Rewinding the tape of life

Here’s another of those Dawkins questions.

Stuart Kauffman’s thought experiment: If evolution could be re-run 1000 times, would certain patterns predictably recur? Humanoids?

Only I already answered it a few weeks ago! I know that Dawkins is more sympathetic to the idea of evolutionary convergence than I am, but I don’t think you’d get recurrence of humanoids. If we could reset everything to the precise state the world was in during the Cambrian, half a billion years ago, I think it would be safe to say we’d get a planet full of molluscs and arthropods, but that’s about all we could say — tetrapods are not inevitable. If we could rewind to a few billion years ago, before the evolution of eukaryotes, we could talk about a planet of algae and bacteria, but other derived forms would be so contingent on chance that no prediction is possible.

The best examples of actually doing this experiment come from the Lenski lab and their work on bacteria, where generations could be frozen and restarted at will, and the answer is…no, it isn’t inevitable that a lineage will emerge that carries even an expected optimal simple biochemical pathway.

Refreshingly vigorous

We’ve been battling the stupid philistines within our own communities so long that it’s easy to forget the atheist tone police — those people who like to chide atheists for being too harsh on religion, who make excuses for faith, and who recoil from confrontation with nonsense. Alex Gabriel will have none of that.

It is a form of privilege to be an atheist who’s never experienced religious abuse, as many of us have who are antagonistic.

It is privilege blindness to expect — without a clue what we’ve experienced or what it means to us — that we give up our self-expression so that you can form alliances with faith communities that deeply injured us.

It is tone-policing if when you’re not telling us to shut up about it, you’re telling us how to talk about it. How dare you tell us to be more respectful.

It is splaining if your answer when we detail histories of religious abuse is ‘Yes, but’ — or if you tell us we can’t blame religion for it since not all believers do the same. We know the details. You don’t.

Ah, excellent. I’ve never been fond of the milquetoast approach to atheism.

I’m one of the privileged people in the first line quoted. I used to think I’d been brought up religious, but I revised my opinion as I met more people who really had been abused by dogmatic religion as children — my liberal Lutheranism and secular parents with only nominal associations with religion was more of an inoculation with a dead virus than an exposure to the real disease. But it was enough to trigger a strong reaction when I did encounter religious stupidity.

Just yesterday, I got in my car to run some errands, and the radio had been left on to a local station (my wife listens to music on her commute), which on Sunday was broadcasting a sermon. It was a generous and liberal sort of sermon — the guy was going on about how we have to be open to change, and receptive to new ideas, which I thought was a nice message…until he started yammering on about why we should be that way. We need to be generous in thought because that’s how Jesus was. Jesus, Jesus, Jesus — he started spinning out this revisionist biography of Jesus that fell just shy of declaring that Jesus had been a gay democrat who campaigned to save the whales.

It annoyed me. I could change the tuner and probably find a Christian preaching a wrathful Jesus, or a law-and-tradition-abiding Jesus, or an American Jesus who wants the brown people executed. Jesus, the Stretch Armstrong of Christianity.

I didn’t experience the pain of a religious upbringing, but I did experience a science education, and I will say this: how you know something matters. If you want a mind that adapts and responds intelligently to changing evidence and circumstances, you don’t get it by telling your children to worship and obey a myth. You don’t invent imaginary heroes who were paragons of perfection and tell the kids to follow them — even if you are promoting ideals I personally find copacetic, you are committing child abuse by short-circuiting their capacity for critical and independent thinking.

So I agree with Alex, but for different reasons…and I respect those differences. Fight on, everyone. And don’t try to demand that everyone on your side must have the very same perspective on the struggle that you do.

Let’s not forget that Nixon was a horrible person

Just a reminder that the president I grew up despising had blood on his hands.

Nixon’s newly revealed records show for certain that in 1968, as a presidential candidate, he ordered Anna Chennault, his liaison to the South Vietnam government, to persuade them refuse a cease-fire being brokered by President Lyndon Johnson. 

He was responsible for the death of American soldiers, as well as Vietnamese civilians.

He paved the way for Reagan to use a hostage situation for political ends, and for Bush to lie and immerse an entire generation into a futile war.

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.

Why would you support a policeman who shoots unarmed people?

There is a protest going on in St Louis, in support of Darren Wilson, the policeman who shot Mike Brown ten times. I don’t understand that at all. Best case scenario, he executed a man for shoplifting; worst case, he’s a trigger-happy racist. There’s really no possible way to justify what he did.

wilsonsupporters

But just in case you’re worried that these citizens might get out of control, the police are on the case — riding bicycles.

cops_on_bikes

Hey, where are the armored personnel carriers and the assault rifles? Don’t they think those protesters deserve a few shots of CS gas?

(via Jon Swaine)

How to shut Sye Ten Bruggencate up

His only trick is to tell everyone else that they aren’t certain that they are right, while he is absolutely certain that he is right, and therefore he must be right. Most of this video is taken up with wordy attempts to pin him down, but the simple solution comes up at the end: just tell him to knock if off with his one and only line of argument, and then he jumps up and goes away.

We now need to compile a list of magic words that make other creationists disappear.

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:

wonder-al-Daniel-Boone-Nat-Forest-KY-c868b4_z-300x200

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.

Time to arrest the police

I’ve been away for 10 days, and trying to catch up with the nightmarish news from Ferguson, Missouri is rage-inducing. I’ve decided that the only possible solution is to declare martial law, call in the National Guard, and let the tanks roll in…to shut down and arrest the police force. These trigger-happy militarized goons need to be stopped, and not just in one town in Missouri, but all across the country: no more drones, armored personnel vehicles, SWAT teams, and thugs playing soldier — those aren’t the police. We need something in between open-carry idiots deputizing themselves to enforce the peace, and these paramilitary pseudo-soldiers who believe their job is to suppress people they don’t like.

Once upon a time, it was people in blue uniforms who were supposed to avoid drawing their weapons in all but the most dire circumstances. Now it’s a race to make the police increasingly lethal, which should not be their mission.

And then, just to get yourself even deeper in a fug, read the opinions of white people in St Louis. We’re screwed.

(By the way, I’m closing this thread full of Ferguson news…now you can fill up this one.)

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.