How to examine the evolution of proteins

In my previous post, I described the misguided approach Gauger and Axe have taken to criticizing evolution, and one of the peculiarities of their criticism is that they cited another paper by a paper by Carroll, Ortlund, and Thornton which traced (successfully) the evolutionary history of a class of proteins. Big mistake. As I pointed out, one of the failings of the Gauger/Axe approach is that they’re asking how one protein evolved into a cousin protein, without considering the ancestral history …they make the error of trying to argue that an extant protein couldn’t have directly evolved into another extant protein, when no one argues that they did.

The tactical error is that right there in the very first paragraph of their paper, Carroll, Ortlund, and Thornton point out the fallacy of what the creationists were doing.

Direct comparisons among present-day proteins can sometime yield insights into the sequence and structural mechanisms that underlie functional differences. Such “horizontal” comparisons, however, cannot determine which protein features are ancestral and which are derived, so they are not suited to reconstructing the events that produced functional diversity.

They don’t mention Gauger and Axe, of course — this paper was written before the creationists wrote theirs — but a methodological flaw is still spelled out plainly, the creationists reference it so I presume they read it, and they still charged ahead and did their flawed study, and then had the gall to claim their work was superior.

Ah, silly creationists. They just assume their target audience won’t bother to read the work they’re citing, and isn’t competent to understand it anyway. And they’re usually right.

The crew doing the work in the Carroll paper did not make the same mistakes. They are doing ancestral sequence reconstruction (ASR), so the effort to work backward to trace ancestral states is implicit. The bulk of the paper describes the sequencing of homologous and paralogous genes in more organisms (in this case, especially cartilaginous fishes), and the analysis of synthesized, reconstructed ancestral proteins, so it’s built entirely on an empirical foundation. And their answers actually advance our understanding of the base-by-base changes that led to the evolution of the current set of proteins. I think they were courteous and sensible (and probably, the idea didn’t even occur to them) in not comparing their work to that of the creationists — it would have been less than gracious to point out how ugly, cheap, and cheesy the stuff coming out of the Biologic Institute looks.

What the real scientists were studying is a class of receptors that respond to mineralocorticoid and/or glucocorticoid hormones. These proteins are similar in sequence and structure to one another, and are clearly paralogous: they arose by an ancient gene duplication event, somewhere around 450 million years ago. The two copies have since diverged to have different roles in hormone physiology.

The two receptors are called MR, for mineralocorticoid receptor, and GR, for glucocorticoid receptor.

MRs are activated by adrenal hormones, aldosterone and deoxycorticosterone, and to a lesser exent, cortisol. The receptors are extremely sensitive to the hormones. These hormones are important in regulating salt balance, and you might well imagine that in our fishy ancestors, as well as ourselves, regulating the concentrations of salts in our blood and tissues is a very important function. Deviations can cause death, after all.

GRs are activated by high doses of cortisol; these receptors are much less sensitive, requiring high doses of the hormone to trigger a response. They are important in regulating stress responses: they adjust the immune system and sugar metabolism. These aren’t ‘twitchy’, fast response functions like maintaining salt balance is; they are long-term, ‘last-ditch’ reactions to growing stresses, so functionally it makes sense that activation requires high levels of accumulated hormone.

Using ASR techniques — phylogenetic analysis and estimating the most likely sequence of the ancestral protein — the investigators have put together a picture of the receptor before MR and GR diverged. This protein is called AncCR, for Ancestral Corticosteroid Receptor, and it has been synthesized in the lab, so we know about its properties. AncCR is a lot like MR: it’s sensitive to low concentrations of hormone, and it responds to low concentrations of a broad spectrum of hormones.

