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Indian Style Beef Curry

November 23, 2011 No comments

This is a very common recipe in northern India. This is basic meat “curry” – the way meat is most commonly cooked in homes every day, with no frills or fancies. I’ve described the procedure in some detail for people (like myself) who don’t know much about the kitchen and prefer to have everything spelled out. If that seems like excess detail to you, please be patient.

Meat

The choice of meat is really important to having it turn out well. I’m only going to talk about beef, though you could easily replace it with lamb or chicken.

Think of this as Indian style stew. So the best cuts of meat for this curry are the same as you would use in a stew. This mean cuts with some fat in them – the more the marbling, the tastier will be, and the less the meat will dry out during the cooking process.

I think that chuck (meat from the shoulder) is best for stew. In many supermarkets, pre-cubed beef for stew is unlabeled as regards its origin, so you have no idea what part of the animal it’s from. Often, it’s actually round (round is meat from the hindquarters). The top part of the round is relatively tender, but the bottom round or the eye of round can also be sold as stewing meat. This is really the worst cut for making stew, in my opinion, since it’s low in fat and also pretty tough. It tends to require long cooking times, and can become even tougher and drier after cooking. Avoid round if you can help it.

That said, this is stew, which is prepared through moist cooking. So it can be pretty tolerant of even the tougher and leaner cuts, if you take the time and trouble.

There are a few methods for tenderizing lean and tough cuts of meat. You could use a tenderizer, or you could marinate it for 24 hours. Brining also works, as does braising over very low heat (in a crockpot) for several hours. If you are familiar with these methods, by all means try them. My personal favorite is to use a pressure cooker, which is pretty darn amazing at tenderizing tough cuts of meat, not to mention saving a lot of time.

However, these methods are outside the scope of this recipe, so for the best results, please stick to well-marbled chuck for this recipe, unless you are familiar and comfortable with cooking tougher cuts of meat.

Ingredients

  • 2 pounds of beef for stew, as 1″ cubes
  • 2-3 medium onions, chopped finely
  • 1 ripe tomato, chopped
  • 0.5 cup of plain whole milk yogurt
  • 1.5 teaspoons ground cumin
  • 1.5 teaspoons ground coriander
  • 1 teaspoon ground turmeric
  • 1 teaspoon whole cumin seeds
  • 1 teaspoon ground red pepper
  • 1 bay leaf
  • 5-6 cloves garlic, crushed
  • Vegetable oil
  • salt to taste

Directions

Pick a large, heavy pot with a well-fitting lid to cook this. We’ll be adding a lot of water later, so make sure the pot is big enough. You don’t want to overfill it. Heavier pots hold heat better and more evenly.

Start by heating the pot over medium heat. When it’s nice and hot (but not smoking), add a few tablespoons of vegetable oil. Wait a minute for the oil to heat; then drop in the whole cumin seeds. If your stove is on medium, the seeds will start to brown and crackle and pop in about 20 seconds. Add the chopped onions and fry them to a golden brown, stirring frequently. Don’t let them burn!

After they are browned, add the crushed garlic and the chopped tomato. Continue stirring until most of the water is gone from the tomatoes, and the oil separates, about 2-5 minutes on medium heat.

Turn the heat down to medium-low. Now add all the powdered spices plus the bay leaf. Fry the spices for about 1-2 minutes, stirring constantly so that the spices don’t stick to the bottom of the pan and burn. Don’t let anything turn very dark brown or black; or it will taste horrible.

Now add the yogurt, and raise the heat back up to medium. Continue to fry while stirring constantly until the yogurt blends in with the rest of the ingredients, loses its water, and the oil starts to separate.

Finally, we are ready to add the meat. Don’t drop it all in at once. Start with 4-5 cubes, stir constantly to coat the meat on all sides with the spice/onion mixture. The goal now is to fry the meat in this spice mixture, until it’s lightly browned.

You can turn up the heat a bit at this point to speed up the process, provided you stay at the stove and continue stirring. It’s very easy to burn the spice mix if you aren’t careful. Don’t bother so much about turning the meat over so it browns on all sides – this will happen automatically if you concentrate on the real purpose of stirring. The real purpose is to not let food stay/stick to the bottom of the pan. The stirring actually consists of scraping the bottom of the pan with the plastic or wood spatula, to make sure nothing sticks there. Keep adding the rest of the meat, 5-6 cubes at time, waiting 30 seconds or so between each addition to make sure the previously added meat has warmed up and is coated evenly.

After all the meat has been added, continue frying for another 5 minutes or so, stirring constantly. You may have to fry a bit longer if your stove isn’t set to high enough heat. The idea is to first reach the point where not much bubbling is going on if you observe a piece of meat at the bottom of the pan (bubbling means there’s significant water present, which means the meat isn’t actually frying yet) and the oil separates, and then to fry for another 3-5 minutes after that.

Now add the water. The amount of water is variable, and depends upon the cut of meat, the type of pot, and the cooking time:

  • If you use well-marbled chuck, the cooking time can be as short as 60 to 90 minutes. With a good, heavy pot with a well-fitting lid, you shouldn’t lose a lot of water in that short time. So 3 cups of water might be fine. Just bring the water to a boil, lower the heat to simmer, cover the pot with the lid and let it cook. Check after 60-70 minutes; and then again at 90 minutes if it isn’t done the first time.
  • If you use leaner or tougher cuts, which are really not recommended, you will need a lot more water and lot more time. Bottom round or eye of round will be very tough and dry after an hour, pretty much inedible. All meats can be tenderized if cooked long enough. For some cuts you may need 4 hours of cooking, with copious amounts of water. When cooking such cuts, there is no recommended amount of water, it purely depends on how fast the water evaporates, given your stove, your exact heat setting, your pot. The general rule is to have enough water to keep the top of the meat covered at all times. Check every 30-45 minutes, add more water if too much has evaporated away.

As mentioned earlier, if you are cooking tough cuts of meat you should really use a crockpot or a pressure cooker. Crockpots take all day to cook (8-12 hours or even longer), so if that’s okay with you, go for it. Pressure cookers are the opposite; they cook the food in a very short time. Both can turn out incredibly tender meat from even the toughest cuts.

From my own experience, cooking stew made from eye of round using a regular pot took about 3.5 hours. The stew was tasty enough, but I wouldn’t do it again. The problem was that at 3.5 hours, the meat starts to shred, with fibers flaking off. Unless you are purposely making shredded beef, this is a bad idea. However, if you cook for a shorter period to avoid shredding, then the meat is too tough and somewhat dry.

Compare that to a pressure cooker. It takes about 15 minutes per pound to cook the same cut. For 2 pounds of eye of round stew, I’d cook it for 15 x 2 = 30 minutes at 15 psi (pounds per square inch pressure), plus 5-10 minutes extra to make it even more tender. Not only does the pressure cooker speed things up considerably, all that pressure inside the cooker tends to keep the moisture inside the meat, so it doesn’t dry out. The result is extremely tender and flavorful. If you are trying to cut down on fat and prefer leaner cuts of meat, this can be a great way to go.

Some tips and final thoughts:

  1. Always keep half a cup of fresh water next to the stove when you’re frying the spices. Small mistakes at this stage can ruin the food. You absolutely do not want the spices to burn. If they look like they’re about to burn, simply turning down the heat will probably not be enough. The pot (and the heating elements on electric ranges) retain a lot of heat, and that carryover heat is enough to burn the spices even if you turn it down or off. In such emergencies, just add a tablespoon of water. It will cool down the spices enough to prevent burning/sticking. It only takes a few seconds for that water to evaporate, so you can resume frying as soon as you have the heat under control.
  2. This recipe is for basic meat stew. You can add vegetables for variety if you like. In my opinion, traditional stew vegetables like carrots don’t go well with Indian spices. Anything with even a hint of sweetness is not good. I get the best results with adding potatoes (chopped into 1” cubes), or chopped spinach. You can also add zucchini, or any non-sweet squash. Just add them to the stew at the appropriate time before it finishes cooking. For example, if potatoes take 30 minutes to cook, add them to the stew 30 minutes before it finishes cooking. Remember to raise the heat to high after you add the potatoes to quickly bring it back to a boil, then reduce heat and simmer.
  3. You can add more elaborate spices if you like. This recipe consists of the 4 basic spices – cumin, coriander, turmeric and red pepper. Some other spices that provide variation include cloves (add 3-4 cloves along with the water), ginger (slice 1” cube of peeled fresh ginger into thin strips, add along with garlic and tomato), cardamom (add 5-6 green cardamom seeds along with the water). Other things to add: chopped fresh cilantro (sprinkle a handful on top after the stew has cooked, let sit 10 minutes), chopped nuts (either roast cashews or slivered almonds) that can be added along with the water.

That’s it! Always let the meat rest for about 15 minutes after cooking before you serve it. This allows liquids that have been forced out of the meat during the cooking process to seep back in, making the meat more tender. Serve with some Indian Basmati rice, or with Indian style bread (in a pinch, you can use warmed up tortilla shells in place of Indian bread – just make sure they are flour tortillas, not corn).

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The Math of Cooking Perfect Rice

July 31, 2011 No comments

Rice is one of the easiest things to cook, but many people are afraid of it because they’re turned out overcooked soggy mushy rice in the past, and don’t know how to fix that. The problem is that there are so many recipes available for such a simple thing, and all of them are different. One recipe printed right on the plastic bag of rice I bought calls for 2 cups of water per cup of rice, another says only 1 cup of water is needed. Others say you should use 1.5 cups of water per cup of rice.

Some recipes don’t even measure water in cups, they just say “add water until the level is about 1/2″ above the level of the rice in the pot”. Some call for pre-soaking rice, others say you should never pre-soak.

So who is right? Why so much variation? You could follow two recipes on the web, and produce perfect rice with one and mushy crap with the other. Does that mean one was good and the other was bad? Maybe for you, but it’s possible that for someone else, the results are reversed, and the crappy recipe produces perfect rice, while your perfect recipe doesn’t.

The reason is because even if both of you follow the recipes exactly, there are still differences in the cooking range/stove you used, the pot you used to boil the rice, the exact amount of heat, etc. No cookbook or recipe can account for all these differences. This is why people’s results can vary so much.

I like a bit of math and science in my cooking, so I decided to put together this post. At the very least, it’ll explain why people’s results vary so much and why recipes are so different. Hopefully, it’ll help you produce perfectly cooked rice every time, without any guesswork.

What happens when rice cooks?

Uncooked dry rice grains have some moisture, but not a lot. The usual rice you buy in stores, both long grain and short grain, has about 12% moisture content, meaning each grain is 12% water by weight. Aged rice has a lower moisture content. If you buy aged basmati rice, for example, the moisture may be as low as 7-9%, depending on how long it was aged.

Cooking does two things to the rice. First, it hydrates the rice grain (adds moisture to it), making it swell and increase in size. Second, the heat cooks the rice grains, making them soft and slightly gelatinous.

Properly cooked rice has a moisture level between 58% and 64%. Anything below that range will feel hard and uncooked, and anything over that range will be mushy. You may prefer one end of the range rather than the other, depending upon the type of rice and your personal tastes.

So the goal of cooking is to increase the water content of the rice from 12% to about 60%, and also heat the interior of each grain for a sufficiently long period that it is cooked.

How much water should you add?

Water is used for two things – to hydrate and cook the rice, and to make up for water losses during cooking. The amount of water needed to hydrate the rice is fixed and based solely on the amount of rice, and can be calculated based on desired hydration levels. But the water lost during cooking is very variable, and depends on things such as:

  • length of cooking time
  • temperature of rice during cooking
  • shape and size of the pot in which the rice is cooked
  • how tightly the lid fits on the pot

Water for hydration

Let’s start with the easy part first, which is water needed for hydration.

Normally, we measure rice and water in cups. One cup of water is 240 ml, or 240 grams. One cup of rice varies, depending on the type of rice:

1 cup long grain rice = 185 – 190 grams

1 cup short grain rice = 195 -210 grams

Short grain rice can be packed tighter in the cup, so 1 cup of it weighs more than the same volume of long grain rice.

In order to hydrate this, we need:

1 cup short grain rice = 0.94 to 1.24 cups of water (for 58% – 64% hydration)

1 cup long grain rice = 0.85 to 1.12 cups of water (for 58% – 64% hydration)

You can pick the middle of the range and say that 1 cup of long range rice needs 1 cup of water for hydration, while 1 cup of short range rice requires a bit under 1.1 cups of water for hydration.

 Water losses during cooking

Next we need to figure out how much water will be lost during cooking, and make up for that. Water is lost during cooking due to evaporation. Ideally, we want to lose as little water as possible to evaporation. We can do this by:

  • use pots which have tight fitting lids
  • choose pots which are narrow and tall, rather than short and wide
  • use high heat to bring water to a boil quickly, then immediately lower heat to simmer
  • try to minimize cooking time

Consistency is the key to cooking rice, so don’t use a different pot each time you cook rice. Pick one pot and stick to it, so you can learn its quirks and adjust accordingly for them. The most important feature is should be the lid – pick one that has a tight fitting lid that doesn’t allow much steam to escape. The heavier the lid, the better. A tall and narrow pot will lose less steam than a wide and shallow pot.

Rice needs to cook at a simmer, which is a point just short of a boil. The temperature of a “simmer” is not that much lower than a boil, it’s just that the rate of heat delivery is such that the temperature is barely maintained, rather than having to keep losing excess heat through big clouds of steam. A “simmer” would be about 94-98 °C, as opposed to a boil which is 100 °C.

The easy way to do this is to bring the rice and water to boil, then reduce the heat drastically until it’s just enough to make bubbles slowly pop at the surface, and to produce a thin cloud of steam on the surface. Cooktops vary, so you will need to find the simmer setting on yours. On a typical cooktop that goes from 1 to 10, simmer might be somewhere between 1 – 3. You have to experiment and find out.

