(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

There is no doubt that Darwin’s ideas about evolution by natural selection carry a huge emotional impact. For many people the idea that “we are descended from apes” is too awful to contemplate and is sufficient reason alone to dismiss any claim that natural selection holds the key to understanding how we came about. (Of course, we are not descended from apes. The more accurate statement is that apes and humans share common ancestors, making them our cousins, but even this refinement does not take away the stigma that supposedly comes with being biologically related to animals such people consider inferior.)
[Read more…]

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

Richard Dawkins in his book The Ancestor’s Tale (2004) tells a fascinating story. He models his book on a journey that, rather than moving through space to a particular destination, is moving in the temporal dimension, going steadily back in time. He calls it a “pilgrimage to the dawn of evolution.” He starts with present day humans and follows them back into history. One reason he gives for going back in time instead of starting at the beginning and going forwards as is more commonly done is to avoid a common trap of perception. When you tell the story forwards, it is hard to avoid giving the impression that life evolved purposefully, that human beings were somehow destined to be. This is counter to evolutionary theory that says that evolution is not directed towards any goal. It tells us how the present emerged from the past. It does not tell us how the future will emerge from the present.

Dawkins points out that the another advantage of telling the story backwards is that you can choose any of the current species and go back in time and tell pretty much the same story.

As I have mentioned earlier, we quickly (in just 2,000 years) reach the time when the most recent common ancestor lived and soon after that (about 5,000 years ago) reach a point when all our ancestors were identical.

But this convergence of ancestry is not just for humans, it is for all species. If we go far enough back in time, even my dog Baxter and I share the same ancestor, which I find a very appealing notion.

Anyway, here is a concise summary of the landmarks on this pilgrimage back in time, along with some other landmarks.

[Read more…]

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

In a previous post, I discussed the fact that although all of us have the identical set of ancestors who lived just 5,000 years ago, this does not mean that we have the same genes. The fact that we are different is due to the fact that if most of the mating occurs within a group, then this can result in certain features becoming emphasized. In extreme case, this initial isolated mating pattern can result in a new species being formed that cannot mate with other groups that it could have done in the past.

I had always thought that the two organisms belonged to different species if they were biologically different enough that they either could not produce offspring or, as in the case of mules produced by horses and donkeys, the offspring were infertile and thus not able to reproduce.

But I learned from Richard Dawkins’ book The Ancestor’s Tale (2004) that two things can be considered different species even if they are perfectly capable of producing fertile offspring. All that is required for them to be considered to be different species is that they are not found to mate in the wild for whatever reason.

Normally, this happens when there is some kind of barrier that separates two groups of the same species so that they cannot mate. “No longer able to interbreed, the two populations drift apart, or are pushed apart by natural selection in different evolutionary directions” (p. 339) and thus over time evolve into different species. But the separation can also occur due to sexual selection.

He gives a fascinating example of this on page 339. He describes experiments done with two species of cichlid fish. The two species live together in Lake Victoria in Africa and are very similar, except that one has a reddish color and the other bluish. Under normal conditions, females choose males of the same color. In other words, there was no hybridization between the two colors in the wild, thus meeting the requirements for being considered different species. But when experimenters lit the fish in artificial monochromatic light so that they all looked dirty brown, the females no longer discriminated among the males and mated equally with both kinds of males and the offspring of these hybrids were fully fertile.

He also describes ring speciation using the example of the herring gull and lesser black-backed gull (p. 302). In Britain, these two kinds of birds don’t hybridize even though they meet and even breed alongside one another in mixed colonies. Thus they are considered different species.

But he goes on to say:

If you follow the population of herring gulls westward to North America, then on around the world across Siberia and back to Europe again, you notice a curious fact. The ‘herring gulls’, as you move around the pole, gradually become less and less like herring gulls and more and more like lesser black-backed gulls, until it turns out that our Western European lesser black-backed gulls actually are the other end of a ring-shaped continuum which started with herring gulls. At every stage around the ring, the birds are sufficiently similar to their immediate neighbors in the ring to interbreed with them. Until, that is, the ends of the continuum are reached, and the ring bites itself in the tail. The herring gull and the lesser black-backed gull in Europe never interbreed, although they are linked by a continuous series of interbreeding colleagues all the way around the other side of the world.

Dawkins gives a similar example of this kind of ring speciation with salamanders in the Central Valley of California.

Why is this interesting? Because it addresses a point that sometimes comes up with skeptics of evolution. They try and argue that there is a contradiction if we had evolved from an ancestor species that was so different from us that we could not interbreed with that species. Surely, the argument goes, doesn’t speciation imply that if species A evolves into species B, then must there be a time when the child is of species B while the parent is of species A. And isn’t that a ridiculous notion?

