Why do all cells have the complete genome?

Ophelia has summarized a series of science questions Richard Dawkins asked on Twitter. Hey, I thought, I have answers to lots of these — he probably does, too — so I thought I’d address one of them. Maybe I can take a stab at some of the others another time.

I like this one, anyway:

Why do cells have the complete genome instead of just the part that’s needed for their function? Liver cells have muscle-making genes etc.

My short answer: because excising bits of the genome has a high cost and little benefit, and because essentially all of the key exaptations for multicellularity evolved in single-celled organisms, where modifying the DNA archive would have serious consequences for all the daughter cells.

This is an interesting issue, though: different kinds of cells in the same organism express genes that are qualitatively and quantitatively different. Here’s a set of nice graphs in which the relative fraction of different classes of genes in gene transcripts in different cell types were measured. Notice in the list of biological processes that a lot of them, such as the genes involved in transcription and translation and metabolism, are going to be used in all cells, but some, such as neuron-specific or testis-specific genes, are only going to be expressed in some cells.

(A) Pie graphs show estimated fraction of cellular transcripts deriving from genes belonging to a set of top-level Gene Ontology Biological Process categories for 7 human tissues and 1 cell line. Fractions were estimated from read density (RPKM) of Ensembl transcripts for each gene. Names of categories, distribution of transcriptome fraction across the samples (each line is a sample), and the coefficients of variation are shown at right. Biological processes with significantly higher or lower densities in individual tissues and cell lines are denoted by arrows. (B) FRACT analysis of sub-categories of the top-level ‘Development’ category in brain and testes.

(A) Pie graphs show estimated fraction of cellular transcripts deriving from genes belonging to a set of top-level Gene Ontology Biological Process categories for 7 human tissues and 1 cell line. Fractions were estimated from read density (RPKM) of Ensembl transcripts for each gene. Names of categories, distribution of transcriptome fraction across the samples (each line is a sample), and the coefficients of variation are shown at right. Biological processes with significantly higher or lower densities in individual tissues and cell lines are denoted by arrows. (B) FRACT analysis of sub-categories of the top-level ‘Development’ category in brain and testes.

It also gets complicated because some genes are found in very different forms: there is a kind of universal myosin, myosin I, for instance, that is expressed in all cells as part of the intracellular transport machinery, and then there is a myosin variant, myosin II, that is expressed only as a part of the contractile machinery in muscle. So you might think that it would be more efficient for a skin cell to simply cut out and throw away Myosin II, since it’ll never use it, and keep Myosin I.

But how does the cell determine which genes it will never use? Where does it draw the line? All those testis development genes, for example — I never used many of them until I hit puberty. Wouldn’t it have been terrible if my young toddler testicles threw out a set of unused genes, and then a dozen years later discovered that they had a use, after all? There are a great many genes regulated by timing and signals, and as can be seen in that figure above, every cell has a different expression profile. There are a variety of cells in my skin that are busy replicating and making keratin proteins as a matter of course, but they only switch on cellular repair mechanisms if I cut myself. There are also many genes that get reused in complicated ways, too: the gene even-skipped is first switched on as part of the segment forming process in flies, but it later is switched on again in making neuroblasts, and later still is expressed in axons during pathfinding. Cells would rather recycle genes than throw them away.

These properties are not unique to us mammals, either. Bacteria regulate which genes are turned off and on, too — they change their biochemical behavior in response to signals in their environment. The ability to switch on and switch off genes, without eliminating the DNA, is a solved problem. Life figured that one out a few billion years ago. Key molecules required for multicellular patterns of gene expression first evolved in bacteria — they worked out how to have a cell with the same genetic material behave differently in different circumstances. We came about ready made with a toolkit equipped to have one set of genes turned on in livers, and a different set turned on in muscles, easy.

But, you might think, wouldn’t it be so much more cost-efficient if cells in multicellular organisms just got rid of genes they’d never turn on in their lifetime, once they’ve committed to a certain tissue type? Muscle cells will never make sperm recognition proteins, and liver cells won’t ever have to lift weights, and you could probably cut the amount of DNA in differentiated cells in half with no effect on function.

