Chromosome 2

Posted on July 29, 2012 by Michael

It has been proposed and well evidenced that human chromosome 2 is the result of a fusion event between two chromosomes in our evolutionary past. Briefly, here is the evidence:

All great apes except humans have 24 pairs of chromosomes. We only have 23. That means we need an explanation for such a difference that dates back only a relatively short period of time (5-7 million years). As it happens, human chromosome 2 shows strong evidence of being two fused chromosomes. The way we know this is that all chromosomes have telomeres and centromeres. Telomeres are repeating units of DNA that serve to protect the ends (and therefore middles) of chromosomes, sort of like a good pair of shoes and a strong helmet. Centromeres are DNA units located somewhere between the telomeres of chromosomes, generally relatively close to the center. Their function is to help assemble the two parts of a chromosome during cellular replication and reproduction. In human chromosome 2, we see that there are actually two telomeres fused together in the center. There are also telomeres on the end, but between each end and the center are centromeres. That means we have three telomeres (one of which is fused) and two centromeres.

I bring this up because I was recently reading yet another excellent post by The A-Unicornist and he was dealing with this stuff:

ID is really nothing but an argument from ignorance – it claims that certain things simply cannot be explained by science, so it must be ‘best explained’ by a designer instead. Take for example this post from The New Creationist. I often point creationists to the Ken Miller video where he explains the Chromosome-2 fusion in humans, because it’s a perfect example of the theory of evolution making a falsifiable prediction that ended up being powerful evidence that evolution is true – something that ID has never done and in principle cannot do, which is why it will never be a science. Now, this “new creationist”, who incidentally sounds just as credulous as the old ones, argues that such a fusion is impossible – that the chromosome should never have been able to fuse at all.

Being that I’m not a biologist, I have no idea how to directly refute what he’s arguing. But it’s conspicuously odd that rather than, I dunno, ask a biologist or two (like, golly I dunno, write a letter to Ken Miller?), he simply frames his argument as though the unanswered question itself creates a major problem for the theory of evolution.

Since I’ve used chromosome 2 as an argument for evolution, I am familiar with the creationist responses. As such, I want to address what the blogger known as The New Creationist is arguing:

If the fused chromosomes in an end-to-end fusion are ripped apart by the centromeres during cell division and cells must divide to produce an embryo then how does an embryo develop with two previously fused but now ripped apart chromosomes? We know that the loss of just one chromosome would be lethal and here we have the loss of both of the two
fused chromosomes. If fused chromosomes do not make it through cell division then how could a fused chromosomal configuration be a result of common descent since there would be no descendants by a biological pathway. Such would be miraculous. Indeed, I believe it is a miracle not only because it can not be explained by any natural pathway but also because it is contradicted by experimental data.

What he is trying to say (and what he later says a little more clearly) is that two centromeres would cause division and assembly to occur in two separate places. This would be an all around mess that would prevent not only mitosis, but meiosis as well. So what could the solution be? Well, he answers it himself:

Now, it has been proposed that the deactivation of one of the centromeres in the fused chromosome would prevent the rupture and subsequent loss of the newly formed fusion…

And that is the case. One of the centromeres has been deactivated. One possible reason for this could relate to the fact that the area near the deteriorated centromere (the pericentromeric sequences) has gone through a large number of duplication events, but this isn’t known and requires certain confirming evidence around other deactivated centromeres. I don’t know if any significant research has been done in this area since the 2006 paper about chromosome 2.

The New Creationist continues:

…but this poses another equally lethal problem during the pairing off of homologous chromosomes.

Let’s say that if C2A fused with C2B forming C2 (which has 2 centromeres) in the paternal germ line, the male’s sperm. Now, that sperm would have to fertilize an egg where both C2A and C2B not having been fused would have to pair off with the paternal C2 BUT if C2 has been prevented from being ripped apart because one of its centromeres has been deactivation then the corresponding maternal C2B (or C2A) will not combine with C2 in the mother’s egg because that centromere would have been deactivated.

In other words, he is saying that if two ancestral primates had offspring with the fused chromosome, then that offspring would have 23 chromosomes whereas the rest of the population still had 24. Mating between the two could not occur as a result, thus the fused chromosome could never make it beyond a single generation.