The herring gulls and salamanders are the counterexamples in space (which we can directly see now) of the counterargument in time (which we can only infer). What it says is that as descendants are produced, they form a continuum in time. Each generation, while differing slightly, can interbreed with its previous generation, but over a long enough period of time, the two end points of the time continuum need not be able to interbreed.

Thus it is possible for an organism to be intermediate between two species.

Coming back to the question of why we look so different if we all shared common ancestors so recently, it is likely that the kind of selectivity practiced by the cichlid fish has resulted in certain features being shared by groups that interbreed within a restricted domain bounded by distance and geography and culture, although the process has not become so extreme that we have formed into distinct species.

I apologize for boring those readers who had had a much more extensive biology education than I have because all these things which I have been writing about recently on evolution must be well known to them. But I find all this perfectly fascinating and novel.

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

In the previous post in this series, I reported on a paper by Douglas L. T. Rohde, Steve Olson, and Joseph T. Chang and published in the journal Nature that said that if we go back about 5,000 years, the ancestors of everyone on Earth today are exactly the same. This date is called the IA point, where IA stands for ‘identical ancestors’.

One question that will immediately arise in people’s minds is that if all our identical ancestors lived so recently, how is it that we look so different? If you take four people from China, Sri Lanka, Sweden, and Malawi, they are usually fairly easily distinguishable based on physical appearance alone, using features such as skin color, hair, facial features, etc. How could this happen if they all had identical ancestors as recently as 5,000 years ago?

The answer lies in the fact that while it is true that we all share the same ancestors, it does not mean that we all received that same genetic information from that common ancestral pool.

It is true that each of us gets exactly half our genes from our fathers and half from our mothers. But when we pass on our genes to our children, while each child gets exactly half from each parent, that does not imply that they get exactly one quarter from each grandparent. What is true is that on average each child gets one quarter of the genes from each grandparent.

The reason for this is because when a sperm or egg is formed, the genetic information (say in the egg formed in the mother) that goes into it undergoes a process of recombination in which the genes the mother obtained from her parents get mixed up before the transfer into the egg. It is thus theoretically possible, though unlikely, that a child will have zero genetic information from one of her four grandparents.

[Read more…]

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

In the previous post, I discussed the calculation of Joseph T. Chang in which he showed that the most recent common ancestor (MRCA) of all the people living today lived around 1100 CE, while around 400 CE everyone who lived then was either the ancestor of all of us or none of us. The date when this occurs is called the IA (identical ancestor) date.

Chang got these results assuming that the population is constant over time at some value N, that the generations (with each generation lasting 30 years) are discrete and non-overlapping (i.e. mating took place only between males and females of the same generation), and that mating was random (i.e., there was equal probability of any one male in a generation to breed with any female of that same generation.)

What happens to these dates if you relax these unrealistic assumptions? One practical difficulty of going to more realistic models is that exact mathematical calculations become impossible and one has to resort to computer simulations. This was done by Douglas L. T. Rohde, Steve Olson, and Joseph T. Chang and their results were published in the journal Nature (vol. 431, September 30, 2004, pages 562-566).

[Read more…]

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

In order to find the date of the most recent common ancestor (MRCA) of all the people living today, Chang started out by constructing a simple mathematical model of population mixing. (See <the previous two posts for some background.)

He assumed that the population is constant over time at some value N. He assumed that the generations are discrete and non-overlapping (i.e. mating took place only between males and females of the same generation). He also assumed that mating was random. In words, that there was equal probability of any one male in a generation to breed with any female of that same generation.

Of course, none of these assumptions is realistic. The size of a population changes with time for a variety of reasons. People also do not mate at random, being more likely to choose from those nearby, and from people within their same groupings whether those be economic, social, cultural, class, religion, etc. And cross-generational matings are not uncommon.

But for the purposes of mathematical simplicity, and to get a rough idea of the timescales involved, Chang’s simple model is worth looking at because it enables him to do a rigorous mathematical calculation for the date of the MRCA. What Chang found, to everyone’s surprise, was that the date of existence of the MRCA of all the humans living today was very recent. He found that the number of generations that one has to go back to get an MRCA was log₂N, which stands for the logarithm to base 2 of the population size N. He further found that even though this was a statistical calculation, the result was very sharply peaked about this value, meaning that it was highly unlikely that the MRCA date would differ by even 1% from this value.

If you take a population N of size one million, the number of generations you have to go back to get to our MRCA is only 20. If you take a population of one billion, our MRCA existed about 30 generations ago, or around 1100 CE (for an average generation span of 30 years).