To reduce total cooking time, it’s important to bring the rice to a boil quickly. So use the high heat setting on your stove (and stand there and watch, or at least, don’t leave the stove for prolonged periods). As soon as it comes to a boil, reduce heat to simmer, and let it cook covered for the recommended amount of time.

To pre-soak or not?

This factors directly into cooking time, so I’m going to mention it here. In fact, we can also ask “should we wash the rice or not” while we’re at it.

What’s the difference between washing and pre-soaking? In washing, you add water to rice, swirl it around with your fingers, then drain the water out. Washing removes any loose starch grains adhering to the rice, and also removes any vitamins that the rice has been fortified with.

In the US, by law, all rice is sold fortified with certain B vitamins. This may or may not be useful to you. If you have a varied diet, if you occasionally take vitamin/mineral supplements, or if you already eat other foodstuffs supplemented with vitamins (anything made from flour, cereals, etc. will have added B vitamins), then you don’t really need the little bit of vitamins that were artificially added to the rice.

I always wash rice for 2 reasons:

  • washing gets rid of loose starch granules, which make rice sticky after cooking
  • washing can get rid of dirt and dust, after all, rice is a raw agricultural product

As I said, the downside is that you also lose those added vitamins. I don’t care about them because they are very minor, and I get enough vitamins from other foods anyway.

Now, what about pre-soaking? Yes, rice can be pre-soaked without washing. All you have to do is to not add an excess of water during the pre-soaking, so you don’t have to throw any water away. This way you can pre-soak, and then use the same water for cooking. Any vitamins that leach out remain with the water, and so are absorbed back into the rice when it cooks.

I think pre-soaking is a must, if you have the time. For any kind of rice, pre-soaking will always reduce the cooking time. Why? Because pre-soaking “wets” the interior of the rice grains, which allows them to cook much faster and more evenly.

When you cook rice, the heat has to get from the outside of the grain to the interior. This can take time. Let’s say you cook the rice for 15 minutes. While the outside of each grain reached cooking temperature right when you brought the heat down to a simmer, the inside doesn’t reach full cooking temperature until much later. So you can have the outside cooking for 15 minutes while the inside only cooks for 5 minutes. This means that either the inside is not fully cooked, or else the outside is overcooked and mushy.

Soaking allows water to reach the inside of the grains, which greatly improves heat transfer into the grain. So the inside starts cooking much sooner, compared to rice that wasn’t pre-soaked. This allows the total cooking time to be reduced, and for each grain to be cooked as evenly as possible.

Remember, the shorter the total cooking time, the less water you will lose during cooking, and the better the rice will taste, all else being equal.

So in summary, my recommendation is:

  1. Always wash the rice first in a couple changes of cold water, specially if you are cooking long grain rice. Long grain rice should not be sticky, and washing makes it less sticky at the end.
  2. Always pre-soak rice in cold water for about an hour, if you have the time. It will make the rice cook much more evenly, and can reduce cooking time in half.

You may choose not to wash or pre-soak the rice, but in that case, keep in mind the caveats mentioned above.

So, how much water do you need?

To figure the total amount of water needed, you should add the water required for hydration and the water losses during cooking. For long grain rice, you need 1 cup of water for 1 cup of rice, and for short grain rice you need 1.1 cups of water per cup of rice. This is hydration water only.

Next, you need to add water for cooking losses. This will vary greatly with your setup, the size and width of the pot, the lid, the temperature, etc. All those things mentioned above. If you wanted to be very exact, you could even perform an experiment:

  1. Fill the pot with a measured amount (say 3 cups) of water – water  only, no rice. Close the lid, put it on the stove, bring to a rolling boil.
  2. Immediately lower the heat to simmer, and note the time.
  3. Wait for 30 minutes, then turn the heat off, and remove the pot from the stove. Let it sit on a counter top while it cools to room temperature.
  4. Measure the amount of water left in the pot.

Let’s say you started with 3 cups and you end up with 2 cups after 30 minutes of simmer. So your rate of water loss  due to evaporation was 1 cup per 30 minutes. So if you expect to cook your rice in 15 minutes, you should plan for 1/2 a cup of lost water during cooking. For cooking 1 cup of long grain rice, you would add 1 cup of water for hydration plus 1/2 a cup for water loss, making 1.5 cups of water per cup of rice, for example.

If you don’t want to measure the rate of water loss, you will have to discover the right amount of water through trial and error. Here’s some brief pointers on how to begin:

All cooking times are measured from the point when you turn the heat down to simmer.

Rice that has not been pre-soaked typically cooks in 15 – 20 minutes, while rice that has been pre-soaked cooks in about 8-10 minutes.

If your pot is really bad in terms of retaining heat (loose fitting lid, too wide and shallow), it will probably lose about a cup of water to evaporation over the 15-20 cooking time of non-pre-soaked rice. This is the maximum amount of water you should start with (for example, cooking 1 cup of long grain rice = 1 cup water for hydration + 1 cup water losses = 2 cups water total). Chances are, your pot isn’t that bad, so you need to adjust down from 1 cup.

Typically, the range is:

  • the best professional dedicated  rice cookers – very tight lids, zero water loss
  • the worst random lidded pot found in the average kitchen – about 1 cup water loss per 20-30 minutes
  • pot without a lid – all bets are off, your mileage will vary. Not recommended at all.

Depending on the pot you use, you’ll be somewhere in that zero to one cup range for water loss. I’d split the difference and figure on half a cup of water loss and adjust up or down from there through trial and error.

A note on proportions

Unless you cook exactly 1 cup of rice at a time, you will need to scale these amounts up or down. Let’s say you figure out through trial and error (or through the procedure described above) that you need exactly 1.5 cups of water per cup of long grain rice to make the perfect rice. Now let’s say you decide to cook for friends, so you end up cooking 3 cups of rice instead of 1. Can you scale up the water from 1.5 cups to 4.5 cups (3 x 1.5)?

If you’ve read this far, you know the answer is NO.

Remember, only the water needed for hydration scales with the amount of rice. The water needed to cover water  losses only scales with the cooking time, not with the amount of rice.

When you arrived at that 1.5 cups water per 1 cup rice number, what you were really doing was using 1 cup of water for hydration, and 1/2 a cup of water to cover water losses during cooking. So when you scale this up to 3 cups of rice, you will need 3 x 1 = 3 cups of water for hydration, but still only 1/2 a cup of water to cover water losses during cooking. Water losses during cooking only depend on the length of cooking time, and that hasn’t changed. Yes, it will take longer for 3 cups of rice plus water to come to a boil than it took for 1 cup of rice plus water to come to a boil, but we don’t measure that time anyway, we measure cooking time from after it’s come to a boil and the heat is reduced to simmer. This time doesn’t change whether you’re cooking 1 cup of rice or 3.

So in this case the correct amount of water needed for 3 cups of rice was 3.5 cups, and if you used 4.5 cups based on the simple calculation of multiplying everything by 3, then you used too much water and your rice will be soggy and mushy. This is one of the commonest mistakes that people make and why rice so often turns out bad.

In this respect, the older method of describing water quantity by “inches of water covering the rice was better. The idea there is that water mixes  with rice in a roughly 1:1 proportion, and the water level above the level of the rice represents water that will be lost during cooking. So if you know half and inch of water is lost during cooking, then no matter how much rice you have in the pot, half an inch of water on top of that will still be the cooking losses.

This method is also very hit and miss when it comes to sharing recipes, because nobody can say “half an inch on top of the rice works well” without seeing the pot you’re cooking with. This is because half an inch of a wider pot is a lot more water than half an inch of a narrow pot. If you use the same pot regularly, then you may make an observation that half an inch works well for that pot, or maybe 1/3 of an inch, or 2/3rd. This can serve you well for as long as you use the same pot, you’ll never have to measure water anymore. Just drop in the rice, add enough water to cover the rice plus 1/2 an inch over, and you’re all set. But if you change pots, you’ll need new numbers for the new pots. I don’t like this method much because eyeballing half an inch isn’t very accurate, I get much better results with measuring volumes in a measuring cup. But it still beats scaling up single  cup recipes naively, without separating out water of hydration and water losses of cooking.

What’s a good cooking time to aim for?

Rice tastes best when it’s cooked in the shortest time possible, but evenly (inside/outside of each grain cooked to the same degree).

Pre-soaking reduces cooking time, and for this reason alone I think it’s worth doing whenever you have the time to pre-soak. Always pre-soak for at least 1 hour.

Washing rice is generally a good idea, unless you are making certain short grain varieties that are meant to be sticky. In which case I would still pre- soak, but not wash (not drain the pre-soak water, just use it for cooking).

In my kitchen, when cooking basmati rice (my favorite) which has been pre-soaked for 1 hour, it takes about 8-10 minutes to cook the rice. The time is measured from after I’ve brought the pot to a rolling boil and lowered the heat to a simmer.

I use a heavy stainless steel pot for cooking rice. Since I have an induction cooktop which requires ferromagnetic pots, the pot is actually triple layered (magnetic stainless steel on the bottom, copper in the middle, regular stainless steel on the inside). I bring the pot to a boil on high heat (the highest setting on the cooking range), then immediately lower the heat to a simmer. The cooktop can be set by power level ( 1 to 10) or by temperature, and I set the simmer by temperature at 210 °F (boiling point is 212 °F). This is what I would call a “high simmer”, meaning that it cycles between just below boiling to a mild boil and then drops down again. A low simmer would be more like 200 °F. At these settings, it takes 8-10 minutes of simmer to cook the rice, regardless of the quantity of rice.

After cooking, always leave the rice on the stove (just turn the heat off), and let it sit covered and undisturbed for about 10 minutes before serving.

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Ancient Bacteria

September 22, 2010 No comments

Here’s an interesting question: how long can living organisms survive in hibernation? We know that many animals such as bears, squirrels and bats hibernate seasonally, but I am talking about bacteria, which can enter a state of suspended animation and survive for very long periods. By “very long” I mean possibly millions of years. Hundreds of millions of years.

This question is interesting for several reasons. First, just what kind of chemistry does it take to do that? We know that DNA degrades over time. The random influences of temperature, radiation, or environmental chemistry ought to degrade any huge and complex molecule over such long time spans. How could bacterial DNA survive intact for millions of years?

Second, if it is true that bacteria can survive so long, what a remarkable opportunity this would be to investigate the process of evolution! Consider the organisms alive today. Although it is generally believed that archeobacteria found in certain inhospitable environments (such as mid-ocean ridges, or deep beneath the Earth) are the oldest forms of life, they can offer only limited insight into what early life might have been like. All forms of life continue to evolve, including archeobacteria. Although such bacteria look very primitive to us, they have also evolved and changed continuously for 3-4 billion years. Who knows what they looked like 3 billion years ago? Or even 100 million years ago? How could we know, unless we found a 100 million year old bacterial spore, and were able to sequence it? Since bacteria do not reproduce while in the spore state, they are not evolving. Their DNA is essentially unchanged. Such an organism could provide a 100 million year old snapshot of evolution, frozen in time. If we could then sequence its genome and compare it to similar life forms today, we would see how a hundred million years of evolution have brought about their changes.

It is also interesting from the point of view of panspermia – the hypothesis that life was seeded to Earth from space. Or even the reverse – life from Earth reaching other planets or other extraterrestrial habitable environments. We know that certain things (like large impact events) can propel material into space at speeds exceeding escape velocity. However, because of the immense distances involved, such material could take thousands of years to reach another solar planet, or millions of years to reach nearby stars. But if there are bacteria that can hibernate for millions of years, then such ideas become more practical.

I was reminded of these questions today when I read a story on New Scientist about bacteria found on the sea floor near Svalbard, an island off the coast of Norway. These are arctic bacteria, so you’d expect them to grow at cold temperatures. However, when the scientists incubated them, they had a surprise. In addition to the expected growth peak at about 20 °C, they observed a second growth peak at 55 °C.

Obviously, the sample contained different types of bacteria, one of which was thermophilic, with spore activation at 50 °C and peak growth at 55 °C. Why do these bacteria exist on the arctic sea floor, where the temperature never reaches 55 °C?

The DNA of these bacteria showed that they resemble bacteria known to exist deep under the Earth’s crust, where the temperatures are warmer. Typically, such bacteria are found associated with petroleum deposits. This might just be coincidence though, since most of our drilling underneath the sea floor is to look for oil. At any rate, the conditions in their normal habitat are hot and anoxic. So what were they doing on the arctic sea floor?

The temperature at the deep sea floor is near zero. It continues to rise in the Earth below the sea bed, at a rate of about 2-3 °C per 100 meters depth. So the normal habitat of these bacteria, with a peak growth rate at 55 °C, would be about 2 to 3 kilometers beneath the sea floor. Note that there are bacterial species that live at different depths below the sea floor – mesophiles, thermophiles (like these bacteria), and hyperthermophiles (in even deeper and more ancient sediments). It has been estimated that about 1/2 to 5/6 of the Earth’s entire bacterial biomass lives in the Earth beneath the sea floor[ref 1]. Some studies estimate that 1/10 to 1/3 of the Earth’s entire biomass is contained in these sub-sea-floor bacteria. So we are talking about very large bacterial populations, and an extremely diversified ecosystem.

There are a few different ways in which bacteria from deep sub-sea-floor regions could move to the ocean floors, and vice versa. The ocean floor constantly accumulates sediment, and therefore anything on the sea floor will be eventually buried deep beneath the sea floor. But this process takes millions of years, even hundreds of millions of years. So if these bacteria are in their normal life cycle, it would take up to a hundred million years for them to be buried deep enough to have a satisfactory environmental temperature in which to germinate. Can they live that long?