The most obvious solution to this problem is that several members of a population experienced a fusion event. It could have been a completely chance event, or it could have been due to a particular mutation that had spread down the line. That is, my money is on a mutation existing in a population that caused the fusion between two specific chromosomes. Perhaps all the pericentromeric duplications (which pre-date the fusion event, incidentally) gave rise to a gene that was free to mutate neutrally in the population. After some time, it managed to survive the generations, and made a marked difference. (That’s what has happened, minus the specific duplication events, with Richard Lenski’s E. coli.) Or maybe a mutation popped up just out of completely random chance, as opposed to being connected to any particular type of event. It’s hard to say just how any of this happened, but there are good hypotheses to be had on the question.

To conclude, the first argument presented here was defeated before it was even made. One of the two centromeres was deactivated long ago, as stated in the original paper. Indeed, that very paper even suggested a correlating factor in centromere deactivation that could be useful for future research. As for the second argument, I’m going to give Mike the last word:

[T]he fact that an explanation is either unknown or not immediately apparent would not refute the fact that the theory of evolution made this falsifiable prediction, nor would it suggest that there cannot be a rational explanation at all. Our new creationist seems to think that because he does not know how to explain it that a rational explanation is not merely unknown, but in principle impossible. Ergo, Goddidit. That ain’t how science works, kids.

Filed under: Biology, Creationism, Evidence, Evolution | Tagged: , , , , , , | Leave a comment »

tigtog doesn’t get it

Posted on January 7, 2012 by Michael

I recently came across an old post from hoydenabouttown.com that referenced an argument about rhetoric I made on Pharyngula. Basically, I was saying that one’s argument should match one’s goals. The sexist goals of PZ and others do not match their goals of making people more aware of what they see as sexism, thus their rhetoric is just awful. That isn’t to say it is awful for their in-group discussions. I expected to see harsh rhetoric from PZ and his followers. That’s what his audience wants, so he delivered. The problem is when they want to appeal to anyone else. No one is going to listen. Try getting an event organizer to book more female speakers by calling him a sexist, privileged pig who wants to take away women’s rights to vote. See what happens. So once I made my argument and everyone thoroughly misunderstood it, I cited Cicero who made the same basic point all day long: rhetoric should match goals. Unfortunately, author “tigtog” of hoydenabouttown.com doesn’t seem to get it:

Using this quote as if Cicero thus obviously advocated politely rational rhetoric is so hilariously ignorant about how Cicero actually used rhetoric in practice to garner an audience and persuade them to his will! Nobody who was actually familiar with Cicero’s most famous successes as an orator could possibly imagine that he was recommending civil argumentation.

(I didn’t actually use a quote, but I digress.)

tigtog then went on to discuss specific tactics Cicero used. None of it got to my point. Again, rhetoric needs to match goals. The times when Cicero used harsh rhetoric matched his goals and spoke to his audience. If he did the same thing in 21st century American politics, he may have been seen as just another asshole who is petty and flies off the handle. Or not. All politics are local, so – as always – it all depends on his audience.

People just don’t seem to get it. I’m all for harsh tones when harsh tones work. I feel they are more honest, so I prefer them. Just look at the hilarious lashing Richard Lenski gave to creationists. The second letter he sent to the morons at Conservapedia was far from nice, but it’s hard to deny its greatness. And, oh gee, look at his third sentence:

I expect you to post my [second] response in its entirety; if not, I will make sure that is made publicly available through other channels.

In his first response he was fairly cordial. He was just responding to a few silly creationists. However, his second response was designed to be seen by scientifically-oriented people. That’s why he explicitly said he would make it public one way or another. So in each letter we see appropriate rhetoric: in the first he answered nicely so as to more easily move on from the situation while remaining professional; in the second he ripped them apart so everyone could laugh. That pretty much nails the sentiments and arguments of Cicero in every regard.

So, again, my argument is simply that one’s rhetoric must match one’s goals. In fact, that was Cicero’s argument. This makes tigtog wrong twice. First, she has implied that I would not advocate for harsh tones. Saying as much is to willfully disregard everything I have said. Harsh tones are great when used correctly. Second, I never argued what Cicero thought was the best or worst specific rhetoric one way or another anyway. That’s just poor reading comprehension on her part.

Oh, and using an embarrassing misunderstanding of another person’s argument as a premise for one’s own argument is also bad rhetoric. I don’t know if Cicero ever felt the need to be explicit on that point, so maybe tigtog can enlighten us all.