But that’s penny-wise accounting. In bacteria, only about 2% of the cell’s energy budget is invested in replication — so removing a bit of DNA here and there is only going to shave a tiny amount off the cost of cell division. On the other hand, an amazing 75% is spent on transcribing and translating genes, so efficient mechanisms of simply turning off unused genes reaps huge savings for the cell. Evolving a complex process to pare away unused DNA in terminally differentiated cells simply does not make sense energetically, while simply taking advantage of an already fully implemented and refined process for regulating gene expression…heck, that’s what evolution does best, reusing what’s already there.

By the way, not all cells carry the complete genome: there are also a few cases where the DNA of an organism is modified — the CRISPR system in bacteria, and the somatic recombination system used in vertebrates to generate diverse immunoglobulins. In both of those cases, though, it’s not a mechanism to cut away unused DNA. It’s a specialized process to create variation during an organism’s lifetime to cope with environmental challenges.

Lane N, Martin W. (2010) The energetics of genome complexity. Nature 467(7318):929-34.

Ramsköld D1, Wang ET, Burge CB, Sandberg R (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5(12):e1000598. doi: 10.1371/journal.pcbi.1000598.

There are no living pterosaurs, and “ropen” is a stupid fantasy

I was recently getting dunned by kooks insisting that a live pterosaur had been found. I’d love to see a pterosaur, but I’m afraid they’ve been extinct for over 65 million years; I’d also like to have a conversation with my great-great grandfather, John Page Hurt of Saylersville, Kentucky (I’m pretty sure he fought in the Civil War…on the wrong side), but I think we can be realistic about the likelihood of that happening. I took a look at the pterosaur information anyway, though, and discovered something interesting. There isn’t any evidence. There’s just one fanatic.

Here’s the kind of evidence they present. You’d expect a blurry photo of some flying creature, right? Or maybe claw marks, or scattered fewmets…none of which would be particularly persuasive. But no — we don’t even get that much. We get photos like this:

Professor Peter Beach tells Whitcomb how the bright light quickly flew up from the tree

Professor Peter Beach tells Whitcomb how the bright light quickly flew up from the tree

That’s it. Not a picture of the creature, but a picture of a guy pointing to a place where he claims to have seen a glowing light. Or sometimes we get this:


A generic picture of some trees in Kentucky, where some guy said he saw a pterosaur. Twice, no less.

These stories are terrible and pointless. There is no evidence here.

And then something else emerges — all the sources sound dreadfully familiar. Here’s a list of some of the sites I found, and the authors’ names where available.

Same stories, same pedantic, boring style, same lack of understanding of what constitutes evidence. It turns out that they’re all by the same guy, Jonathan Whitcomb, who’s been busily dropping turds all over the internet to make it look like there is an active community of researchers tracking down the wily pterosaur. There isn’t. And he confesses to rampant sock puppetry!

If you had Googled something like “live pterosaur” in 2005, the first page may have included a site that included the words “stupid,” “dinosaur,” and “lies” in the URL. Yes, it was libel, and that site is probably still out there; but try searching on “live pterosaur” today and you won’t see that libelous site listed on the first three pages of Google. You will find that most of the pages are positive about the possibility of modern living pterosaurs. The few that are negative are at least not libelous.

My purpose in using the pen name “Norman Huntington” differed from that of Alice Sheldon, but is was equally valid. I got around potential bias in readers by using that name instead of my own. The difference is this: I was trying to attract attention to the basic idea of modern pterosaurs, not to my own writing ability. (In fact I altered my writing style for those blog posts using “Huntington.”)

But it’s OK that he’s playing these circular SEO games, because he’s not trying to peddle his writing commercially — it’s just so gosh-darn important that everyone know about these pathetic pterosaur stories, so he’s just got to play these sneaky games to avoid criticism and get his essential story told.