Another, somewhat faster process, involves the circulation of ocean water into the deep sediments below the sea floor. This takes about a million years, which is much faster the burying of sediments, but still pretty long. This could give the microbes a boost, take them at least part way through their journey down to 2500 meters. It could also explain how they happened to end up on the sea floor, through the deep sea bed circulation.

The article itself [PDF of the full article can be found here] concludes that the bacteria are engaged in their normal life cycle. Depending upon which cycle we are talking about (burial under accumulating sediments until they reach their target depth, or movement through oceanic sub-sea-floor circulation, or some combination of the two), this would mean that the normal life cycle for these bacteria ranges from a million to possibly a hundred million years.

There are other putative examples of extremely long-living bacteria, but the claims tend to break down upon further examination. For example, Vreeland and others found a species of Bacillus enclosed in the brine inside a salt crystal in the Salado salt formation in New Mexico [full PDF here]. These crystals are from the Permian, 250 million years old. Their team was able to successfully revive the bacterial spores and grow them in culture, and named them Bacillus strain 2-9-3, subsequently called B. permians. However, it was not clear whether these are actually 250 million year old bacterial spores trapped inside the salt crystal, or if they are bacteria that only recently migrated into the salt crystal.

Salt crystal from which B. Permians was extracted.

There are some studies that cast doubt on the age of the bacteria. The gene for the 16S ribosomal subunit was sequenced, and has been compared to the same gene from modern day halophilic bacteria. One study reports that “The B. permians sequence differs from that of S. marismortui by only one transition and one transversion out of the 1,555 aligned and unambiguously determined nucleotides” [ref 2].  S. marismortui is a moderately halophilic species from the Dead Sea. It seems very unlikely that a 250 million year old bacterium would differ from a modern species by only 2 mutations on that gene. Phylogenetic studies comparing B. permians to closely related organisms do not place B. permians at an ancestral position in the phylogenetic tree. So at best, there are serious doubts about the 250 million year claim.

Another example is the claim by Cano et al that they revived spores from many bacterial species found in the stomach of a bee that had been trapped in amber. The amber was mined in the Dominican Republic, and is 25-40 million years old. One of these strains was identified as Bacillus sphaericus, which is a common species even today, and is often found inside the bodies of insects. B. sphaericus is listed as a single species, but like many bacteria, it is really a complex of several different subgroups. There are at least 5 recognizable DNA subgroups in various strains of B. sphaericus. The type isolated from the ancient amber was named BCA16, and eventually 1482 base pairs from its 16S ribosomal subunit gene were sequenced. These have been compared to various types of modern B. sphaericus.

There is about 80% similarity to one modern strain – NRS 592 [ref 3]. This sort of leaves the question open – it’s not possible to definitely conclude that the spores found in the amber are millions of years old, but it’s not possible to rule it out either. Interestingly, the NRS 592 type that is most similar to the ancient strain is not primarily an insect pathogen. Other types of B. sphaericus which are known to be insect pathogens today share much smaller similarities to BCA16.

Another species isolated from ancient amber by Cano and his group was tentatively named Staphylococcus succinus [full PDF here]. The 16S ribosomal subunit gene for this bacterium differs from its closest modern day homologue (a urinary tract pathogen called Staphylococcus saprophyticus) by 19 substitutions out of 1525 aligned base pairs. This is certainly far larger than the reported homology for B. permians, which is supposed to be even older (250 million years). I don’t know if this is enough to support the ancient origin of S. succinus, but it certainly seems to deny the claim for B. permians. If a 25-35 million year old bacterial spore differs from modern species by 19 substitutions on that gene, how could a 250 million year old spore only differ from modern relatives by only 2 substitutions on the same gene?

There are a number of other similar claims, which I will not cover. Here are some of the papers if you are interested:

DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. DeSalle R, Gatesy J, Wheeler W, Grimaldi D. Science 1992 Sep 25; 257 (5078): 1933-6.

This was one of the first papers about supposedly ancient DNA (25-30 million years old). Unlike the previous examples, this is not bacterial DNA, this is from a termite, which makes it harder to believe. On one hand, the fossil was preserved in amber, which is good. On the other hand, it’s not a spore, it’s a whole multicellular organism, which makes it hard to believe that the DNA could survive that long. The 18S ribosomal subunit gene was sequenced, and was found to be similar to modern termites and roaches.

Amplification and sequencing of DNA from a 120-135-million-year-old weevil. Cano RJ, Poinar HN, Pieniazek NJ, Acra A, Poinar GO Jr. Nature 1993 Jun 10; 363(6429): 536-8.

This one is from another insect, the weevil. This is even older, the weevil was found in Lebanese amber that is 120-135 million years old. Both 16S and 18S ribosomal unit genes were sequenced. Two short fragments from the 18S show that it’s possibly from some extinct weevil.

PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus). DeSalle R, Barcia M, Wray C. Experientia 1993 Oct 15; 49(10): 906-9.

More from the DeSalle group, also 30 million year old termites preserved in amber.

Here are some papers that talk more generically about extracting ancient DNA:

  1. Very old DNA. DeSalle R, Grimaldi D. Curr Opin Genet Dev 1994 Dec; 4(6): 810-5.
  2. Ancient DNA: using molecular biology to explore the past. Brown TA, Brown KA. Bioessays 1994 Oct; 16(10): 719-26.
  3. Implications of ancient DNA for phylogenetic studies. DeSalle R Experientia 1994 Jun 15; 50(6): 543-50.
  4. Rapid isolation of DNA from fossil and museum specimens suitable for PCR. Cano RJ, Poinar HN. Biotechniques 1993 Sep; 15(3): 432-4, 436.
  5. The range of life in amber: significance and implications in DNA studies. Poinar GO Jr. Experientia 1994 Jun 15; 50(6): 536-42.

So how plausible are these accounts of finding ancient DNA and being able to sequence it? Many modern microbiologists consider it very implausible. The main reason is that DNA is a very large and complex molecule, which degrades rapidly in the environment. The problem is radioactivity in the soil and rocks. Even small levels of radioactivity which are naturally found everywhere, should degrade DNA within a few hundreds of years. Bacterial spores contain no active DNA repair enzymes. How could the DNA survive that long?

A bacterial spore is a remarkably hardy entity. The thick walls offer considerable protection to the contents. The core, which contains the nuclear material and other cellular machinery is very low in water content, which also helps in preserving the material.

We know that live bacteria can take a lot of abuse. For example, Deinococcus radiodurans can stand cold, vacuum, acid, dehydration, and massive amounts of radiation. It has been shown to tolerate 10,000 grays of radiation (5 grays are lethal to humans). It’s not obvious why such an organism should evolve – after all, there are no habitats on Earth with such extreme radioactivity. The highest natural radiation is found in some areas of Iran, and it’s only about 260 milligrays per year. A year is far in excess of a bacterium’s lifetime, and even so the total cumulative radiation in a year would be far below the capacity of this organism to tolerate.

Some people have suggested that resistance to radiation and resistance to drying use the same mechanism, so the bacteria were really selected for resistance to drying, and resistance to radiation was just a side effect. This is certainly possible, but the fact remains that many of the mechanisms for the resistance depend upon the organism being alive and active. D. radiodurans, for example, has multiple copies of its genome for redundancy, and very active DNA repair enzymes. It has special mechanisms for annealing split strands. However, these are all active mechanisms, and don’t occur in bacterial spores.

What about passive mechanisms? We know that in D. radiodurans, the DNA is very tightly coiled into toroids. Does this confer some extra resistance? Some studies have found high levels of manganese associated with the DNA. Manganese complexes can act as antioxidants. Some researchers have also suggested that the chief damage from ionizing radiation is not to the DNA, but rather to the associated proteins. Manganese complexes could be protecting the proteins. These passive mechanisms would work in bacterial spores, but are they enough to ensure survival for millions of years? Who knows.

The amber fossils may be similarly protected. We know that amber slows down the degradation of biological material. This has been shown in studies on proteins. Proteins in all life forms on Earth are made of amino acids which are “left handed”, that is, they are levorotatory stereoisomers. However, simply over time, all amino acids racemize – spontaneously convert from one stereoisomer to the other. In living organisms, this is not a problem, because proteins are constantly being destroyed and replaced. Since all new proteins are formed with levorotatory amino acids, this is the predominant stereoisomer seen in living organisms.

However, after the cell dies, no new proteins are being synthesized. In time, all the remaining amino acids racemize, and after an extended period of time, the amino acids will be about half and half – roughly 50% in the levo form, and the other 50% in the dextro form. But it has been shown that this process of racemization is significantly slowed down if the organic material is preserved in amber. So if amber can protect proteins, perhaps it can protect DNA as well. Again, the question is for how long, and under what conditions. Could DNA protected by amber, then buried in inert rock or inside a salt crystal, with a low ambient radioactivity level survive for a long time? For millions of years? How about a whole bacterial spore, presumably with manganese complexes, or something functionally equivalent that preserves it?

I don’t think this question has been answered yet, but it seems like people are slowly chipping away at the notion that DNA (or bacterial spores) couldn’t survive beyond a few hundred years.

References:

1. Leg 201 synthesis: Controls on microbial communities in deeply buried sediments. Jørgensen, B.B., D’Hondt, S.L., and Miller, D.J. (Eds.). Proceedings of the Ocean Drilling Program, Scientific Results Volume 201. [PDF]

2. The Permian Bacterium that Isn’t. Graur, D and Pupko, T. Mol. Bio and Evolution. (2001) 18(6): 1143-1146. [PDF]

3. DNA similarity analysis of a putative ancient bacterial isolate obtained from amber. Yousten, AA and Rippere, KE. FEMS Microbiol Letters. 152 (1997): 345-347. [PDF]

biology, science none

The Origins of “YHWH”

September 1, 2010 2 comments

I read an interesting theory about the origin of God’s name “YHWH” in the Hebrew Bible. I am not enough of a scholar to know all the pros and cons, but for it’s worth, I present it here.

Many secular historians, as well as the Bible itself, agree that at the time of Moses (around 1200 BC), the ancient Hebrews worshipped many gods. There are several instances in the Bible of Moses warning his followers about worshipping false gods, and many other instances of various misfortunes on the Hebrew people being blamed on the fact that they worshipped other gods besides YHWH. Archeological evidence shows that this practice of worshipping multiple gods continued very late.

Archeological digs of sites as late as the 6th century BC (right before the Babylonian captivity) have revealed thousands of statues of various gods. Written inscriptions from the period confirm this as well (there is a well-known tomb inscription from the 8th century BC saying “blessed be <this dead guy> in the name of YHWH and Asherah”. Asherah was the old Canaanite mother goddess. It’s hard to judge the prevalence of such beliefs from archeology alone, but it seems certain that not all of the Israelites were monotheistic at this time – they worshipped other gods as well. It’s only after the Babylonian captivity that they underwent a radical change. After this period, statues and mentions of other gods disappear from the record.

The assumption among Biblical scholars has been that YHWH was a popular god at the time, but one among many. The Hebrews made their contract with this one god, and decided to worship him alone and no other. However, the name YHWH only appears in the Hebrew Bible. It does not appear in any Canaanite text or inscription of the period. So where did YHWH come from? What people worshipped him at the time?

The first non-Biblical mention of the Israelite people comes from an Egyptian stele – the Merneptah Stele, which is inscribed with the victories of the Pharaoh Merneptah in his campaign against Libya. Although much of the inscription is about his victory over the Libyans, it does contain this one line:

Canaan is captive with all woe. Ashkelon is conquered, Gezer seized, Yanoam made nonexistent; Israel is wasted, bare of seed.

This stele, dated from 1208 BC contains the first non-Biblical mention of people called the Israelites living to their east, in Canaan. So if we take the Biblical account as true, this was after Moses led them to the Promised Land, and therefore after the exodus.

The question of when (and if) the exodus happened is difficult to settle, since there is no historical or archeological evidence of it. However, on the North Wall of the Temple of Karnack, there is an inscription describing the victories of Seti I (the father of Ramses the Great, who many believe to be the pharaoh of the exodus). One of the victories mentioned by this inscription is over a people called the Shasu, who lived in southern Canaan (today the region of Jordan and northern Saudi Arabia). These people had a town, mentioned on the inscription as “Yahoo”. In those days, towns were often named after gods; so historically, “Yahoo” is considered both the name of a settlement, and a god (the local god of that town).

In Hebrew, for lack of vowels, “Yahoo” is written as YHW. The Bible also mentions the Shasu, whom it refers to as the Midianites. This is especially interesting for a couple of reasons:

  1. After Moses killed the Egyptian overseer, he fled to Midian, where he lived as a shepherd for 40 years (this was before the exodus).  There he was hired by the Midian priest Hobab (also known as Jethro) to look after his flocks, and he married Hobab’s daughter Zipporah. It seems likely that living with a Midian priest, he would learn something about Midian gods.
  2. The incident of the burning bush where Moses had his first encounter with god happened in Midian.

After these 40 years in Midian, Moses went off to have a word with the Pharaoh, which led to the exodus. As he led his people out of Egypt, Moses made his way back to Midian, to Mount Sinai/Horeb, where he had first encountered the burning bush. There he stayed for 40 days and 40 nights, while god gave him the 10 commandments. However, when he came down from the mountain, he saw his people worshipping the golden calf, and that made him mad, so he smashed a couple of the tablets. Then god offered to give him a copy of the two tablets he had smashed, so he went back up the mountain for another 40 days and 40 nights, and finally brought back the 10 commandments that were later put in the Ark of the Covenant. Then Moses and the Israelites spent another 40 years wandering the desert, after which they finally came to Canaan. As you can see, the ancient Hebrews liked the number 40.