So according to Chang’s model, our MCRA lived far more recently than anyone had imagined, and way more recently than Mitochondrial Eve (~140,000 years ago) or Homo erectus (~250,000 to one million years ago). It is fascinating to think that every single one of us living today share at least one ancestor who was living in the Middle Ages. I have been wondering who that person was, and where he or she lived, and what he or she was like.

But that was not the only surprising thing that Chang found. Once you get an MRCA, then that person’s parents are also common ancestors for all of us, as are his/her grandparents and great-grandparents, and so on. In fact, just as the number of our ancestors increase rapidly as we go back generations, so do the number of our common ancestors once we go further back than our MRCA.

Chang found that if you go far enough back, you reach a point when every single person living at that time is either the ancestor of all of us or none of us (i.e., that person’s line went extinct). In other words, there is no one who lived at that time who is the ancestor of just some of us. It is an all-or-nothing situation with an 80% chance of the former and 20% chance of the latter. To be perfectly clear about this (because it is an important point), at one particular time in the past, 20% of the people who lived at that time have no descendants alive today. Each one of the remaining 80% of the people has the entire world’s population today as descendants.

So all of us have the identical entire set of ancestors who lived at that time. Chang calls that time the IA (standing for ‘identical ancestors’) time.

Using the same assumptions as before, Chang’s calculations for the number of generations to reach the IA date is 1.77log₂N. For a billion people, it amounts to about 53 generations ago. This works out to 675 CE for a generation span of 25 years and 410 CE for 30 years.

It seems amazing (to me at least) that all of us living right now have identical ancestors that lived so recently, roughly around the period when the Prophet Muhammad lived (570-632 BCE). In fact Mark Humphrys, a professor of computer science at Dublin City University in Ireland using a different technique estimates that Muhammad, the founder of Islam, appears on the family tree of every person in the Western world. (Thanks to commenter Steve Lubot for this link.) But it is important to realize that there is nothing special about Muhammad or about the Western world.

So taking Chang’s results at face value, all the people who fight over religion today are highly likely to be descendants of each and every religious leader who lived from the time of the Prophet Mohammed and earlier. So in a very real sense, they are killing their own cousins.

Of course, Chang’s results were based on a highly simplified mathematical model. In the next posting in this series, we’ll see what happens when we create more realistic scenarios of population changes and mating patterns.

POST SCRIPT: File under things I don’t understand

What is the book most often stolen by shoplifters at bookstores? The Bible.

The article also seems to suggest that shoplifting is a routine activity among young people of all social classes in the US, almost a rite of passage. Could this be true?

(My latest book God vs. Darwin: The War Between Evolution and Creationism in the Classroom has just been released and is now available through the usual outlets. You can order it from Amazon, Barnes and Noble, the publishers Rowman & Littlefield, and also through your local bookstores. For more on the book, see here. You can also listen to the podcast of the interview on WCPN 90.3 about the book.

Because of the holidays and travel overseas where internet access will be sporadic, I am taking some time off from writing new posts and instead reposting some of my favorites (often edited and updated) for the benefit of those who missed them the first time around or have forgotten them. New posts will start again on Monday, January 18, 2009.)

In 1999, Joseph T. Chang published a very interesting paper in the journal Advances in Applied Probability (vol. 31, pages 1002-1026) titled Recent Common Ancestors of all Present-Day Individuals. To understand the paper, it helps to reflect a little on the mathematics of genealogy.

One rock-solid fact of ancestry is that every person has two, and only two, biological parents. They in turn each have two parents so going back two generations gives a person four ancestors. If you go back three generations, you have eight ancestors and so on. Each generation that you go back doubles the number of ancestors in the previous generation.

We all know that this kind of geometric progression results in one reaching very large numbers very soon and by thirty generations, the number of ancestors one has acquired has ballooned to over one billion. In forty generations, we have over one trillion ancestors.

Conservatively allowing for each generation to span 30 years (which is a little large), going back thirty generations takes us back to about 1100 CE where the population was only about 300 million, and forty generations takes us back to 800 CE where the population was less than 200 million. (If we take each generation as averaging 25 years, 30 generations takes us back to 1250 CE when the population was 350 million and in forty generations we reach 1000 CE where the population was 200 million.)

Having more ancestors that the total population leads to the clear conclusion (which is not that surprising once one thinks about it) that all our ancestors cannot have been distinct individuals but were shared. In other words, my great-great-great-grandfather on my father’s side had to be the same person as my great-great-grandfather on my mother’s side, or something like that.