The pedigree of these proteins is illustrated below.

i-8821726c17d966da50a695e8a1d903b7-grmr_phylo-thumb-500x280-70023.gif
(Click for larger image)
Simplified phylogeny of corticosteroid receptors. Ancestral sequences are shown at relevant nodes: AncCR, the last common ancestor of all MRs and GRs; AncGR1, the GR ancestor of cartilaginous fishes and bony vertebrates; AncGR2, the GR ancestor of ray- and lobe-finned fishes (including tetrapods); AncMR1, the MR ancestor of cartilaginous fishes and bony vertebrates. (AncGR1.0 and AncGR1.1 are different reconstructions of node AncGR1, inferred from datasets with different taxon sampling.) Black, high sensitivity receptors; gray, low sensitivity receptors. Single and double gray dashes mark functional shifts towards reduced sensitivity and increased specificity, respectively. Support values are the chi-square statistic (1 – p, where p equals the estimated probability that a node could occur by chance alone) calculated from approximate likelihood ratios. The length of branches from AncCR to AncMR1 and to AncGR1, expressed as the mean number of substitutions per site, are indicated in parentheses.

The MRs are similar in function to the AncCR, so they aren’t particularly interesting in this context — there’s no big question about how the MRs retained similar properties to their ancestor. The interesting questions are all about the GRs: what changed to make GRs different from the ancestral protein? What amino acid changes set AncGR1 apart from AncCR?

The investigators have an answer. The first step was the evolution of reduced hormone sensitivity, so that these receptors only responded to very high concentrations of the hormone, and the second step was a loss of sensitivity to the mineralocorticoids, already handled by the MRs, so that they only respond to high doses of cortisol, which at this point became exclusively a stress hormone. And they know exactly which amino acids changed to confer the reduced sensitivity.

They identified three changes: the conversion of a valine at position 43 into an alanine, called V43A; the conversion of an arginine at position 116 into a histidine, R116H; and the conversion of a cysteine at position 71 into a serine, C71S. They also know the effect of the mutations. V43A and R116H each loosen the structure of the receptor so that it’s less sensitive, and when both mutations are present the effect greatly reduces sensitivity about 10,000-fold…too much! They make the mutant hormone too insensitive, and much less insensitive than their reconstructed AncGR1.

The most interesting change is C71S. It basically does nothing to the sensitivity; make the C71S change to AncCR, and you get a receptor protein that is essentially indistinguishable in its response. This is effectively a neutral mutation. It can spread freely through a population with no deleterious or advantageous effect.

C71S does have one significant effect in cooperation with the other two mutations: it buffers both V43A and R116H. When all three mutations are present, the desensitizing effects of V43A and R116H are reduced to produce the level of sensitivity expected for the AncGR1 protein. This means we can reconstruct the order of the amino acid changes in evolution. First came C71S, because it doesn’t cause any particular adaptive change, and because if either V43A or R116H came first, the resulting receptor would be generally non-functional. The existence of C71S first means the subsequent V43A/R116H changes produced receptors that are still functional, but simply operate only at higher concentrations of the hormones.

All of these changes are perfectly compatible with an evolutionary model of their origin. No sudden leaps, no deleterious intermediates are required — everything hangs together beautifully and is backed up by solid empirical evidence. In addition, the work explains the mechanics of receptor-hormone interactions, stuff I haven’t explained here, but if you’re a biochemist, there’s much to savor in the paper.

It’s an amazing contrast to the Gauger and Axe paper, too. No wonder I’m not a creationist!

Carroll SM, Ortlund EA, Thornton JW (2011) Mechanisms for the evolution of a derived function in the ancestral glucocorticoid receptor. PLoS Genet.7(6):e1002117. Epub 2011 Jun 16.

How not to examine the evolution of proteins

The Discovery Institute has me on a mailing list for their newsletter, Nota Bene. That’s probably unwise: usually I just glance at it, see another ignorant bit of fluff from Luskin or Nelson or one of the other usual suspects, and I snigger and hit ‘delete’, but sometimes they brag about how they’re really doing science, and I look a little closer. And then I might feel motivated to take a slap at them.

The latest issue contains an article by Ann Gauger, babbling about her recent publication disproving Darwinism, written with her colleague Douglas Axe, published in their tame ‘science’ journal, Bio-complexity, and edited by Michael Behe. It’s not work that could survive in a real journal, I’m afraid.

The work focuses on a diverse family of enzymes, the PLP-dependent transferases. These are all paralogs, or genes produced by duplication and divergence, as determined by their similar sequences. They picked two members of this family that use different substrates and catalyzed different reactions, and asked how they could possibly have evolved from each other…and they did it all wrong. The mistakes they made were fundamental, obvious, and amazingly stupid.