Filed under: Language/Rhetoric | Tagged: , , , , , | 1 Comment »

Hold your horses

Posted on July 9, 2011 by Michael

People like fast things. Our amusement park rides zip on their tracks. We jump from planes for fun. Our video games have names like Need for Speed. We’re even willing to watch bad movies so long as they’re called Speed. But that doesn’t mean there isn’t value in taking things at a pace reminiscent of the olden days. Sometimes we like to slow things down. Sometimes we like to take the time to smell the roses. And sometimes bloggers will engage in hackneyed stock expressions, both in title and content, in order to slowly build up a contrast between quickness and slowness.

As I’ve explained in the past, Richard Lenski is running a 20+ year evolutionary experiment with E. coli. He has published some fantastic results (much to the chagrin of overwhelmed creationists), and now his lab has utilized his bacterial lineages to further probe how evolution works.

[Co-author Tim] Cooper and his colleagues looked at two Escherichia coli clone lineages, sampled after 500, 1,000 and 1,500 generations of evolution. They came from a long-term bacterial evolution experiment running in the lab.

By looking for the presence of five beneficial mutations, the researchers found that ‘hare’ bacteria had more advantageous genetic changes than ‘tortoises’ after 500 generations, suggesting they were more likely to go on to successfully survive and reproduce, and to eventually wipe out their competitors altogether.

The terms “hare” and “tortoise” refer to the speed with which each group experienced mutation. The more quickly mutating group would change so rapidly that it was unable to achieve the same beneficial mutations as the more slowly mutating group. Here’s how I like to think of it.

In the late 90’s, several children were treated with gene therapy for various diseases. This is when a virus is used as a vector for a gene that has the ability (hopefully) to correct whatever is wrong with the child. It’s how researchers cured color blindness in monkeys in 2009. Basically, a gene is missing, resulting in some malady. When the virus is inserted, so is the missing gene. This usually helps or fixes the given problem. However, in a number of the children from the 90’s, insertional mutagenesis occurred. This is where the inserted gene causes a mutation (for reasons we can skip). In these cases, it caused a downstream mutation. The result was leukemia years after the fact.

The reason I’m seemingly rambling is that it was a complex interaction of genes that caused the cancer. It happens often enough that one gene is mutated and it is the loss of function of that gene that causes cancer, but that wasn’t the case in the 90’s. Think of mosquito genocide. Ultimately it’s all such a complex question that the specific results cannot be known ahead of time.

The reason Lenski’s lab found that the slower mutating group of E. coli out-competed the faster group was because the faster group had too many changes. The high number of mutations prevented it from obtaining other certain mutations. A change in one location can have long-reaching implications for future change in another location, in a way superficially similar to that of children from the 90’s, it turns out; it isn’t the case that just any gene can jump into a genome or population and be beneficial, or even work.

This research is important because it is generally assumed that high mutational rate means high evolvability. And that is still going to remain the assumption. But this gives factual credence to the idea that genetic background matters in a very deep way. In fact, Lenski’s earlier work with the same E. coli demonstrated that mutations themselves can be very much contingent. What this all means is that life doesn’t proceed with a single ‘strategy’. High mutation rates have their advantages, but just the same so do lower rates. It’s like driving through the city versus walking through the city. Plenty can be seen and much ground can be covered by car, sure, but a stroll by foot reveals doors and windows and alleys and other things that otherwise could have gone unnoticed.

Filed under: Evolution | Tagged: , , , , | Leave a comment »

Are humans “more advanced” than other organisms?

Posted on January 2, 2011 by Michael

I recently had a discussion with a friend where he asserted that he was more advanced than, say, a plant. By the common connotations that come from the word “advanced”, we would have to agree that his statement was true. But it asks an interesting question: What do we really mean when we say we’re advanced?

To put the discussion in a proper framework, think in evolutionary terms. That means we can’t compare Albert Einstein to Sarah Palin and say, “Why, yes, he was more intellectually advanced than she is.” Of course that is true, but if we’re going to discuss evolution and what it means to be advanced, we’re necessarily comparing species, not individuals. That is what makes my friend’s initial comparison to plants a reasonable starting point.