But the interesting point is that each one of us has over a trillion ancestors in just forty generations, which must mean that you, the reader, and I must have some shared ancestors as recently as a thousand years ago, unless the huge population of your ancestors were entirely isolated from the huge population of my ancestors, with no mixing at all between them. Given the large numbers of ancestors involved, this kind of isolation seems highly unlikely unless there was some major geographical barrier separating the populations. We know that this is not the case, since by 1000 CE people were able to travel pretty much all over the inhabited world, and all you need is just one person from my group of ancestors mating with one person from your group of ancestors to break the isolation, because then all the ancestors of that pair are shared by both of us.

So if you and I (as just two people) share common ancestors, then we can see that if we go back far enough in time, all of us living on the world today should share at least some common ancestors. One question that Chang was investigating was that of finding out, from among all the common ancestors, when the most recent common ancestor (MRCA) of all the people living in the world today lived.

The concept of the MRCA is interesting. My siblings and I share all our ancestors so the MRCA is not meaningful. The MRCA of my first cousins and I are the one set of grandparents that we have in common. As my cousins get more distant, the MRCA goes back in time but it is not hard to see that an MRCA must exist for those whom we commonly refer to as ‘blood’ relatives.

For those who take the Bible literally, definite common ancestors would be Noah and his wife. Since everyone except the two of them and their sons and their sons’ wives were killed by god in the flood, all the current inhabitants of the world should have Noah and his wife as common ancestors. But they may not be the MRCA because their sons’ descendants may also have intermarried, creating a more recent MRCA.

For those of us who accept evolution, it is not hard to get our minds around the concept of all of us having an MRCA, and the fact that we must have a shared ancestor in an earlier species has a rigorous proof (see the previous post) and is fairly easily accepted. What people thought was that this person probably existed around the time of our ancestor Homo erectus, perhaps a million years ago.

But when analysis was done on the mitochondrial DNA, and its mutation rate was used to triangulate back to the time when all the current mitochondrial DNA converged on a single individual, people were surprised that the calculations revealed that the MRCA deduced from this analysis, (nicknamed Mitochondrial Eve) lived much more recently, only about 140,000 years ago, probably in Africa. All present-day mitochondrial DNA is descended from this single individual. A similar analysis can be done for the Y chromosome to trace back to ‘Y-chromosome Adam’, and that person lived about 60,000 years ago (Richard Dawkins, The Ancestor’s Tale (2004), pages 52-55).

But as Dawkins cautions (page 54):

[I]t is important to understand that Eve and Adam are only two out of a multitude of MRCAs that we could reach if we traced our way back through different lines. They are the special-case common ancestors that we reach if we travel up the family tree from mother to mother to mother, or father to father to father respectively. But there are many, many other ways of going up the family tree: mother to father to father to mother, mother to mother to father to father, and so forth. Each of these pathways will have a different MRCA.

Our normal concept of genealogy traces back through both sexes and thus the web of ancestral pathways becomes increases tangled and complex as you go back in time. As a result there is a greater chance of my ancestral pathways intersecting with the ancestral pathways of other people. It is thus reasonable to suppose that if we look at all these pathways, we will find a more recent MRCA than Mitochondrial Eve or Y-chromosome Adam. But this kind of calculation using mutation rates is not easy to do for things other than sex-specific chromosomes like mitochondrial DNA.

In order to try and fix the date of existence of the MRCA of everyone living today using the lines through both sexes, Chang used the tools of mathematics and statistics rather than genealogical charts or DNA mutations. And he found something very surprising, to be discussed in the next posting.

POST SCRIPT: Praying for defeat of health care

Congressperson Michele Bachmann (R-Loony) leads a group of people in a creepy prayer. Watch Tony Perkins, head of the Family Research Council that organized the event, drink some coffee in the middle of the prayer. You shouldn’t have done that, Tony. Jesus just hates it when people eat and drink when they should be groveling before him. Actually, Tony seems to show a remarkable lack of enthusiasm, not standing up and holding hands at the end.

If the health care legislation is defeated, they will no doubt attribute it to their prayers. But what if the health care bill that they are earnestly praying against actually passes, what will they conclude? That god wanted it to pass? Nah. That god was playing golf at that time and so missed their prayer? Nah. That god wanted to punish Tony Perkins for drinking coffee during the prayer? Nah.

Like all religious people when their prayers are never answered, they will ignore the issue (since no one usually asks them because the faith of religious must not be disturbed) or they will say that god agrees with them (isn’t it amazing that god agrees with every religious person?) but that he has a cunning plan that we cannot fathom.

It is all so predictable.