How to make a funny-looking mouse

I’m going to tell you about a paper that was brought to my attention by some poor science journalism, so first I have to complain about the article in the Guardian. Bear with me.

This is dreadfully misleading.

Though everybody’s face is unique, the actual differences are relatively subtle. What distinguishes us is the exact size and position of things like the nose, forehead or lips. Scientists know that our DNA contains instructions on how to build our faces, but until now they have not known exactly how it accomplishes this.

Nope, we still don’t know. What he’s discussing is a paper that demonstrates that certain regulatory elements subtly influence the morphology of the face; it’s an initial step towards recognizing some of the components of the genome that contribute towards facial architecture, but no, we don’t know how DNA defines our morphology.

But this is disgraceful:

Visel’s team was particularly interested in the portion of the genome that does not encode for proteins – until recently nicknamed “junk” DNA – but which comprises around 98% of our genomes. In experiments using embryonic tissue from mice, where the structures that make up the face are in active development, Visel’s team identified more than 4,300 regions of the genome that regulate the behaviour of the specific genes that code for facial features.

These “transcriptional enhancers” tweak the function of hundreds of genes involved in building a face. Some of them switch genes on or off in different parts of the face, others work together to create, for example, the different proportions of a skull, the length of the nose or how much bone there is around the eyes.

NO! Bad journalist, bad, bad. Go sit in a corner and read some Koonin until you’ve figured this out.

Junk DNA is not defined as the part of the genome that does not encode for proteins. There is more regulatory, functional sequence in the genome that is non-coding than there is coding DNA, and that has never been called junk DNA. Look at the terminology used: “transcriptional enhancers”. That is a label for certain kinds of known regulatory elements, and discovering that there are sequences that modulate the expression of coding genes is not new, not interesting, and certainly does not remove anything from the category of junk DNA.

Alok Jha, hang your head in shame. You’re going to be favorably cited by the creationists soon.

But that said, the paper itself is very interesting. I should mention that nowhere in the text does it say anything about junk DNA — I suspect that the authors actually know what that is, unlike Jha.

What they did was use ChIP-seq, a technique for identifying regions of DNA that are bound by transcription factors, to identify areas of the genome that are actively bound by a protein called the P300 coactivator — which is known to be expressed in the developing facial region of the mouse. What they found is over 4000 scattered spots in the DNA that are recognized by a transcription factor. A smaller subset of these 4000 were analyzed for their sequential pattern of activation, and three of these potential modulators of face shape were selected for knock out experiments, in which the enhancer was completely deleted.

The genes these enhancers modulate were known to be important for facial development — knocking them out creates gross deformities of the head and face. Modifying the enhancers only leaves the actual genes intact, so you wouldn’t expect as extreme an effect.

One way to think of it is that there are genes that specify how to make an ear, for instance. So when these genes are switched on, they initiate a developmental program that builds an ear. The enhancers, though, tweak it. They ask, “How big? How high? Round or pointy? Floppy or firm?” So when you go in and randomly change the enhancers, you’d expect you’d still get an ear, but it might be subtly shifted in shape or position from the unmodified mouse ear.

And that’s exactly what they saw. The mice carrying deletions had subtle variations in skull shape as a consequence. In the figures below, all those mouse skulls might initially look completely identical, because you aren’t used to making fine judgments about mousey appearance. Stare at ’em a while, though, and you might begin to pick up on the small shifts in dimensions, shifts that are measurable and quantifiable and can be plotted in a chart.

Attanasio-face-enhancers-9

This is as expected — tweaking enhancers (which are not, I repeat, junk DNA) leads to slight variations in morphology — you get funny-looking mice, not monstrous-looking mice. Although I shouldn’t judge, maybe these particular shifts create the Brad Pitt of mousedom. That’s also why I say that implying that we now know exactly how DNA accomplishes its job of shaping the face is far from true: Attanasio and colleagues have identified a few genetic factors that have effects on craniofacial shaping, but not all, and most definitely they aren’t even close to working out all the potential interactions between different enhancers. You won’t be taking your zygotes down to the local DNA chop shop for prenatal genetic face sculpting for a long, long time yet, if ever.

Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. (2013) Fine tuning of craniofacial morphology by distant-acting enhancers. Science 342(6157):1241006. doi: 10.1126/science.1241006.