When Moses brought the 10 commandments to his people, he explained to them that their god was YHWH, and they better not have any other gods before him. This is an interesting connection, seeing that these events happened in Midian – the same Midian of the god YHW (or “Yahoo”). Further, there are other interesting associations. Right about this time, who should decide to join Moses, but his old buddy and father-in-law, Jethro/Hobab, who brought along his daughter (Moses’ wife) Zipporah. If you recall, Jethro was a priest of Yahoo, the Midianite god. He apparently had some hand in setting up the Old Testament religion too. The Bible mentions that when Jethro saw Moses holding courts and passing judgment, he suggested that Moses delegate some of this work, and this is how Moses came to appoint Judges.

Admittedly, this is all circumstantial, but it makes for a pretty solid case. The name YHWH had to come from somewhere. It was not a local Canaanite name; none of the Canaanite texts mention it. But there WAS a god YHW nearby in Midian, the same place where Moses lived for 40 years, working for a priest of YHW, marrying his daughter. The same place where Moses saw the burning bush, and later received the 10 commandments. So I call it a good working hypothesis.

Of course, nothing good lasts forever. In time, Moses got angry with the Midianites, and attacked them. This is one of the great massacres of the Bible, with god telling Moses:

  • NUMBERS 31:2 Avenge the children of Israel of the Midianites: afterward shalt thou be gathered unto thy people.
  • NUMBERS 31:3 And Moses spake unto the people, saying, Arm some of yourselves unto the war, and let them go against the Midianites, and avenge the LORD of Midian.

Again, the mention of “avenge the LORD of Midian” seems suspect. The “LORD of Midian” was Yahoo. Did Moses think the Midianites had been naughty towards their god, so the god needed avenging? Who knows. It is certainly suggestive. The war did not go well for the Midianites:

  • NUMBERS 31:8 And they slew the kings of Midian, beside the rest of them that were slain; namely, Evi, and Rekem, and Zur, and Hur, and Reba, five kings of Midian: Balaam also the son of Beor they slew with the sword.
  • NUMBERS 31:9 And the children of Israel took all the women of Midian captives, and their little ones, and took the spoil of all their cattle, and all their flocks, and all their goods.
  • NUMBERS 31:10 And they burnt all their cities wherein they dwelt, and all their goodly castles, with fire.
  • NUMBERS 31:11 And they took all the spoil, and all the prey, both of men and of beasts.

After which, the Lord rewarded his own:

  • NUMBERS 31:15 And Moses said unto them, Have ye saved all the women alive?
  • NUMBERS 31:16 Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the LORD in the matter of Peor, and there was a plague among the congregation of the LORD.
  • NUMBERS 31:17 Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.
  • NUMBERS 31:18 But all the women children, that have not known a man by lying with him, keep alive for yourselves.

That’s how the lord was, sort of a finicky fellow. With you one day, out for your blood the next. Anyway, perhaps we are closer to settling on his name. The lack of written vowels in old Hebrew has always made the pronunciation of “YHWH” a bit of a mystery. But now that we have a phonetic spelling from the Egyptians, I propose that we tentatively start calling him “Yahoo”.

religion none

On “Science Turns Authoritarian”

July 28, 2010 No comments

I read an article in The American claiming that science is losing its credibility because it has adopted an “authoritarian tone”. The author, Kenneth P. Green, asserts that science used to be in the business of simply stating facts neutrally; but now it has become increasingly assertive about drawing conclusions from the facts, that is, telling us what we ought to be doing.

For those unfamiliar with the magazine, The American is published by the American Enterprise Institute, a right wing think tank. While I have no idea how scholarly they pretend to be, this particular article is so full of errors and strawmen that it demolishes any credibility they may have as a serious think tank.

Here is the gist of it. They performed an “experiment”, in which they searched for certain phrases in the Lexis/Nexis database. The phrases were:

  • science says we must
  • science says we should
  • science tells us we must
  • science tells us we should
  • science commands
  • science requires
  • science dictates
  • science compels

They narrowed the search by date, and reported cumulative results for each year, from 1980 to 2009, and graphed them. Here is the graph:

adapted from article at American Enterprise Institute

The steep green line at the top is the cumulative total for all phrases. The next two lines, which show a significant increase over the years are for “science tells us we should” in purple, and “science requires” in brown. The rest of the lines are scrunched up at the bottom and do not show any sharp increases in the frequency of those phrases.

From this molehill of “experiment”, the author derives far reaching conclusions. He says that the graph shows that the occurrence of these phrases has increased sharply over the years since 1980, which reflects an increasingly “authoritarian” slant to science. He says:

“In other words, around the end of the 1980s, science (at least science reporting) took on a distinctly authoritarian tone. Whether because of funding availability or a desire by some senior academics for greater relevance, or just the spread of activism through the university, scientists stopped speaking objectively and started telling people what to do.”

Now consider how laughably unscientific this experiment is. If you have children in middle school, consider if your average 10-14 years old could have designed a better experiment. Then understand that Mr. Kenneth P. Green, resident scholar at American Enterprise Institute failed.

I’ve described some problems with their “experiment” below.

The Graph is Meaningless Unless Normalized

It’s a fair bet that between the period covered by the graph (1980-2009), the size of the Lexis/Nexis database grew tremendously. Recall that back in 1980, people used 300 baud modems, and hard drives in gigabyte sizes arrived from IBM on a palette, and cost thousands of dollars. The web as such barely existed. Now consider the situation today, when 2 terabyte drives are available by mail order for a couple hundred bucks. Obviously, databases have grown. A lot more is being stored in the Lexis/Nexis database today than used to be the case in 1980. Here’s a brief history of Lexis/Nexis, showing how they have grown by incorporating more and more publications into their database.

Anyone interested can do their own search, but 2 minutes on Google turned up these facts:

  • By 1983, the LEXIS database had 12.5 million pages, including the full text of federal and state laws, court decisions, and much of British and French law.
  • Today, to serve its user population of about 5 million subscribers, LexisNexis hosts over 100 terabytes of content on its 11 mainframes (supported by over 300 midrange UNIX servers and nearly 1,000 Windows NT servers) at its main datacenter in Miamisburg, Ohio.

This is not even going as far back as 1980, the date the author uses, when the database would have been even smaller. In 1983, it was 12.5 million pages. Even at a generous 100 kilobyte per document (100 kilobytes is a good sized novella), the size of the database was about 1 terabyte in 1983. Realistically, it was probably much smaller than 1 terabyte. Terabyte size databases were exceedingly rare in 1983. Today it is 100 times larger. This is because Lexis/Nexis is indexing a vast number of magazines, journals, legal documents and other texts today, than it was in 1980.

With a much larger number of publications being indexed today, it’s no surprise that any given search phrase produces more hits. This is why graphs such as these are completely and utterly useless. If the author had even a little bit of common sense, he would have taken the trouble to contact Lexis/Nexis, and ask them specifically “how many gigabytes per year do you add to your database today? How many gigabytes per year were you adding to your database in 1980?” If the difference between 1980 and today is 10 fold, then simply divide today’s numbers by 10 to obtain a normalized result for today. If you want to plot a point for every year between 1980 and 2009, then you need to ask the same question for each year – how many gigabytes of data per year were you adding in 1989? In 1990? In 1991?”

If this was too much trouble, I can suggest a simpler test, which is not as accurate but better than nothing. Pick a phrase that has nothing to do with science, such as “I like cookies”. Do a search for it in the same way, year by year. I am willing to bet cookies to peanuts that he will find the exact same result – that the frequency of occurrence of this phrase increases yearly. This is simply a result of the increasing number of resources indexed by the database, and has nothing to do with whether cookies are really more popular today than in 1980.

So pick half a dozen such non-science phrases. “I like cookies”. “Cars are fun”. Whatever. Get some numbers for how those phrases have changed in frequency, then normalize to those numbers. Better than nothing.

Results Show the Opposite of What Author Claims

Mr. Green makes fleeting reference to the increasing size of the database:

“Some of this may simply reflect the general growth of media output and the growth of new media, but if that were the case, we would expect all of the terms to have shown similar growth, which they do not.”

He gets zero points from me for this. No, we wouldn’t expect all phrases to show similar “growth”. First, as I explained above, no “growth” was demonstrated. You cannot demonstrate growth unless you normalize the numbers, which he failed to do. However, if he had normalized the numbers, even then, any growth (or shrinkage) does not need to be even. Language is an evolving thing. Over time, some phrases become popular. Others become archaic or obsolete. This graph stretches 30 years, over a generation long. That’s plenty of time to see statistical effects in the popularity of phrases.

But the funny thing is that even if you grant him his point, it shows exactly the opposite of what he claims. What are the phrases that are becoming more popular, according to his graph? They are:

  • science tells us we should
  • science requires

Compare that to which phrases are at the bottom, that did not become more popular:

  • science commands
  • science dictates
  • science compels

Which is more authoritarian? “Science commands”? Or “science tells us we should”? The fact is that the most authoritarian phrases (commands, compels, dictates) are the ones that have grown the least in popularity. If anything this is a sign of decreasing authoritarianism in science. If he had bothered to normalize his numbers, these phrases would probably all have negative growth. But somehow he misses all that and just merrily goes on his way.

Some of the phrases are particularly poorly chosen, such as “science requires”. This could easily be part of a statement such as “… credit in science requires that you take three 101 levels courses in physics, chemistry and biology …” which doesn’t have a darn thing to do with the “authoritarianism” of science, just some school listing its requirements. Or it could be “what science requires of time“, meaning what are the scientific constraints on our understanding of time that need to be taken into account. Again, not an “authoritarian” directive telling people they better not smoke or they’ll get lung cancer, or they better watch the greenhouse gases (Mr. Green’s pet peeve) or the Earth will get hot. Or “Mercury Mission Shows Science Requires Patience“.  This is precisely the content that’s getting indexed in Lexis/Nexis, and is showing up on the graph.

One click on Google turns up a hundred thousand hits, and from what I can see precious few have anything to do with Mr. Green’s thesis about authoritarianism. If you pick such a commonly used phrase, of course you’ll see its use spike as more material is indexed. But it says nothing about authoritarianism in science.

The Lexis/Nexis Database Doesn’t Represent What Scientists Say

The Lexis/Nexis database consists of popular magazines, TV reports, business journals, legal documents, and other texts of this nature. What it does not include are scientific journals. In other words, the material in the Lexis/Nexis database represents the words of journalists, not so much scientists. If you want to see what scientists actually say, better databases would be those which index scientific journals.

So really what he’s claiming is that journalists are using these phrases more often than they used to, that journalists are becoming more “authoritarian” about science. Perhaps in some cases the journalists are actually quoting scientists, but certainly not in all. Journalists also editorialize the words of those they interview. They also present their own viewpoints. Without any effort to differentiate between what the scientists said and what the journalists said, how could you draw any conclusions about scientists? You wouldn’t, if you cared about the truth. Obviously, Mr. Green is not so burdened. He has an agenda to push, and he gets busy pushing it.

The Agenda

So what is Mr. Green trying to do? He works for the American Enterprise Institute, a right wing think tank. They produce reports that are cited by right wing politicians, to support right wing agendas. The science he particularly hates is climate science, specifically global warming. He mentions it specifically:

“The climate community is probably the biggest user of the authoritarian voice, with frequent pronouncements that “the science says we must limit atmospheric carbon dioxide concentrations to 350 parts per million,” or some dire outcome will eventuate.”

This is what he’s fighting against. Apparently, he’s not happy with the gl0bal warming reports, and he doesn’t want any legislative actions taken. So what is he really saying?

When he says “science should be neutral”, what it amounts to is that scientists should just state the facts as they see them, and then shut up. In particular, they should never make any suggestions about what ought to be done. They should have no political voice.

Who then has the political voice? Who makes the decisions? If the scientists shut up, then it’ll be the non-scientists making the decisions. In other words, in the most complex technical matters, when it really helps to have an understanding of science to know what you’re talking about, he wants to silence the most technically qualified people. He wants the only people who are allowed to make “ought” statements to be the most clueless – hacks like himself, politicians of all stripes, whatever. So long as they’re not scientists.

This sort of viewpoint, overwhelmingly silly though it may be, comes from a very real resentment that people like Mr. Green have. Science is outside their understanding, specially highly technical matters such as climate science, where you need a technical understanding of an immense body of data to even sound half-intelligent. Being unable to use science himself, Mr. Green wants to deny it to his opposition as well. He wants to have a shouting match between people as clueless as himself, with the scientists all locked out of the discourse, because if they participate, they’re “tainting” science, don’t you know.

science none

Mass Effect 2

July 11, 2010 No comments

I’ve been playing Mass Effect 2, the latest action RPG from BioWare/EA. If you like computer gaming, you’re probably aware of BioWare, which has made some of the best action RPGs (role playing games) ever, including Baldur’s Gate and Neverwinter Nights. More recently, they made Dragon Age: Origins, also an excellent RPG, which I recently completed twice.

Mass Effect 2 is the latest in their series of big budget RPGs for PCs and consoles. It continues the story began in the original Mass Effect, from 2007. Mass Effect 2 is bigger and better in almost every way, with beautiful visuals, great audio, good game design with useful skills and talents, and plenty of atmosphere. Combat is great, almost FPS-like, with different weapons and ammo, a good targeting system with double damage points for head shots, etc. The weapons are well thought out and feel different, each with its advantages and disadvantages, each requiring adjustments to your strategy.