  • The cousin problem. You should have picked up on the key problem from my short description above: they picked two extant proteins and then asked how they could have evolved from each other. Imagine if I picked one of my many cousins — say, the tall, red-headed Mormon fellow from Oregon, or the slender fan of horses in California — and started enumerating our many differences and declared that I couldn’t possibly have evolved from either of them. You would rightly stop me and suggest that maybe my problem is that I didn’t evolve from my cousins — that maybe the smarter approach would be to look at our respective parents, and the grandparents we have in common, and trace the lines of descent.

    And you’d be right, of course. A more sensible way of looking at this problem is to start with a valid premise, and examine parental and grandparental states. Gauger and Axe don’t do that at all. They speculate about the huge number of possible intermediate states between two cousins, and decide that there are so many possibilities that the path from one to another is so improbable that it couldn’t have happened in the history of the planet. You might be able to say the same thing about me and my very different cousin, if you disregarded the fact that there actually were known intermediates.

  • The bridge hand problem. Creationists pull this one all the time. Here’s the situation: you are dealt 13 cards in a hand of bridge. What’s the probability that you’ll get the hand you’ve got? Obviously, the probability of getting a hand is 1.0, but the probability of getting any one specific arrangement of 13 cards is less than one in 635 billion. The silliness of the creationists is to point at a number like that and announce that the arrangement must have been designed. Gauger pulls this same stunt.

    …we calculate that the waiting time for a bacterial population to acquire seven specific mutations in a duplicated gene, none of which provide any functional benefit until all seven are present, is something like 1027 years. That’s a ten with 27 zeros after it. To put this in perspective, the age of the universe is believed to be on the order of 1010 years.

    If I played bridge very, very fast, dealing out one hand every minute, that means I’d still have to wait 1.1 million years to get any particular hand you might specify ahead of time…and my life expectancy is only on the order of 102 years. Therefore, bridge is impossible. Similarly, if you add up all the nucleotide differences between me and my cousin, the likelihoods of these particular individuals is infinitesimally small…but so what? We’re here.

  • The talentless critic problem. Let’s pretend that the prior problems don’t exist (I know, that’s an awfully big hypothetical leap to make, but try). Let’s pretend therefore that the Gauger and Axe paper actually accomplishes what they claim: that neo-Darwinian mechanisms are inadequate to explain the origin of the family of PLP-dependent transferases. Now what? They’re here, obviously — how did they get here? They don’t say. They don’t even speculate; “intelligent design” is a phrase studiously avoided. Lord knows, their experiments and simulations aren’t even designed to reveal alternative mechanisms. This is their conclusion:

    …answers to the most interesting origins questions will probably remain elusive until the full range of explanatory alternatives is considered.

    Yeah, but…if Ann and Doug aren’t considering them in their papers, let alone putting together experiments to test them, why should I? And given that their protocols are so deeply flawed and built on faulty premises, I don’t think they’ve ruled out natural evolutionary mechanisms at all. I’ll be much more interested when they actually try to explore their unstated “explanatory alternatives” and show me a novel mechanism.

  • The much more attractive friend problem. I was surprised at one thing: usually creationists assiduously avoid the possibility of comparisons by, for instance, shutting off comments and not bothering to cite their critics, but in this case, Gauger actually links to a paper by Carroll*, Ortlund, and Thornton. It’s a terrible tactical mistake. Gauger and Axe are saying, “Ooh, we shit in a pot and we couldn’t even get mushrooms to grow in it,” and then pointing to the flourishing, hugely productive garden that Thornton has cultivated and saying, “…and they’re doing it all wrong.” It’s crazy. It just tells me my time is much better spent reading PLoS than Bio-complexity.

That other paper is so much better than the creationist paper, let’s talk about it.

*Sean Michael Carroll. No, not the physicist Sean M. Carroll who works at CalTech, and not the developmental biologist Sean B. Carroll at Madison, but another Sean Carroll at Harvard. It’s so confusing. If there was a secret research project decades ago to clone a set of hot scientists, you’d think they’d have at least had the decency to append a plate and well number to the ends of their names.