Do better. Please just do better.

It’s been a rough couple of weeks in the community of science bloggers, with the abrupt downfall of Bora Zivkovic, a very well liked (I consider him a friend) and influential leader. If you haven’t been following it, here’s a summary and timeline of recent events. The simple version of the whole story is that one of the major pioneers of science blogging and one of the people most instrumental in forging a community online has been found to have abused his privileges to sexually harass women members.

I’ve been processing how I feel about it all. As I say, Bora is a long-term friend; I remember when he joined us at Scienceblogs, and I also remember meeting him for the first time — he was a genuinely enthusiastic proponent of bringing people together and building a new platform for science communication. So this is a real tragedy that he has managed to undermine his own talents.

At the same time, though, here’s what I feel now: discouragement and despair and cynicism. We’ve been through this before in the skeptic/atheist communities. It was beginning to be my expectation that any grand attempt at building new organizations and improving communication was eventually going to collapse into the sewer of patriarchal sexual politics — that this pattern of sexual inequity was hardwired into the culture as a whole, and anything rising up out of it was going to be infected with the taint and eventually succumb to it. Same ol’, same ol’, I thought — the hard slog is never going to end.

But I was surprised: the science community’s response has been strong and appropriate. There’s no excusing his behavior, and rising up and demanding better is exactly what needed to be done, painful as it was. And they did it. There’s hope? Really? The struggle might actually lead to progress?

There has been a lot of writing on this topic in the last few weeks, but I thought Scicurious captured it particularly well.

Bora is not the man I thought he was. And the science communication community was not the place I thought it was.

The whole week has been full of downs. But toward the end. I started to see #ripples of hope. Not just the hashtag (though that alone is brilliant), but from other bloggers, saying, we can, in the future, be better. We want to be better. We WILL be better. People taking decisive action.

And I have been incredibly impressed with many of my colleagues. Yes, people fought, and jumped to conclusions, and etc. But there have been no death threats or rape threats, and compared to some communities I’ve seen…well I’m impressed. I always thought I wrote with and worked with some amazingly good people. Now, I KNOW it.

I contrast that with the atheist community. We also have some amazingly good people — as I travel around, I run into them all the time, at all levels of organization, and all doing good work — but we also have a substantial number of amazingly awful people…and as it turns out, it doesn’t take many sexist jerks clawing at the structure of your organization to distract and disrupt and impede progress. We have enough atheist asshats to provide shelter and support to exploiters — and too many of us are willing to overlook the content of our leaders’ characters, as long as they are willing to say the right words about the sacred atheist cause.

I’ve been astounded at how many people demand that we plaster over an atheist’s human flaws simply because, well, he’s The Man. We’ve been building up a body of revered saints, rather than recognizing that every one of us is human and needs to be held accountable. Face reality: if Bora had chosen to be a leader of the atheist community, rather than the online science community, right now there would be a huge battle going on, with loud voices shouting that “He only talked to these women; aren’t they strong enough to resist?” And the women who spoke out would be flooded with death threats and rape threats, and would be endlessly lampooned on our little hate nests scattered about the internet. Youtube would be full of videos expressing outrage that a Good Man should have been chastised by the Shrill Harpies of Feminism.

We’ve all seen it. Every atheist woman who dares to challenge the privileged status quo and ask for a little respect gets the treatment: just ask Rebecca Watson, or Jen McCreight, or Ophelia Benson. So I feel mixed: there is the despair at the failure of atheism to motivate real change, and hope that the science online community will set a model for everyone to follow.

But I also fear that atheism’s problems are rooted too deeply. This community is full of people who are already convinced that they are better than everyone else. But to be a good person, you have to always want to be better than yourself right now.

Who do you trust to tell you lies?

Here’s a simple experiment: separate two people. Give one person, the sender information about two packets of money, a small sum and a larger sum. Let them then tell the other person, the receiver, about the two packets, and give them the choice of which one they can have. Will the sender lie or not, in order to trick the receiver into picking the smaller packet?

The result in college students in Canada is that roughly 50% of the subjects lie. Before we go on, be sure to put this in context: this result is only valid in one particular culture. Related economic tests have found that there are many other cultures that value giving over receiving, and that would skew the interpretation of this one, so we’re not looking at broader human properties, but solely at the properties of products of one narrow culture. OK? OK.