Mass Effect 2 is a space based RPG, which borrows elements from a lot of cinematic history. People will find parallels to Firefly (the chief villains are aliens called “Reapers” which sounds suspiciously like the “Reavers” in Firefly, not to mention a wild-west sort of frontier much like Firefly, and Star Wars before that). There are elements of Blade Runner in the cityscapes on different worlds. The “Collector” ship (“Collectors” are another group we’re fighting in this story) has distinct touches of the Alien movies, with organic looking architecture vaguely reminiscent of H.R. Giger, Alien-like sound effects, and even “pods” that reminded me of the eggs in Alien. There are even elements of previous computer games like Starcraft.

I don’t say any of this to detract from Mass Effect 2. While it borrows heavily from different sources, it’s not a clone of any of them, and all the elements are well integrated into the story. The game is very polished and feels that way.

However, there is one problem that annoys me tremendously. In fact, that was what provoked me to write this blog entry. And that problem is the inability to fast forward through the dialog.

First, let me say that I am only writing about the PC version. I understand that the XBox version is different, and does in fact have a way to fast forward through dialog. So please don’t worry about it if you’re only playing Mass Effect 2 on the XBox.

Mass Effect 2 is an RPG, which means it has a strong story line. This is good – in fact, it’s considered a mark of great RPGs to have a story which can interest the player and draw him into the game. The downside of it is that the story is told mainly through dialog and cut scenes. Mass Effect 2 is an incredibly long game, taking many hours (many days of many hours) to complete. Unfortunately, a large portion of this is dialog.

Now I understand that not everyone may have a problem with dialog. After all, there are people who love the old D&D games, which are almost purely dialog – reading stuff on the screen. Not to mention there are many RPG fans to whom story and dialog are an essential part of enjoying the RPG genre. If the game doesn’t provide a sufficient story element, these people make it up on their own.

I point to World of Warcraft as proof – not only does it have an incredibly detailed background spanning multiple games from Blizzard, it also has tons of in-game information about the story, factions, events, and characters available for anyone interested. But since it’s primarily an action RPG, you don’t really need to know any of that in order to play the game. You pick your faction, you roll a character, you start playing. The guys with the red name tags are enemies, you kill them. Sure, there’s some dialog from quest givers. But it’s short and sweet. There is no waiting – the text appears along with the dialog, if you read faster than the dialog is spoken, you can click right in the middle of the dialog and move on. If you’re playing your second or third character and know what choice you’ll make, you can skip the reading too, you already know where to click. This keeps the action moving for those of us who like the “action” part of the action RPG genre.

Yet even in this very action oriented game, the story and background are there for those who care about such things. Blizzard simply leaves it up to the player to determine their own level of interest and tolerance for things such as story and background, which get in the way of gameplay.

To get back to my point – even when the game doesn’t force you to spend a lot of time listening to dialog and involving yourself in the story, some people create ways to do that for themselves. This is why Blizzard has role-playing servers, and there are multitudes of people who create guilds that deliberately build a mythos that relates to the story line. These are people who love fantasy, obviously, and to them a good part of the enjoyment of the game is fantasizing about their character, the story, the events. I’ve heard of people getting kicked out of their guild for “breaking character” – the offence of repeatedly talking as if they were Joe the Computer Gamer, rather than Aragorrrn the Magnificient on a quest to retake Alliance territory from the evil Horde.

Now while I don’t grudge these people their fantasy – their money is just as good as anyone else’s, and they have just as much right to enjoy themselves as anyone else – I have to say that I am not one of them. Very emphatically not. I like stories as much as anyone else, but the fact is that when I’m playing a computer game, I want to play a computer game, not listen to an audio book. If I’m in the mood for a story, I’ll read a novel. That’s not to say I think computer game writers are cheap hacks. Some of them might be good writers. But I am not playing a computer game to read pages of text on my screen, or to listen to hours of dialog. That’s what books and movies are for, in my opinion.

This is why I have such a problem with Mass Effect 2. This game has way too much dialog, too many cut scenes. In short, there is too much time when the game takes over my keyboard and mouse, and turns me into a passive reader/listener. This is not why I play games.

In case you are not a gamer and wondering why this is such a big deal, let me explain. Since the game is a well-designed RPG, events unfold very much based on the choices you make. Typically, RPGs tend to build upon the motivations of your character. In fact, they have a vocabulary assigning your character to a spectrum ranging from Lawful Good through Chaotic Neutral to Lawless Evil. It’s sort of a continuum, with characters being lawful, neutral or lawless, and good, neutral, evil. What kind of character you are depends upon the choices you make in the game, and this in turn affects how other people in the game respond to you. These differences can be quite dramatic, with whole parts of the story arc or side quests being closed to one kind of character but open to another.

This is also true for Mass Effect 2, which uses the words “paragon” to describe “good” and “renegade” to describe “evil”. It doesn’t matter what words a game uses, RPG gamers know that every time they talk to a character and try to reason with him instead of shooting him (and vice versa), they are making a choice to fulfill their role as “good” or “evil” and that this choice will have consequences for game play. In other words, they have to pay attention to such matters.

The problem happens when the game makes you sit through a screenful of text, 2 minutes of dialog, a lengthy cut scene, before you are allowed to click a button and make your choice. Now imagine this happening over and over and over throughout the game. You begin to realize you are spending a lot of your time just sitting back, listening to inane chatter and dramatic declamations, waiting for a button to appear on your screen. But we’re not done yet.

The consequences of a choice might not be apparent until the dialog is complete, and you see the message flash up “You just won 15 Paragon Points!” No matter how carefully you listen to the dialog, you’ll still make mistakes. Or maybe you just got bored the 36th time this happened, and your attention wandered. At the end, the message flashes “You just won 15 Renegade Points!” Damn. You just moved 15 points into the evil column instead of 15 points into the good. Or the other way around, if you were trying to be evil. What do you do? Well, the only thing you can do is to load from the last save you made, and play some portion of the game again, to come back to this dialog, so you can pay more attention and make the right choice.

It gets to the point where players get into the habit of automatically hitting the “save” button before any such dialog. Of course, you can’t always predict when the dialog will happen, so you’ll find yourself replaying significant portions of the game just because you clicked the wrong button on a dialog screen, because you were so damn tired of listening to the characters squawk that you had stuffed your ears with your fingers. No, I’m not kidding, I have actually done that with Mass Effect 2. Usually the second or third time I was forced to replay the same dialog to pick a better choice.

This turns the game from pure fun to alternating periods of pure fun and pure torture. Since we humans can’t instantly switch our emotions at will, even the periods of pure fun are marked by long slopes where the fun is admixed with irritation at the dialog you had to sit through a minute ago.

What does it take to avoid this, if BioWare had chosen to avoid it? Simple, it just takes two things:

1. Keep dialogs to a minimum. No matter how much you’re paying your writers, no matter how spiffy you think your dialog is, no matter whether you hired Hollywood talent to speak the voice parts for you. Remember, you’re selling a computer game. Not a book. Not a movie. Keep dialogs to a minimum. Mass Effect 2 has about 5 – 10 times as much dialog as is needed.

2. Always present the choices along with the dialog. Do not impose a delay, where the whole dialog has to be spoken before the choice buttons appear. After all, users have the choice to turn on subtitles to the dialog. They can read. If they can read faster than your voice talent speaks (which everyone does), they already have the information needed to make the choice long before the characters are done speaking. Let them make the choice when they are ready to make it. Don’t force them to wait for the whole tedious thing to be voiced out before you present them with choice buttons.

That’s all there is to it. But Mass Effect 2 breaks both these rules. Dialog is excessive. There no way to stop it. At least, not on the PC.

When I started this game, I picked “Soldier” as the class I wanted to play. Since the game is otherwise so excellent, very soon after I started I decided that I would play it again, as one of the other available classes. This is a great feature of RPGs, that you can replay them as another class for a whole new experience.

However, by the time I was about half way through it, all I wanted was for the game to end. There is no way on earth that I would sit through all that dialog again. It’s like getting a root canal. Two root canals. And then having the tooth pulled by a pair of rusty pliers just after you went through the trouble of getting the root canals.

It amazes me how game designers who spend millions of dollars on a game make such foolish choices. How willing they are to ruin the game experience for thousands of people (and I know I am not alone in this), for lack of a simple feature that would have been trivial to implement.

Again, please don’t take this as a rant against RPGs, or against people who love story lines, who love to listen to hours of dialog, who want cutscene after cutscene to the point where the game begins to look like a movie rather than a game. I have no problem with such people. It’s possible to give these people exactly what they want, but for the sake of those of us who want control back on our keyboards, just give us a fast forward button. You’re taking nothing away from anyone else if you do that.

computers, reviews none

What’s all the fuss with Mirror Neurons?

June 27, 2010 3 comments

Mirror neurons have been in the news a lot lately, performing a dizzying array of functions, from the fight against pornography to explaining why World Cup Football is a good thing, to explaining the banking crisis. It seems like people love to use mirror neurons to explain just about anything they want to, it doesn’t really matter what. And they don’t seem to know a whole lot about mirror neurons, other than vague associations with “empathy” and “imitation”. These are common enough things in human affairs that mirror neurons can intrude anywhere, make any opinion seem more scientific.

This profligacy is not limited to lay people and journalists. Scientists have implicated them in things as varied as understanding intentions, empathizing with others, the development of language, a possible role in autism, and a host of other things. Hundreds of papers on these subjects have been published.  Can mirror neurons indeed have such near-miraculous explanatory powers?

What are Mirror Neurons?

What are mirror neurons, and why all this fuss about them? In brief, mirror neurons are certain neurons in the brain that fire not only when the individual performs an activity, but also when the individual observes someone else perform that activity. They were discovered in the 90’s by an Italian scientist named Giacomo Rizzolati, in the macaque monkey. He observed that in the F5 region of the monkey brain (part of the premotor cortex, a region concerned with planning actions); there was a certain population of neurons which had some peculiar properties:

  • They fire both when the monkey performs an action, and when the monkey sees another monkey (or human) perform that same action. Typical actions in which such activity is observed are things like reaching for an object, or grasping an object.
  • They fire only when the actions are goal-oriented, meaning when there is a perceptible goal to the action, some object towards which the action is directed, for example, reaching for food. They do not fire when the monkey observes another monkey performing meaningless actions, such as waving its arms randomly.
  • Further, they fire only when the monkey knows what the goal is. Performing a pantomime (reaching for food when food is not there) will not produce any activity in these neurons. However, if the monkey knows the object is there even though he cannot see it, then they will fire. For example, if the observing monkey sees the food, but then a screen is placed in front of the food, and he sees the acting monkey reach for the food behind the screen, these neurons will fire, even though the object (food) is itself hidden at the time. This is because the monkey saw the food previously, and knows it’s there.
  • They don’t fire when tools are used to perform the actions. For example, if food is delivered simply by pressing a button, there is no activity in the mirror neurons when this is observed. Only the observation of direct, goal-oriented action will provoke the activity of the mirror neurons.
  • They don’t respond to partial activity. They won’t fire if you show the monkey the food, or show the monkey another monkey looking at the food. Only when the other monkey reaches for the food will they fire in the observing monkey. Further, the response is quite specific for the type of activity. For example, consider two actions – reaching for an object and placing it in one’s mouth (as with food), and a different action, picking up an object and placing it in a container. Both are goal-directed activities, and both can generate mirror neuron responses in the observer, but different populations of neurons are involved in each response. The mirror neurons which fire when the monkey observes another monkey reaching for food and placing it in its mouth are different from the mirror neurons which fire when the monkey observes another monkey picking up some object and placing it in a box.
  • The neurons will fire as early as the initiation of activity (as soon as the monkey observes another monkey initiating the activity), even before the action is complete. In other words, they fire as soon as the monkey observes another monkey reaching for the food, before it has actually reached the food, grasped it, brought it back to its mouth, and deposited it there. Now it’s possible that some actions could be ambiguous, for example, a monkey may reach for an object either to place it in its mouth, or to place it in a box. However, in most tested examples where the activities are clearer cut, the appropriate population of mirror neurons for that activity begins to fire at the initiation of that activity, suggesting that the observing monkey is predicting the subsequent course of the action.
  • They don’t fire during imitative activities. Adult macaque monkeys do not imitate, but juvenile ones do. Imitation is not a “goal oriented” action in the previous sense. A juvenile monkey will imitate any meaningless action, for instance, if you stick your tongue out at it, it will stick its tongue out back at you. In juvenile macaques, mirror neurons do not fire during imitative activities – not during observation of the activity, and not during subsequent performance of that activity.
  • They don’t fire in preparation for the activity, only when the activity occurs. This is important because there are areas nearby in the monkey brain (for example, area 6) which have “set neurons” that fire in anticipation or preparation for an action, before the action is initiated. This is not true for mirror neurons.
  • They don’t seem to represent covert activity, that is, activity which happens in the brain but is not implemented by the body. More specifically, covert activity would be the brain going through the motions of reaching for an object, and yet the hands don’t move, the monkey doesn’t actually reach for the object. Covert activity is ruled out by the observation that during the mirror neuron firing, there is no corresponding activity in the primary motor cortex. For covert activity, one would expect some activity in the primary motor cortex, which does not get translated into movement of arm muscles because it’s sub-threshold, or because it’s blocked in some way. Such covert activity is not recorded.
  • Finally, it’s important to remember that mirror neurons are only a subpopulation of the neurons in the F5 area. Different estimates put them at somewhere around 20%-40% of population. The rest of the neurons in F5 which do not show mirror activity are called “canonical” neurons. Of the subpopulation of mirror neurons, some might respond only to visual stimuli, some only to auditory, and some only to somatic sensory information. Further, of those that respond to say visual stimuli, some might respond only to certain kinds of actions and others to a different kind of action, as mentioned earlier.

These observations on macaque monkeys were the basis of our understanding of mirror neurons. Any theory about mirror neurons must explain these observations. So, what are these mirror neurons, what are they doing, and why?