But it is only a starting point. Because what are we comparing exactly? In terms of brain development, yes, he beats that plant handily. But what about in terms of ability to photosynthesize? Well, the plant just got a knockout in that round. Clearly there is a difficulty in making useful (and, in my view for this discussion, any) comparisons between species. Maybe we need to find a species that is closer in relation to humans. (It certainly would help for it to have a brain in the first place.) The animal I chose for the discussion and the one I am choosing for this discussion is the skunk. Jerry Coyne is the inspiration.

It does not always [evolutionarily] pay to be smarter, either. For some years I had a pet skunk, who was lovable but dim. I mentioned this to my vet, who put me in my place: “Stupid? Hell, he’s perfectly adapted for being a skunk!” Intelligence comes with a cost: you need to produce and to carry that extra brain matter, and to crank up your metabolism to support it. And sometimes this cost exceeds the genetic payoff. A smarter skunk might not be a fitter skunk.

A skunk is vastly more well adapted to life as a skunk than any human ever could be. All the things it takes to be a skunk? A skunk has them nailed down pretty well. The counter to this point was to say that if humans decided to destroy all skunks, we could. True enough. But does that make us more advanced? Of course our intelligence allows us to wipe out many other species, but the whole point of bringing up a skunk and its adaptation is to say that a comparison of intelligence is not valid for purposes of this discussion in the first place! (As always, you know I mean it when I use the lazy-man’s exclamation point.)

When we choose to compare intelligence in order to define what it means to be advanced, we have two massive assumptions going on. First, we’re assuming that intelligence is better than toothiness or having sharp claws or any other characteristic we see in nature. This assumption is untenable because some environments might call for all or any of those characteristics over intelligence. To put things in perspective, try thinking on an evolutionary timescale. So far I have only been comparing humans to other extant organisms (plants and skunks). But what if we go back 100 million years? 200 million? 500? 600? Any human put into an ancient enough environment would die. We know this because the right foods would not be available or because there would be no proper shelter or because the atmosphere would be poisonous or because our immune systems would not be evolved to cope with the bacteria and viruses present at the time or because…and so on. The assumption that intelligence is better than anything else is clearly wrong once we recognize that evolution and the ability of a species to survive depends largely upon environment.

The second assumption in this whole discussion is that we can even say something in evolution is “advanced”. We can say more complex or better suited to a particular environment, but “advanced”? That implies evolution is on the march towards some goal, to some end. That is not true. Science has demonstrated this again and again by showing what a contingent process evolution is. Take the Lenski experiments, for example. (I’m rather disappointed I never wrote about them here.) Richard Lenski and his researchers followed several lineages of E. coli for 20 years (in fact, they’re still following them). They would freeze samples every 500 generations so they could go back and re-run the tape of evolution should some fundamental change occur. And, eventually, such change did occur. Some E. coli were able to consume a natural by-product of their environment after nearly 30,000 generations. Lenski et al. unfroze the old generations to see just what enabled the bacteria to obtain their new found skill. As it turned out, they had to go back many thousands of generations; it wasn’t just one mutation, but at least three. The first two were effectively random. But they were necessary in order to get to the third mutation – the one that opened up a new food product for the colonies. But in the re-running of the tape, not all lineages re-evolved the new mutations. The chance involved in the process was too great to be inevitable; evolution is contingent.

So my answer to the question, Are humans “more advanced” than other organisms?, is to say it is an inappropriate question in the first place. There are several things we should not be assuming:

  • Intelligence is the best trait (whether to this point or in terms of possibility)
  • Evolution is goal oriented
  • The ability to destroy other species and still survive is a mark of advancement

I mentioned the argument for point three, but I have yet to address it. This one is pretty straight-forward, I think: We may be able to destroy many species, but that really only applies for large organisms. The vast majority of life is microbial. Since we would never be able to destroy it all (or even a minute fraction of it), does that mean it is more advanced than we are? What about all the bacteria we need to keep us alive? We certainly could not destroy all the mitochondria of the world and still survive.

Evolution is a contingent process that has no march towards any end. It is about the ability to survive. Our genes are interested in propagating themselves and that is why we are here. Life may mostly (though not entirely) be more complex since it first sprung forth nearly 4 billion years ago, but it always depends upon its environment – and that makes some characteristics more valuable than others. Sometimes.

Filed under: Evolution | Tagged: , , , , , , , | 16 Comments »