stage of the aquarium setup. That might seem slow, and, as I get a feel for it, perhaps the frequency of the posts will increase. But one of the tricks to setting up an aquarium is to take it slowly. If, in a single day, you purchase an aquarium, set it up, and put the fish in, there’s a high probability that you’ll waste a lot of money and kill the fish.

If anyone is going to follow along, I would appreciate getting feedback. What was clear? What wasn’t clear? What was too difficult for your child to understand? What was too simple? What was too expensive? What better ways are there to do this? A comment section is available at the end of each article. I’ll make every effort to answer questions and learn from any suggestions.

Pittsburgh Podcamp 8

Right now, I’m at Pittsburgh Podcamp 8. This is a social media get-together where we can learn about various aspects of online interactions. I wasn’t going to mention this day. UnSpace is about science.

What was I thinking? As a child, computers were huge machines that took up rooms and required several technicians to keep running. The average person didn’t have access to these computers. None of the science fiction stories envisioned something like Twitter and Facebook.
Continue Reading…

Science Links from Around the Web

I stalled yesterday trying to write another article on geoengineering to reduce global warming. There were two problems:

  • I wanted to mention that the Martians attempted to “martiform” the Earth in H. G. Wells’ “War of the Worlds.”
  • The origin of the word “terraform” is to give something the “likeness” (form) of Earth (Latin “terra”). “Geoengineering” is “Earth (Greek “ge”) engineering.” Terraforming and geoengineering refer to concepts so similar (changing the surface of a planet using technology) that they tend to be used interchangeably, which is technically wrong from a grammatical standpoint.

I got stuck on the grammar technicalities and editing. One of the reasons I created the UnSpace blog was to recover my writing skills that I lost when my focus was on editing. I’m still learning.

In the meantime, here are a bunch of fascinating links from around the web.

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2nd Law of Thermodynamics Permits Evolution

2nd Law of Thermodynamics Permits Evolution

Creationists repeatedly claim that the Second Law of Thermodynamics prohibits evolution. Buzz. Wrong. False. Incorrect. This claim has been around at least back to when I was in college, back when disco was popular. It was wrong then and it’s still wrong.

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Pittsburgh’s Day of Giving

Pittsburgh’s Day of Giving

Tomorrow, October 3, 2013 is Pittsburgh’s Day of Giving. This is the 5th year for the Day of Giving. As the PittsburghGives.Org website says,

PittsburghGives is an initiative of The Pittsburgh Foundation.  The aim of this initiative is to:

  • Increase the level of knowledge about nonprofits in our region
  • Leverage or increase individual funding or organizations or an issue in our community
  • Spotlight the charitable trends in our region.  Where are people giving?  What are your community’s nonprofits saying is vital and needed right now?

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Weather Wars

Weather Wars

There’s an interesting exchange beginning at 41:08 on the YouTube video of the recording of the NASA Hangout: Ask A Climate Scientist on 30 September 2013. The video starts a few seconds before the 41:08 mark:

NASA Hangout: Ask a Climate Scientist

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