Rizzolati and others initially explained mirror neurons as a form of “action understanding”.  In Rizzolati’s words:

“Each time an individual sees an action done by another individual, neurons that represent that action are activated in the observer’s premotor cortex. This automatically induced, motor representation of the observed action corresponds to that which is spontaneously generated during active action and whose outcome is known to the acting individual. Thus, the mirror system transforms visual information into knowledge.”

Nielsen put it this way:

“A mere visual representation [of an action], without involvement of the motor system, provides a description of the visible aspects of the movement of the agent, but does not give information critical for understanding action semantics, i.e., what the action is about, what its goal is, and how it is related to other actions.”

What does this mean? They are basically saying that in a pre-language sense, our brain has a certain innate “vocabulary” which it uses in planning. Part of this vocabulary has to do with motor actions, and that is assisted by mirror neurons. So for example, our brain has a “word” or a “concept” or a “symbol” or some discrete “thing” (to be as non-committal as possible) which represents the action of grasping, and that mirror neurons are an automatic mechanism that identifies this action when we observe others do it. By activating the same neurons that we would activate if we ourselves performed this act, we can recognize or identify when others are doing it. This adds to our knowledge in some sense – by observing the other monkey stretch its arm out and grasp the food, we gain the knowledge that the monkey is going to eat the food, because our mirror neurons are firing in the pattern in which they would if we were to reach for the food and grasp it.

This is an interesting point to consider, especially if we generalize it beyond monkeys to humans. But before we do that, let’s consider a few problems with the monkey model. Biology is very messy, and for every case where someone says “X”, another person says “not-X” and often the evidence for both is inconclusive.  So what are some of the objections against this “action understanding” theory?

First, there is some evidence that disruption of the F5 area (the mirror neuron area postulated to be involved with “action understanding”) does not disrupt “action understanding”. That is, if you destroy the area supposedly responsible for this function, the function does not go away. This is sort of fuzzy, because some experiments seem to show that lesions of F5 do indeed disrupt some forms of action understanding, while others don’t support the idea. So I’ll leave this alone for now until we have more data.

Second, we know that action understanding can happen without mirror neurons. The visual system has the job of identifying objects we see, understanding relationships between them, and using that information as the basis for action. This can occur quite independently of F5. For example, the Superior Temporal Sulcus (STS) has cells which are much more sophisticated than the F5 mirror neurons in distinguishing between different types of observed actions, and they respond strongly when monkeys observe other people do various actions. They don’t, however, have a motor component. They do not fire when the monkey himself does the action. So it’s possible to have action understanding without the corresponding motor part.

Third, it now seems that there are mirror neurons in the monkey’s M1 region, or primary motor cortex. This is a problem because we assumed that mirror neurons aren’t simply responding to a covert action, they are actually helping us process information by helping us identify the actions of others. One thing that supported this view was that there was no activity in the primary motor cortex when one monkey observes another monkey act. But now that we know that there are mirror neurons in M1, this foundation is somewhat shaken, and it’s harder to rule out that what we are seeing is simply an associational covert action. Humans do this too, if you observe a sports fan watching his favorite game on TV. He will contort his body into actions mimic the player he’s observing, almost “willing” the player to respond as he does. This does not need to be explained via “action understanding”, but simply by the fact that the sports fan is reacting as he thinks the player ought to act. He may in fact act differently from the player on the screen, because in his judgment a different action was called for.

Mirror Neurons in Humans

This brings us into the problem of generalizing from macaques to humans. While there is some evidence that humans also have mirror neurons, there are a number of key differences, including:

  • Humans show “mirror neuron” activity even for imitation, while monkeys do not. Monkeys only show activity when the action is goal directed, not when it’s random.
  • Humans react to pantomime displays, while monkeys do not. When the object isn’t really there, but the actor does a good enough job of pretending that it is, humans will show mirror neuron activity as if the missing object were really there. Monkeys don’t do that. They need to know that the object is there, even though it may be hidden during the experiment.

Some researchers explain these discrepancies by saying that the human system is more “evolved” and responds to a wider range of stimuli. This may be so. However, it raises two problems. First, it shows that there are significant differences between humans and monkeys in this regard, and therefore research that was done on monkeys should not be uncritically generalized to humans, as it often is. Second, it weakens the original argument for monkeys, which was that mirror neurons are responsible for “action understanding”. Imitative or random behavior is obviously not goal directed in this sense, and therefore there is nothing corresponding to understand. Why then, are human mirror neurons activated in such cases?

The data for humans and monkeys isn’t easy to compare. There are a lot of studies at the single cell level with implanted electrodes that are available for monkeys. Parallel data for humans is non-existent or very scarce, because of the obvious problems with implanting electrodes into human research subjects. On the other hand, there is a wealth of human fMRI data, which is scarce for monkeys, because monkeys can’t easily be trained to perform tasks inside an MRI scanner. This imbalance of the data types makes direct comparisons difficult.

Some tests which can only be performed on humans show other differences as well. For example, Catmur et al performed a TMS/MEP study on human subjects (TMS is trans cranial magnetic stimulation, in which a part of the brain is stimulated with magnets placed on the outside of the skull. MEP is motor evoked potentials, which are small electrical signals recorded from peripheral nerves) which show dissociation between mirror neurons and “action understanding”. The experimental setup was to stimulate specific motor areas of the brain (through TMS) to produce a twitching of the abductor muscles of the hand and fingers (which was recorded by MEP). Under the standard test condition, the subjects watched a video of someone abducting the index finger of hand, followed by abducting the little finger. When the subjects were watching the video of the index finger being abducted, the MEPs recorded from their own index fingers were stronger than those recorded from their little fingers. When they observed videos of someone abducting his little finger, the MEPs recorded from their little fingers were stronger than those recorded from their index fingers. This was the standard response. However, in the test condition, this was reversed. The subjects were trained to trained to move their index finger when they saw the video of someone moving his little finger, and vice versa. After training, the MEPs recorded were reversed. In other words, the “mirror effect” dissociated from the “action understanding”. Given that this is a crude way to compare what was done will skull electrodes in monkeys, but it is still significant.

This sort of training to overcome default congruent behavior is very common among humans. The fact is that we don’t WANT to act exactly the way we observe someone else acting. If you see the same action, say someone tossing a ball at you, your action will be very different depending upon whether you have a bat in your hand, or if you are the catcher. Our expectation of what they are trying to do depends upon our own role and circumstances. How do monkeys deal with this? We don’t know.

The large numbers of fMRI studies have opened up many interesting areas for study in humans. By its nature, fMRI scans large parts of the brain, compared to the single cell recordings done in monkeys. When you are scanning large areas of the brain, other interesting things turn up. Humans apparently have mirror type neurons in many locations. Among the more interesting regions are the anterior cingulate cortex, the anterior insula, and the inferior frontal cortex. These areas are supposed to have roles in mediating emotions, which leads to the speculation about empathy.

Mirror Neurons and Empathy

We know that observing a certain emotion in others can produce the same emotion in ourselves. This has been amply demonstrated in several studies for emotions such as disgust and pain. Further, when we observe someone else feeling these emotions, there is increased activity in areas of the brain (the above mentioned areas) which are activated when we ourselves experience those emotions. This is strong evidence for mirror neurons in these areas.

There are supportive studies as well. People who self-report to having a high empathy in questionnaires show a greater mirror neuron activation of emotion centers in the brain in fMRI when they are exposed to images of other people feeling those emotions, compared to people who self-report to having lower empathy. Further, not only do the self-reporting empathic people show greater activation in areas to do with emotions, they also show greater mirror neuron activation in tests which have nothing to do with emotions, such as the reaching/grasping tasks described earlier. Does this mean that some people just have a stronger mirror neuron system, which they typically experience as “having more empathy”?

There is some evidence in support of this from the opposite end of the spectrum too. Some autistic people (who have very low empathy) have been found to have markedly smaller/thinner cortical regions that are associated with mirror neurons. Autistic people also generally show lower mirror neuron activity in fMRI and EEG experiments. However, the implications of these findings are disputed, and the matter is not settled.

Mirror Neuron Fever in the Media

While this is extremely fascinating stuff, the fact is that our theories about the role and function of mirror neurons are very hazy at this point. Many of the theories were built on monkey models, which have not been proven to apply to humans. In fact, there are a number of ways in which human mirror neurons are different from monkey mirror neurons, so we should not expect the monkey data to simply generalize to humans without modification. These details are often ignored by media and even by scientists, who have a poor understanding of mirror neurons.

For example, consider this article in the Washington Times about a group lobbying Congress to ban porn because of the effect it might have on children. They found a doctor, a “forensic pediatric physician” to bolster their case.

Quoting from the article:

Pornography normalizes sexual harm, Dr. Cooper said. It shows children a lack of any kind of emotional commitment or relationship between two consensual partners, shows unprotected sexual contact and visual examples often of violent rape.

When a child sees this image of adult pornography, the mirror neurons that are in their brain will convince them that they are actually experiencing what they are seeing,” she said.

Children are very vulnerable as compared to adults because of the presence of mirror neurons in the brain, Dr. Cooper said. Mirror neurons are part of the brain that convince us that when we see something we are actually experiencing it.

This is complete nonsense. It is in fact the opposite of what the theories about mirror neurons say. We don’t experience stuff because we see it, we experience stuff when we do it, and then this knowledge can later be used to understand the actions of another. You don’t experience playing a piano just because you see someone else playing a piano, if you have never played a piano yourself. This is the whole point of mirror neurons – that our brains can and do obtain information and make sense of it in many different ways. On an intellectual and analytical level, we can observe a person playing a piano, understand what he’s doing, get some sort of “action understanding” from the observation. If, however, we ourselves have played the piano before, then to this analytical understanding we can add an “experiential” understanding, and perhaps understand better what it feels like to play the piano, and to understand the person we are observing from an experiential level in addition to an analytical level. Even this is just a theory, and is by no means widely accepted. But to go from this to saying that mirror neurons can convince us that we are experiencing what we see someone do is supremely ridiculous. And then to add that “children are very vulnerable as compared to adults because of the presence of mirror neurons in the brain” is a gratuitously stupid statement. Why would children be more vulnerable compared to adults because of mirror neurons? Because they have mirror neurons while adults don’t? No, adults have them too. Because they have more mirror neurons than adults? No, they don’t. All of which assumes that mirror neurons enable these kids to experience what they see on the screen, which is a wrong conclusion based on a poor understanding of mirror neurons.

This is an obvious example of political activism misusing science to push an agenda, but not all such incidents are so obvious. There are plenty of scientists who have caught on to the mirror neuron idea as well, and use it to push their pet theories. Among the worst offenders are “evolutionary biologists”, which is a category that is fast becoming known for having miles of speculation hanging on to an inch or two of fact.

Mirror Neurons and Morality

One common theory these days is that mirror neurons explain how humans evolved a moral code. The idea is that since we can empathize and feel another’s pain, we know when he’s feeling bad. And for various reasons ranging from social cohesiveness to “seeing him feel bad makes me feel bad”, we came up with the idea that we shouldn’t make others feel bad. This, supposedly, became the basis for some sort of golden rule – don’t do stuff to others that would make you feel bad.

I know this sounds very simplistic, and certainly there are many people who express the same idea much more eloquently, but this is in essence what it amounts to. I have some serious problems with this idea.

First, I am not denying that mirror neurons are real. Of course they are. Second, I am not denying that they may have a role in empathy, in understanding how others feel because we can experientially know their emotion since we feel it ourselves. There are plenty of studies which support that too. However, as a basis for morality, this explanation is very lacking.

Mirror neurons are only one of the ways in which we know things about other people. As mentioned earlier, we have much more sophisticated systems (such as the STS) which allow much finer discrimination when judging and interpreting the actions of others. These systems are not based on mirror neurons at all. Secondly, there are many ways of learning that if you hit someone, he will probably hit you back. While it may help to know “oh, that must have hurt him, I know because I’ve felt pain myself” this knowledge is general enough that we don’t need mirror neurons to remind us of it constantly. If you’ve bumped your toe against a rock, you know it hurts. This does not require mirror neurons. It is not a stretch from that to understand that if you hit someone else with a rock, it will hurt him too. Mirror neurons can add to that, for example by seeing the grimace on his face once he gets hit, which may help you understand the extent and severity of his pain better after you have hit him. If you are empathic, you may feel some pain yourself, from watching his reaction. But nowhere near the pain he felt.  And the fact is, while it may have added something to your knowledge, you certainly knew beforehand, before hitting him, before watching him grimace, that it would hurt. That’s probably why you hit him in the first place, to make him hurt.

Now if empathy was strong enough that our own distress while watching someone else in pain would prevent us from hurting anyone, then we might have an argument. But it isn’t. Even the kindest, most empathic mother may occasionally slap her child for misbehavior. We know from experimental studies that empathy (and the corresponding mirror neuron activation) increases towards people we love. So if it’s still not strong enough to prevent us from hurting people we love, how would it prevent us from hurting those towards whom we are indifferent?

On the other hand, there are several ways in which we can derive the same morality without referring to mirror neurons, which make much more sense. For example, we know that if you hit someone, he might hit back. This dissuades us from hitting people very frequently, because the consequences to ourselves would be unpleasant. We also know that if we live in a family where two people are constantly fighting each other, it can get unpleasant for other family members as well. You don’t want to deal with angry individuals, even though they might not be angry specifically at you. This is why when humans live in social groups, as our ancestors did, it benefits everyone to see that peace is maintained, even those who are not involved in the fighting. These are common sense things that we all know. And they are powerful inducements towards “morality”, if morality is reduced to “don’t hurt other people” in mirror-neuron fashion. And this kind of analysis is available to everyone without any mirror neuron imperatives.