Standing up to William Lane Craig

Lately, William Lane Craig has been demanding that Richard Dawkins debate him, and has gotten quite insistent lately as he tours England. I don’t see the point in anyone debating Craig: he’s a nobody who has contributed nothing to the intellectual world; he’s a professional debater and apologist, a rhetorical gunslinger for Christ, and there’s no purpose to enaging him (I know Hitchens took him on…but Hitchens has been our rhetorical gunslinger). Dawkins is a top-flight evolutionary biologist and a masterful craftsman of the English language. I don’t think there’s even anything interesting to discuss with Craig. So Richard Dawkins has taken the time to explain why he refuses to debate William Lane Craig. It’s a terrific put-down. I’m going to have to steal from it next time that importuning dweeb Vox Day starts pestering me to debate him.

I was pleased to see that one of Dawkins’ points was one that is not made often enough: William Lane Craig is a nasty, amoral excuse for a human being.

Why I am an atheist – Samyogita Hardikar

Up till I was 19 I had been dwelling into the murky waters of faith, mainly switching between a haphazard belief in some sort of higher power if not god per se and agnosticism of the ‘If there had been a god, then surely he wouldn’t have allowed all this cruelty and suffering?’ persuasion. Now I really don’t think there is a god. The reasons are many and most of them are obvious to and shared by most other atheists: no real evidence for the existence of god/ gods, a respect for and inclination towards a humanitarian and human-centric idea of morality, too many vulgar disputes amongst the believers themselves about who exactly this ‘one true god’ person that they all keep banging on about might be, to name a few of the top ones. But I vividly remember the moment I started thinking of myself as an out-and-out atheist and it wasn’t any kind of anger or frustration or hardcore empirical analysis that made it happen. It happened when I heard Douglas Adams speculating about the origin of god.

He says that the idea of god probably came into existence because after looking about and seeing what a well oiled machine this world was, we humans made the foolish mistake of asking the most ridiculous, naive and treacherous question: ‘So who made this then?’ ‘This’ being the world, of course. ‘Someone must’ve made it, you know? Like we make stuff?’
And from there we just went on improvising and thinking that since we’re the only ones who ever actually make anything, it must’ve been someone very like us, much more sizable and capable than us, and much more invisible, obviously.

I completely buy that theory and it may seem trivial but if we are to move on from all this violence and disharmony that happens in the name of god, we have to see the whole notion for the triviality that it is. Let’s not- for a moment- try to answer that absurd question with the first thing that comes to your mind and we’ll be fine.

To put forth a simple if slightly cheap analogy, the idea of god is a bit like non-degradable plastic. It’s man-made. It’s not found in nature. It was created by throwing a whole bunch of random stuff together. It’s a relatively recent invention considering how long we’ve been around and even if it may look like it at first glance, our lives do not depend on it. It’s a quick, immediate gratification based solution for an eternal problem which is why it’s dangerous. It seemed like a very good idea at the beginning and most people still think it’s pretty handy but now that we have it, we don’t seem to be able to get rid of it and it’s all beginning to get a bit out of hand. And lastly, living things are suffering and dying horrible deaths because of it. Atheism on the other hand is way more ego-friendly.

Samyogita Hardikar
India

Ritualized child abuse: circumcision

Want to spend an hour cringing and twitching? This is the abridged version of “Cut: Slicing Through the Myths of Circumcision“, and you will suffer if you watch it. It is a wasteful, terrible thing to do to a child.

One rabbi interviewed is at least honest about circumcision: “It’s painful, it’s abusive, it’s traumatic, and if anybody does it who isn’t in a covenant ought to be put in prison…I do abusive things because I’m in covenant with god.” What nonsense. What a wretched excuse for abusing children.

(Warning: lots of shots of babies getting chopped, as well as closeups of adult penises.)

The arguments for circumcision are pathetic and awful.

  • “You either believe [in the covenant of circumcision] or else nothing is true”. I’ve heard that before: it’s the argument creationists use to defend the absolute literal truth of the book of Genesis, because if that’s not true, the story of Jesus falls apart, and therefore the whole of Christianity is false. Yeah, so? Then it’s false.