There’s another motive, too: he’s a creationist who thinks finding a ptersoaur would defeat evolution, and he’s using his book and web pages to promote the Mormon religion.

Consider Helaman 5:50, regarding the conversion of many Lamanites, after the miracle in the prison with the brother-missionaries Lehi and Nephi. Lamanites who did not see the miraculous fire believed the words of the eyewitnesses who did see it: “And it came to pass that they did go forth, and did minister unto the people, declaring throughout all the regions round about all the things which they had heard and seen, insomuch that the more part of the Lamanites were convinced of them, because of the greatness of the evidences which they had received.” Latter-day saints rejoice for those who listen to the spiritual testimonies of those who had received confirmation of the truth by the power of the Holy Spirit. Just as missionaries may appear, on the surface, to differ from those they teach, eyewitnesses of strange flying creatures are from various countries and cultures, appearing to differ from those who have been raised in Western countries in which universal-extinction ideas are taken for granted for dinosaurs and pterosaurs.

Greatness of the evidences, indeed.

There’s also another place where you can find the story of the living pterosaur: the wikipedia article on “ropen”. It’s pure mush regurgitated from Whitcomb’s pages; the only sources cited are from Whitcomb, with the exception of mentioning two paranormal reality TV shows, “Destination Truth” (on SyFy) and “Monster Quest” (on the History channel). It’s a completely credulous and pro-bullshit page, and is a perfect example of why I don’t let my students ever cite Wikipedia. It’s also got Whitcomb’s fingerprints all over it — he was formerly an editor going by the name “jondw”, although he seems to be an ex-editor now. The page that contributes to his PR efforts for the totally fictitious creature “ropen” still stands, though.

Undermining their audience

I just realized that I haven’t tuned into any of the so-called educational channels for years — Nerdy Christie dissects the latest shark week abomination, and I understand why.

Not only is there no support for the show’s entire premise, each of the hypotheses presented are factually wrong or illogical. Sharkageddon’s pointless pontificating doesn’t leave us any closer to explaining why shark attacks occur—or where, or when. Alexander ends on a conservation message, which Discovery, of course, ensures is brief and buried with credits. But this final thought is what Discovery should have focused on all along. Sharks are vital to Hawaiian ecosystems. We don’t need another “documentary” villifying these ecological and culturally important animals—we need one that explains why they matter, what they do for us, and why we should be fighting to save them.

Although SMBC might have an alternative explanation.

Spanking Nicholas Wade

Wade’s li’l book of scientific racism has been repudiated by over 100 scientists working in the fields of evolutionary biology and population genetics.

As scientists dedicated to studying genetic variation, we thank David Dobbs for his review of Nicholas Wade’s “A Troublesome Inheritance: Genes, Race and Human History” (July 13), and for his description of Wade’s misappropriation of research from our field to support arguments about differences among human societies.

As discussed by Dobbs and many others, Wade juxtaposes an incomplete and inaccurate account of our research on human genetic differences with speculation that recent natural selection has led to worldwide differences in I.Q. test results, political institutions and economic development. We reject Wade’s implication that our findings substantiate his guesswork. They do not.

We are in full agreement that there is no support from the field of population genetics for Wade’s conjectures.

Ow, that has to sting. But I know exactly how the Human Biodiversity wackos will respond: all those scientists must actually be acolytes of the New Creationism.

Did I ever tell you how much I despise Ronald Reagan?

Here, have a nice comic that explains the situation in Lake Erie.



When I was a kid, Lake Erie was a joke: it was a polluted cesspool with rivers that caught on fire. Places like Erie and Love Canal were the punchlines of a national sense of disgust with abuse of the environment, and amazingly, people got together and changed things: new tighter regulations, clean up of the worst cases (well, that was begun but never finished), and in general, we saw a reduction in pollution around the country.

Then…fucking Ronald fucking Reagan fucking fucked everything up. Trees cause pollution. Regulation is bad for the economy. And every Republican since has followed the same script, right up to “drill baby drill”. Even the Democrats are getting in the act.

And the end result is that everything is turning to shit again.