The second and more important question to me is whether “don’t hurt people” is a sufficient basis for morality. Or even a particularly good basis. I don’t think it is. Most of us require a concept of justification when it comes to morality. Someone might perform an action and feel bad about it, and through empathy, we may observe this person and feel bad ourselves because he feels bad. But we may still think that he deserves to feel bad, because of the nature of his actions. This is the essence of justice, which is really the foundation of our morality. A killer may feel bad because society locks him up; we may look upon his face and see fear and misery on it, and perhaps that will evoke fear and misery in our own minds. But our idea of morality might be that he deserves his fate, because he took a life. You can call that balancing empathies, if you will – empathy towards the victim versus empathy towards the killer. But if it is empathy, it’s not based on mirror neurons. We don’t have to see the killer’s face, we don’t have to observe the act of the murder, and we don’t have to see his victim’s face. None of the things that mirror neurons might have a role in are required.  All you need are analytical concerns, such as “is this justice” or “he can’t kill anyone else if he’s locked up”.

You can ask the same question in another way. If you cheat on your spouse, and you know that your spouse will never find out, is it okay? If your sole concern was empathy and “don’t hurt people”, then you might consider it okay, since your spouse will never find out and never be hurt by your action. However, many people might disagree based on other grounds. Such as, you promised to be faithful. Why should you keep your promise? If you do, I think it’s because you value integrity. That is the crux, not empathy.

So I don’t consider empathy to be a sufficient basis for morality. Considerations like justice and integrity, concern for the viability of the society in which you live by having rules that promote harmony – these are all essential for a system of morality. And as mentioned earlier, empathy isn’t the greatest or most powerful reason for the golden rule either. As the rule itself says “do unto others as you would have them do unto you” – meaning, the stress is on the consequences, on the “as you would have them do unto you”. What are the implications? That if you want to be treated right, you better treat others right. If you expect consequence Y, do action X. Why? Because that’s justice. Empathy is part of it, but by no means the only part. Nor is empathy even necessary to understand that people might feel bad if you treat them badly.

Mirror Neurons and Philosophy

Finally, I’d like to touch on some philosophical implications of mirror neurons, which I think are pretty exciting. One well known fact (and problem) in philosophy is that each of us only ever has access to his own mind. We never really know what another person experiences, what they feel. We can draw inferences from their behavior, but we cannot directly experience what they experience. This leads to philosophical views that can verge on the absurdly solipsistic – “I am the only person, everyone else is just an entity that responds in certain ways to certain things I do or observe. Perhaps they are not even real; perhaps they are just creations of my mind”.

There is no cure for true solipsism. If everything is a figment of your imagination, then you have no possible way to establish the reality of anything but your own mind. This is technically true, but uninteresting, since it leads nowhere. At best, you have to admit that the figments of your imagination behave in somewhat predictable ways, just as they might if they were real. Whether you continue to call them figments of your imagination or real make little difference to how you behave. If you believe that truck you are imagining can kill you, then you will move out of its way whether it’s real or not. It becomes an exercise in semantics.

However, there is a kernel of a real problem here. Even if we admit that other people exist, we don’t know what goes on inside their minds. There are many approaches people take to overcome this – by making certain assumptions (he’s a human like I am, with the same sort of machinery to think, reason, feel, that I do), and we can interpret their behavior in light of our own experiences. However mirror neurons provide an extra link in this chain. If mirror neurons allow us to experience what the other person experiences more directly, then this is an automatic connection between his brain and ours, in that we have within our own brains a parallel to what is happening inside his brain. By becoming aware of these parallels in our own minds, we have some sort of understanding that is more experiential than simply observing his behavior.

biology, Philosophy none

Deepwater Horizon Oil Spill

May 19, 2010 1 comment

This oil spill in the Gulf of Mexico has been in the news a lot lately. Recently, I came across this satellite photograph from NASA, which shows the oil heading southeast in a long stream. There’s a lot of speculation on what will happen in the days to come if the spill isn’t capped soon. Where will the oil go? Which areas will be affected?

Satellite Photo Showing SpillHere’s a map showing the topology of the sea floor where the Deepwater Horizon was located. As you can see, the site is near a steep incline, where the continental shelf drops off sharply towards the sea floor. The depth of the sea floor was around 5000 feet.

Sea Floor at Deepwater Horizon

I’ve come across a bunch of comments at various websites, with some people saying “oh well, the oceans are huge, so what if we have a spill? If you consider the amount of oil compared to the vast volume of the oceans, it is so tiny it doesn’t matter”. This kind of talk seems singularly uninformed at best and deliberate distortion of the facts at worst to me. It’s clearly obvious if you follow the news at all, that the spill isn’t being distributed evenly among the oceans. Tar balls and oil are appearing on the Louisiana coast. And as the satellite picture from NASA shows, the oil is definitely being channeled in a very specific direction. So I thought to write this note to explain what is happening, and what we might expect in the days to come.

In order to understand what’s happening to the oil as it leaks out, we need to understand water currents and wind directions in the Gulf of Mexico.  These can be summarized as follows:

  1. There is a deep water current that enters the Gulf of Mexico from the south, loops through the Gulf, and then exits through the Florida Strait and curves northwards along the east coast of the US, as the Gulf Stream.
  2. The prevailing winds in this area are the Westerlies, or anti-trade winds, which blow from south west to north east. Winds do not affect deep waters, but they do in fact produce currents in surface waters. It might seem intuitively right that the surface water current should be in the same direction as the wind, but this is not so. In fact, surface water currents flow in a direction 90 degrees to the right of the wind direction, because of a phenomenon known as Eckman Transport. Since the prevailing winds in this region are southwest to northeast, surface currents induced by the winds flow northwest to southeast.
  3. The movement of the oil itself is subject to the Coriolis Effect. This is an effect which happens due to the west to east rotation of the Earth. Air or water or oil flowing in a fluid medium is affected in that its path curves westwards if the flow is towards the equator, and curves eastwards if the flow is away from the equator.
  4. The oil leak is occurring at the bottom of the ocean. The oil rig collapsed to the sea floor. The leaks are in the valve at the sea bed, and also in the riser pipe which is now lying collapsed on the sea floor. So the oil is being released at the sea floor, and then rising slowly to the surface. Therefore, since this oil is traversing the entire depth of the sea, from the sea floor to the surface, it is affected by both deep water and surface currents.

You can see these things in this diagram I made:

Deepwater Horizon Oil Slick

Notice the deep water current displayed in tan. This current enters the Gulf of Mexico from the south, loops around the Gulf, and then exits around Florida, only to swing back north and proceed along the eastern seaboard as the Gulf Stream.

Next, consider the winds, shown in yellow on the map. These are the Westerlies, or anti-trade winds. At these latitudes, they blow from southwest to northeast (as an aside, this is why “weather” in the form of storms tends to move from southwest to northeast in the continental US). Because of these winds, the movement of surface water is from northwest to southeast, as shown by the orange arrow. This is because of Eckman Transport, which tends to push water 90 degrees to the right of the wind direction. Remember, this represents surface water only, since the wind does not affect deep water.

Now in the light of these factors, look at how this oil slick has evolved over time:

Evolution of Oil Slick

These are four satellite images taken by NASA, from May 9th, 10th, 11th and 17th. Note that the images have not been equally scaled. Specifically, I zoomed out on the May 17th image to include the long tail.

As you can see, the slick slowly elongates in a north-south direction, and develops a “tail” pointing south. Between May 11 and May 17, the tail grows enormously, curving southeast. What could explain this effect?

If you look at the diagram I made earlier, you can see that the slick was slightly north of the loop current. The position of the loop current isn’t fixed, it has some daily/weekly variation. During early May, satellite imaging showed that the northernmost extent of the loop current was about 50 miles south of the oil spill, though the strongest currents were about 80 miles south. Since then, as we’ve seen in the satellite maps, the spill has extended far southwards. The satellite image from May 17th shows the slick extending 100+ miles south of its origin. This would put it well within the range of loop current, even if the loop current has shifted somewhat in this time.

So far, BP is still saying that the oil has not entered the loop current. There is still some doubt about this, but some scientists think it may already have entered the loop circulation. We will probably know for sure in a day or two.

Here is how I think the slick has proceeded:

  • Oil leaking from the sea floor rose up and encountered local currents. Since the leak origin was fairly close to the shore where currents are quite turbulent, it initially spread pretty randomly, forming a large patch offshore.
  • As oil continued to pump out from the leak and the volume of the leak increased, some of it drifted southwards. It acquired a slight easterly curve, because surface currents move in a direction 90 degrees to the right of the prevailing winds, due to Eckman Transport. The prevailing winds in this area are the anti-trade winds, or westerlies, which blow from southwest to northeast.
  • This could very well explain the southeastward trajectory of the slick, without needing to invoke the loop current. However, the fact that it’s spread so far south and is either in or very close to loop current trajectory, means that there is a good chance that at least the tail end of it is being pulled along by the loop current, which would carry it eastwards at this point. The sudden sharp bend it makes at the very southern end also suggests that something else happened at this point – perhaps that something else was the slick being drawn into the loop current.

If the slick hasn’t been drawn into the loop current, it seems almost certain that it will, since it’s so very close.

Future Expectations

The size of the spill is under debate. BP has stated that it’s about 5000 barrels per day, but independent estimates from other scientists say that it could be as much as 70,000 barrels per day. The fate of the spill depends upon its size, which means how much oil is being spilled per day, and how many days it continues to flow before it’s capped.

If a substantial amount of oil leaks out, where will it go? As you can see in the maps, the deep water currents loop around the Gulf, and head north along the Gulf Stream, which passes by the east coast of the US. Oil that gets caught in this current and doesn’t make it to the surface until much later may therefore follow this path and only surface off the east coast of Georgia or the Carolinas. But this would take a lot of oil, and perhaps there won’t be so much.

The more immediate danger is to the Florida Keys and the Bahamas, as well as the north coast of Cuba. Because the loop current stays pretty far away from the west coast of Florida, it seems unlikely that much oil could end up there. But it comes very close to land when the current passes out of the Florida Strait. It has to pass through a triangle formed by the Keys to the north, Cuba to the south, and the Bahamas to the east. Those are the likely danger spots.

If there are strong winds in this period, driving strong surface currents, then the Bahamas and Cuba are probably even worse off, since wind-driven surface currents will be in a southeasterly direction. By the same token, if the oil makes it into the Gulf Stream and heads up the east coast of the US, winds may cause the coasts of Georgia and the Carolinas to be spared, since surface currents would push the oil away from the shores.

It’s also important to remember that the paths of these currents and even the wind directions aren’t always constant. There is day to day variation, as well as seasonal variation now that summer is coming. So these predictions are only approximate.

I also wrote a short article on ocean currents which you can read here, if you’re interested.

EDIT: There were some news stories recently that tar balls have washed up in the Florida Keys. These are not from the Deepwater Horizon spill. As you can see from the maps, the spill hasn’t reached anywhere near the Florida Keys so far. The Gulf of Mexico has a lot of oil rigs and many spills have happened here before, so it’s not uncommon for tar balls to show up on any of these coasts.

current news, science , ,

Australopithecus sediba – a new human ancestor?

April 8, 2010 No comments

An interesting story has been making the rounds in the science press today – the unveiling of new hominid fossils, by Lee Berger, of the University of Witwatersrand in South Africa. In two related articles in Science, Berger and colleagues have tentatively classified these as belonging to a new species: Australopithecus sediba.

The fossils represent two individuals – a juvenile male and an adult female, and there is some evidence that these two individuals were associated in life (perhaps mother and son). The skeletons are remarkably complete, even in comparison to such well known specimens as Lucy. An almost complete skull, mandibles, part of a pelvis, and a complete collar bone are included, as well as limb bones, fragmented ribs, and some vertebrae.

Fossils of two individuals (juvenile male on left, adult female on right) of Australopithecus sediba. From Berger, et al "Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa" Science, April 9, 2010.

The fossils date from between 1.8 to 1.95 million years old, which makes them very exciting, since fossils from this period are rare. This is also the period when the genus Homo differentiated from australopithecines, and may therefore cast some light on the otherwise hazy ancestry of Homo.

The original paper in Science (full text available with free registration at their site) describes the fossils in great detail, but the interesting features seem to be:

Skull: A. sediba is different from earlier australopithecines in being less prognathous, having a generally thinner and lighter jaw, smaller teeth. These are all characteristics trending towards Homo. In contrast, the cranial capacity has been estimated to be about 430 cc, which is smaller than the lowest currently accepted range of early Homo (510 cc).

Postcranial: The rest of the skeleton is much like earlier australopithecines, with two significant differences. First, the legs are quite long, making A. sediba somewhat taller than earlier australopithecines (estimated height about 4.5 feet). Second, the pelvis appears to be more adapted for walking. Again, both of these traits seem to foreshadow Homo. In contrast, the arms are long and australopithecine-like, as is much of the rest of the skeleton.

Australopithecus sediba skull. From Berger, et al "Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa", Science, April 9, 2010.

Given this mix of australopithecine and early Homo traits, it was not clear whether these fossils represent a late australopithecine or an early Homo. The authors have chosen to classify them as a new species of Australopithecus, and they go over their reasons in great detail in the paper. I am not qualified to comment on their merit, but from a quick glance at various commentaries on the paper it seems that the anthropological community is divided on the issue.
So why is this issue important and what does it all mean? Well, first we need to understand the context of this discovery. The larger context is the appearance of Homo.  This is not well understood. The earliest member of the genus Homo is generally considered to be Homo habilis. According to the fossil record, H. habilis appeared about 2.3 million years ago, and is hence older than these fossils. However, because of the fragmentary nature of the early remains, it is difficult to be sure that the early remains do in fact represent Homo. The better known and more complete skulls, such as OH 7, OH 24, KNM ER 1805 and KNM ER 1813, are all about 1.7 to 1.9 million years old. For a while, anthropologists did not even agree whether H. habilis represented a separate species, preferring to classify skulls as either australopithecine, or those of H. erectus. These days, H. habilis is more accepted, but because of the wide variation in H. habilis fossils, many people believe that they represent more than a single species. H. rudolfensis is possibly a second ancient species of Homo, with one skull (KNM ER 1470) being dated to about 1.9 million years old.

