Carl Zimmer is defective

But it’s all right, we all are. Zimmer has begun a series called Game of Genomes in which he has had his whole genome sequenced, and is being led by a group of scientists through the analysis. So far he’s made a good summary of the procedure, and a general overview of the state of his genome.

In my own genome, Gerstein and his colleagues discovered 13 genes in which both copies appear to be broken. I have another 42 genes in which only one copy looks like it’s defunct.

It may sound strange that my genome has dozens of broken genes that cause me no apparent harm. If it’s any consolation, I’m no freak. The 1000 Genomes Project revealed that everyone has a few dozen broken genes.

Our genomes are not finely engineered machines that can’t tolerate a single broken flywheel or gear shaft. They’re sloppy products of evolution that usually manage to work pretty well despite being riddled with mutations.

I’ve probably passed down some of my uniquely broken genes to my children. Perhaps, long in the future, one of those broken genes will become more common in humans, and end up in every member of our species. That’s certainly happened in the past. My genome catalog includes about 14,000 genes that have been broken for thousands or millions of years, known as pseudogenes. Once they lost the ability to make proteins, they simply became extra baggage carried down from one generation to the next. Thanks to a genetic roll of the dice, they ended up becoming common. Now these 14,000 pseudogenes are found in all humans today.

As you can tell, it’s a nicely written summary that doesn’t require a huge amount of scientific background to understand. Good stuff!


  1. lepidoptera says

    Thanks for sharing the link, PZ. I’m enjoying reading the Game of Genomes.

  2. einsophistry says

    I’ve long thought the pseudogene argument for common descent is seldom pushed as strongly as it could and should be. Usually discussions on this topic with creationists fizzle out with the creationist gesturing at some cherry-picked study alleging to have found a “function” (in a typically broad, non-sequence-specific sense) for some bit of DNA once thought nonfuctional and making what amounts to a huge promissory note re: the wholesale demise of junk DNA.

    What seems to regularly go underappreciated by both sides is just how much evidence for common descent is contained in even relatively tiny sequences of shared noncoding DNA. Let’s grant, purely for the sake of argument, that 99.9% of the DNA shared by humans and chimps can be explained by common sequence-specific functionality. The lower end of contemporary estimates for the total amount of this shared DNA is around 2.8 billion base pairs (corresponding to a similarity of around 94%). The measly 0.1% of this that we’re allowing to have no sequence-specific functions still corresponds to a sizeable 2.8 million base pairs. Now, assuming independent creation of humans and chimps, and granting that there is no constraint imposed on the sequence of these 2.8 million base pairs by functionality, what is the probability of finding the same sequence in these two species? The lower bound on this figure will be determined by the total number of possible sequences of length 2,800,000 that can be made with the four different base pairs—that is, 4^2,800,000. This is an unfathomably huge number. Now, some of these sequences will have to be excluded because they contain core promoters or other transcription factor binding subsequences. Realistically, this will be a very small subset of the total number of possible sequences, but since I’m in such a bone-throwing mood today, let’s suppose that 99.9% of these possible sequences would have to be excluded. This still leaves us with a probability of around one in 9.5*10^1,685,764, (that’s a 9 followed by a 5 and 1,685,763 zeros) for finding the same sequence in humans and chimps.

    Of course the more typical inference appealed to by creationists is not from common sequence to common function but from common sequence to common designer. The idea, though, that a designer would have willingly written noncoding sequences in patterns of similarity broadly consilient with phylogenetic trees already hypothesized on the basis of morphological and other more surface-level similarities lies in considerable tension with a central assumption of all species of creationism that pretend to scientific legitimacy—viz., that the designer makes his handiwork in the natural world obvious to unclouded eyes (conf. Job 12:7: “But ask now the beasts, and they shall teach thee; and the fowls of the air, and they shall tell thee,” et seq.). Because these sequences are unconstrained by any sequence-specific functions, they could have varied wildly (and in truth even coding sequences admit considerable degrees of freedom in their writing due to many levels of functional redundancy). A designer intent on getting credit for his work could have made our sequences in these regions more similar to those of broccoli than to those of chimps. Or similar to nothing at all. But he didn’t do this. Mysterious ways indeed.

  3. blbt5 says

    I get it, it’s fun to say that everyone has “broken” genes. But the chemical structure is perfectly fine. If there really were an intrastrand break within any chromosome, you’d never have been born. Radiation poisoning really breaks genes, lethal for any living organism. More accurate to say everyone’s full of nonsense.