  • “The mystery of circumcision is profound”. Ignorance should not inspire the kind of awe that motivates one to mutilate another person’s body.

  • The health benefits. Total bullshit. As one of the speakers in the movie explains, there have been progressive excuses: from it prevents masturbation to it prevents cancer to it prevents AIDS. The benefits all vanish with further studies and are all promoted by pro-circumcision organizations. It doesn’t even make sense: let’s not pretend people have been hacking at penises for millennia because there was a clinical study. Hey, let’s chop off our pinkie toes and then go looking for medical correlations!

  • It’s tradition. Grandpa and great-grandpa and great-great-grandpa did it, so I’ll perpetuate the cycle of abuse to my children. I have to reject that: it reduces a decision to do irreparable damage to a child to repetitive, superstitious, mindless behavior.

There is no reason, other than certain rare and specific medical conditions, for maiming anyone’s genitalia. Don’t do it to your children.

(Also on Sb)

Here’s what happens when you reconcile religion with “science”

You get mad raving nonsense.

In my opinion, Adam and Eve were born with a small organ attached to their appendix tube. An organ that produced stem cells which kept their perfect human body perpetually healthy and forever the equivalent age of thirty years old. In my opinion, this now missing human organ is the Tree Of Life depicted in the Bible’s book of Genesis; an organ that grew from a now missing 24th human chromosome in the human genome. To ‘take fruit’ from the Tree Of Life is to live forever… immortality.

As most of us know, Adam and Eve contaminated themselves by eating the forbidden fruit (cells) from the Tree Of The Knowledge Of Good And Bad. The forbidden fruit (cells) was the ingestion of cells, chromosomes, genes and DNA found in the flesh of mammals. This destroyed the 24th chromosome in Adam and Eve’s reproductive cells (sperm and egg), and also destroyed the Tree Of Life organ attached to their appendix tube. With the 24th chromosome gone from Adam’s sperm cells, and the 24th chromosome gone from Eve’s egg cells, hereditary immortality could not be passed on to their offspring, and hence, to all human beings thereafter. To ‘take fruit’ from the Tree Of The Knowledge Of Good And Bad is to positively die… mortality.

Most of us also know that God took a rib from Adam in order to build Eve. The rib was taken before Eve came into existence. The rib was taken before any kind of contamination to the human genome. The rib was human flesh, blood and bone; human cells, chromosomes, genes and DNA. The rib was made of human cells that have the 24th human chromosome that produces the Tree Of Life organ attached to the appendix tube. Adam’s rib cells are immortal human cells with 48 chromosomes (24 pairs), rather than our present 46 chromosomes (23 pairs).

My theories will also show you that Jesus was born from an uncontaminated rib cell. Jesus was born with a 24th pair of human chromosomes in his body cells, which produced the Tree Of Life organ attached to his appendix tube. Adam and Eve were born immortal (to begin with). Jesus was born immortal. My theories will show you that all human beings are destined to become immortal, after the ‘first’ death.

  • An opinion is not a sound foundation for a scientific hypothesis—or even a pseudoscientific one. Show me evidence.

  • There is no evidence of a magical small organ ever being attached to the end of the appendix.

  • We already produce small numbers of stem cells throughout life. They don’t confer immortality, nor is there any reason to expect they would.

  • A large collection of pluri- or toti-potent stem cells might have some advantages in enhancing regeneration. They’d have the disadvantage of also being a source of cancers.

  • Chromosomes don’t map to organs. Organs don’t grow from chromosomes.

  • Other apes do have 24 pairs of chromosomes. They aren’t immortal.

  • Eating fruit, or even magic fruit made of mammalian flesh, won’t selectively destroy a chromosome. And if it did, it wouldn’t have the mild consequence of knocking out an organ.

  • Where did Jesus’ mother get that uncontaminated rib cell?

  • 48 chromosome Jesus just confirms my hypothesis that Jesus was a chimpanzee. You can’t prove I’m wrong!

He goes on for many pages of absurd speculation. Did you know that when Doubting Thomas was poking around in Jesus’ wound, he was actually inspecting his appendicular organ?

(via Adam Rutherford)