Secondly, there is the matter of the persistence of H. habilis. According to the fossil record, H. habilis persisted as late as 1.4 million years ago. This means that for about half a million years, H. habilis co-existed with H. erectus, which is generally reckoned to have descended from H. habilis. Of course, this can be explained by punctuated equilibrium (some population of H. habilis, due to local conditions, rapidly evolved into H. erectus, but other populations of H. habilis continued to exist contemporaneously for a long time). However, if there were in fact habitats for H. habilis to survive so long, it weakens the argument for rapid speciation into H. erectus. Again, this is not a definitive argument against the descent of H. erectus from H. habilis; most anthropologists do in fact believe that H. erectus is descended from H. habilis. It’s just one of those complications that needs to be better understood, and it increases the complexity of the landscape so far as different hominid species are concerned, in which humans involved.

Another point relevant to this discussion: H. habilis had a cranial capacity about half that of modern man, but much larger than australopithecines. Typical numbers are about 650-700 cc for adults, and the low end is about 510 cc. A. sediba has a cranial capacity of about 430 cc, which puts it below the range for H. habilis. This was one of the reasons why the authors preferred to classify the new fossils as australopithecine, rather than human (in anthropology, “human” typically refers to members of the genus Homo).

So what do these fossils say about human evolution? The answer is not clear, but several possibilities can be raised:

  1. A. sediba is the direct ancestor of humans. This seems to be one of the possibilities that the authors lean towards, though by no means do they assert this as fact. To support this, they make certain claims and offer some reasoning. The claim is that previous to the discovery of these fossils, the best candidate for the ancestor of Homo would be A. africanus. Berger has made this claim before, though it is not widely accepted by other anthropologists. Since A. sediba seems to be intermediate between A. africanus and H. habilis in terms of physical characteristics, the argument could be made that the line of descent is A. africanus to A. sediba to H. habilis. The same theory of punctuated equilibrium could be used to explain the persistence of A. sediba to 1.8 million years ago, even though H. habilis appeared 2.3 million years ago. The chronology would then make sense: A. africanus (3.0 to 2.4 million years ago), A. sediba (? to 1.8 million years ago), and H. habilis (2.3 to 1.4 million years ago). This would mean that A. sediba originated somewhere between 2.4 to 2.3 million years ago, which is quite possible, though of course, the only specimens we have are these two fossils dated about 1.8 million years old.
  2. A. sediba is a cousin instead of an ancestor. In this scenario, both A. sediba and H. habilis shared a common ancestor (some other species of Australopithecus). Similarities between A. sediba and H. habilis (such as the more human-like pelvis and skull) could be explained by either positing a more human-like australopithecine ancestor, which is yet to be discovered, or by convergence. After all, the climate and vegetation were changing, grasslands were becoming more common, and these changes might very well have affected two related species which shared the same habitat.
  3. A. sediba is really not an australopithecine, but some ancestral species of Homo. In favor of this theory are a few things – the relatively young age (we know that H. habilis and probably H. erectus were already around at the time of these fossils), the previously mentioned wide variation in H. habilis specimens (which makes it more acceptable to think that this is just yet another variant), and the many human-like characteristics of these new fossils. Against that is the fact that the cranial capacity is smaller than we had previously accepted as the lower limit for Homo, and that the skeleton retains more primitive characteristics than are seen in Homo.

So at this point, it’s hard to say what the true situation is. If we classify these fossils as Homo, it could easily start a debate over whether earlier fossils are correctly classified. As I mentioned earlier, some of the older H. habilis fossils are quite fragmentary, and there have been arguments made in the past that some of them should really be considered australopithecines.

One problem in anthropology is that because of the scarcity of fossils, a lot of classifications are based on “type specimens” rather than any solid statistics. There is a large range of variability in any population (consider humans today, for example). In the absence of a sufficient number of fossils to quantify the extent of variability, anthropologists pick certain fossils with well-defined characteristics as “type specimens”, or “typical” of a certain species. Then when new fossils are found, their classification becomes a matter of relating them to known type specimens, setting up a chain of inferences. If you knock out a link in that chain (for example, declaring some early H. habilis specimen to be australopithecine instead), then there is a cascading effect on the classification of many other specimens, which were in part classified based on some similarity to these fossils.

In short, if we classify the new fossils as yet another variant of H. habilis, we will need to do some rethinking about other early specimens of H. habilis. Rethinking is always good, so this is not a problem. In fact, I am sure that right now there are many anthropologists busily thinking and writing away on just such issues.

Better answers will have to await more fossils. In the meantime, we have added to the richness and complexity of human evolution, and specifically to the period around 1.8 to 2.0 million years ago, which happens to be relatively fossil-scarce. We now have yet another species wandering around Africa at this time period, which is a critical period for the emergence of H. erectus, and the branch of the evolutionary tree leading to us.

EDIT [4/10/2010]: Scientific American has a story up quoting Donald Johanson (the discoverer of Lucy), in which he opines that (1) these fossils have been misclassified as Australopithecus, they are really a new species of Homo, and (2) he thinks it unlikely that this species descended from Australopithecus africanus.

anthropology, biology , ,

The Neanderthal Predation Theory

February 16, 2010 5 comments

I happened across this site, which belongs to Danny Vendramini, a TV producer and scriptwriter, with an interest in evolutionary biology.

Neanderthal face reconstructed by Vendramini, Copyright themandus.org

He has written a book called “Them and Us”, in which he propounds the hypothesis that Neanderthals were:

  • Very different looking from most modern representations – much uglier, hairier, and far less human-like.
  • That they were brutal, intelligent, tool-using predators, who preyed upon modern man in the areas where they came in contact, specifically, the Levant.
  • That being the prey of Neanderthals was the most important factor in human evolution, and that it was responsible for the flowering of art and sculpture, the technological innovations in the tool making industry, perhaps even the flowering of language – all of which happened around 40,000 to 50,000 years ago.
  • And not only that, it was responsible for the evolution of the human body type, including features that distinguish us from other apes, such as decreased hairiness, the development of a prominent and protruding nose, different body posture and gait, etc.
  • Finally, he lists a whole range of human behavioral traits, such as preference for symmetrical faces, fear of the dark, abominable snowman myths across various cultures, etc. as some sort of racial memory of Neanderthals, whom we fear and despise, because they preyed upon us.

Now at first read, this appears to be the work of a misguided though enthusiastic kook. He seems to have no formal qualifications in biology or paleo-anthropology, and is self-taught. He makes the first few chapters of his book available online, and from a quick read, he seems very dismissive of arguments that run counter to his thesis, for example, the loss of body hair in Homo sapiens. He mentions other theories, such as the thermoregulation during the transition from forest living to life on the savannah, but he dismisses them so hastily that it looks like he doesn’t really understand them all too well. Some of the examples he gives (such as big cats are predators, and some of them live in hot climates, why didn’t they lose their hair?) have reasonable answers in the literature, but he makes no mention of them. Instead, he pushes his theory, that we lost body hair because of sexual selection – we didn’t want to look like those ugly, murderous Neanderthals – it became a taboo to look like them.

Profile reconstruction of Neanderthal face, Copyright themandus.org.

Superficially, some of this may make sense. We certainly can’t rule out the role of sexual selection in the loss of body hair. But making the jump from “might be possible in a mundane way” to “it was a response to Neanderthal predation” is a very long stretch. He does this in many, many different areas, not just body hair.

Now I understand that he offers this as a hypothesis. He is not saying this is how it happened, just that this is how it might have happened. Which is fine, but the supporting evidence is very thin. Further, in his enthusiasm to bring in every possible argument to bear, he adds so much speculative and flimsy stuff that it makes it seem like he can’t distinguish between science and fantasy. To name a few, he finds some supposedly “universal” human traits such as xenophobia, preference for bathing and cleanliness, loyalty to the group, self-sacrifice, patriarchy, aggression, and many more, and ties them all into some imagined “prey psychology”, which developed as a result of humans being the victims of Neanderthals.

To be fair, he is not alone in this. Many so called “evolutionary psychologists”, or evolutionary biologists in general, make sweeping generalizations and assumptions, based on the flimsiest evidence. To me, this is an example of science turning into social narrative, the trivialization of science. You don’t need rigor and reasoning based on solid evidence, you don’t need to be cautious, to make no claim beyond the evidence – all you need to do is to tell a good story, preferably sensational enough to get picked up by the popular press, and give you your 15 minutes of fame.

Neanderthal with spear, Copyright themandus.org.

Part of it is the problem of generalists versus specialists. Evolutionary biologists or evolutionary psychologists (*shudder*) are generalists, tying together a lot of details from anthropology, genetics, sociology, psychology, etc. to make some broad claim. But in doing so, they often lack the specialized knowledge of each individual field – they lack sufficient knowledge to not over-generalize, and sometimes end up making silly blunders. They tend to trivialize and gloss over problems that are ambiguous and not resolved, picking the interpretation that favors their own theory, often not realizing that the foundation is very shaky.

And then there are those who disconnect with reality altogether, like Vendramini, when he goes off about connecting “fear of the dark” to nocturnal predation by Neanderthals or similar arguments. The pity is that he doesn’t seem to realize what he’s doing. In trying to add weight to his arguments, he is throwing in every last thing he can think of. And so he’s mixing in things that have some weight and credibility (like, we don’t really know exactly what Neanderthals looked like, perhaps they were more ape like than modern representations; or we don’t know exactly what human-Neanderthal interactions were like, there may well have been violence), with things that are utter nonsense, such as fear of the dark. So the good stuff gets mixed with the bad, and taints everything as trash. Further, it creates a bad impression of the writer, in that he doesn’t seem to be able to distinguish science from fantasy.

To top it all, he really appears serious about this airy-fairy stuff. He has another theory (and another whole website devoted to it), which propounds something he calls “teem theory”. In simple terms, the theory is that nasty stuff that happens to us and creates powerful negative impressions gets imprinted on non-coding regions of our DNA, and thus becomes heritable to future generations. This is what he uses to explain things like fear of the dark, xenophobia, etc. – that these bad experiences with homicidal Neanderthals became imprinted on our DNA, and continues to manifest in modern behavior.

That would be a whole other discussion and a whole other blurb on this blog, so I don’t want to get into it at this time. Briefly, he looks at instinctive behavior of a certain kind, such as certain animals instinctively recognizing their predators and avoiding them, concludes that such behavior must be coded into the DNA, since it’s untaught and not learned, therefore DNA must provide a mechanism for coding our fears. Such ideas ignore a whole realm of evidence, that a huge range of predator-avoidance behaviors are in fact learned, and that interpreting specific instances where they don’t appear to be learned is over-generalizing. Yes, there are instincts that are heritable, but the actual mechanism of how they work, what exactly is coded in the DNA, are very much unknown. Making it out to be something as specific as xenophobia is very imaginative, but poor science.

Neanderthal, hunting. Copyright themandus.org.

I see evolutionary biologists make similarly specific claims, that generosity and altruism are hard coded in our genes – all sorts of stuff like that. I consider it all very unlikely, an over-specification of something much broader. Perhaps what we are inclined for is social cohesiveness, being social animals, and specific instances of it are just a manifestation, they are not individually hard coded. It’s possible to take a population of rats, breed for either aggressiveness or docility, and in a very few generations end up with two distinct populations that are behaviorally very different in that respect. It’s been done. It doesn’t show anything very specific, other than that “fight” responses and aggression are more marked in one population than another, perhaps through some simple hormonal trigger. Going from that to very specific theories about brain centers dealing with aggression, or “cooperation” or something similar is not warranted by the evidence.

While I find his theory not convincing, it did make me wonder about a few things. What exactly do we know about how Neanderthals looked like? Forensic recreations based on bones have to be somewhat an exercise in guesswork, on prior knowledge. I agree with his point that they are not at all comparable to forensic recreations of humans. After all, we have a huge body of knowledge of what humans are supposed to look like, so our guesses are founded in a great deal of prior information. We don’t have a similar body of knowledge of what Neanderthals looked like, so our reconstructions may err on side of making them look too human (or conversely, less human) than they really were.

We have no casts of their soft tissues. We don’t know how hairy they were. We don’t know how much their noses protruded. We don’t know how big their eyes were, how erect their spines, how prominent their musculature. For all of these things, we make educated guesses, but some guesses are more educated than others. For example, the musculature is hinted at by the shape of the bones, the sites of attachment of various muscles to the bones. So this kind of guess can be trusted to a greater extent than say, the guess about how hairy they were, or what their skin was like, or how symmetrical their faces were.

So our picture can’t be very precise, there is some range of possibilities, within the constraints set by the bones. Just how wide that range is, I don’t know, and I wonder if they could have looked like the pictures on his web site. I don’t personally know of any physical evidence that goes against his reconstruction. Perhaps some more knowledgeable people can add to this. But it occurs to me that if Neanderthals looked sufficiently ape-ish, sufficiently non-human, it would explain why we find no evidence of human-Neanderthal interbreeding in the genomes. It would discourage (though not necessarily prevent) the two species from interbreeding.

I look forward to more information which should become available as the Neanderthal genome is fully sequenced and annotated.

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