The interesting result is a finer breakdown of the individuals who were more likely to lie. Mostly, no consistent associations were found, except that membership in any of these three groups were more likely to predict lying: a) Business majors, b) children of divorce, and c) people who say religion is important in their lives. I’m sorry, business majors, but (a) doesn’t surprise me at all. (b) I would not expect; I wondered if financial insecurity played a role, but they report no correlation with socioeconomic status or student debt. Hmmm.

Again, (c) does not surprise me in the slightest. I’ve known too many Christians. Sorry, believers, you’re not all bad, but man have you got a lot of hypocrites in your ranks. I would actually expect that because parasites are more likely to choose to blend in with the dominant group.

I would suggest a variation on the experiment, though. Pair the senders; I’d guess that those students professing a strong religious belief would show a strong reversal, being far less likely to lie, if a co-believer were there to witness. On the other hand, I’d bet that two business majors acting as senders would high-five each other with a successful lie. Put a couple of Libertarians in there, though, and they’d grab both packets and sneak out of the room.

Yeah, I have a hierarchy of well-earned cynicism.

The most depressing thing I’ve read today

Ten years ago, Ivan Macfadyen sailed across the Pacific Ocean. He repeated the voyage recently, and was shocked at the changes: the sea was empty of fish, and thick with garbage. He describes the painful experience, and also sees the trawlers stripping the reefs naked.

The speedboat came alongside and the Melanesian men aboard offered gifts of fruit and jars of jam and preserves.

"And they gave us five big sugar-bags full of fish," he said.

"They were good, big fish, of all kinds. Some were fresh, but others had obviously been in the sun for a while.

"We told them there was no way we could possibly use all those fish. There were just two of us, with no real place to store or keep them. They just shrugged and told us to tip them overboard. That’s what they would have done with them anyway, they said.

"They told us that his was just a small fraction of one day’s by-catch. That they were only interested in tuna and to them, everything else was rubbish. It was all killed, all dumped. They just trawled that reef day and night and stripped it of every living thing."

Macfadyen felt sick to his heart. That was one fishing boat among countless more working unseen beyond the horizon, many of them doing exactly the same thing.

No wonder the sea was dead. No wonder his baited lines caught nothing. There was nothing to catch.

Waste and destruction. Does humanity deserve to continue?

How about a new rule: no idiots allowed in our parks?

This is appalling: a couple of Boy Scout leaders knocked over a rock formation in Goblin Valley. And they were so stupid that they recorded the act and put it on youtube. Here it is; skip it if you don’t think you could bear watching a couple of man-children whooping and hollering while they vandalize a state park.

They now claim that they were acting to protect visitors to the park from a hazard, that the rock could have fallen at any time and hurt someone. Well, golly, I guess that means they ought to go romping through the park and knocking over all those amazing teetering rock formations. Maybe a little dynamite, just to be sure?

My turn

Today is the last day of the Paradigm Symposium, which is good — I don’t know how much more my poor brain could take. But this afternoon, after lunch, it’s my turn to speak. And I’ve been doing my homework, looking into what kinds of things paranormalists often believe about biology and evolution, and it’s been a long exercise in face-palming. They’re all over the map, but there are some common threads: the idea that evolution is inadequate (even while they rather blandly accept it for everything other than humans) and that aliens had to somehow assist us to reach the state we’re in now. Again, there isn’t one simple, coherent formula to describe their ideas — they’re not like the creationists who neatly fall into a few categories — and their hypotheses wobble all over the place. Some believe humans are the aliens, that we immigrated here to Planet Earth hundreds of thousands of years ago. Others believe that we’re hybrids, the product of mating between alien star-lords that we called gods and the common stock. Others think that no, it was planned modification of the ape genetic line by high-tech aliens, who intentionally inserted special genes into our cells to give us higher powers. And some are willing to say we evolved naturally here, but the aliens showed up to give us a technological boost, planting only ideas in human culture. So I’ve got a great big moving target to deal with, and I suspect that if I shoot down one hypothesis people will just glibly shift to one of the other excuses.

Here’s an example of the kind of nonsense I have to deal with.

Why is it that ancient native, cultures all around the world, from the Americas to Africa and Australia speak of advanced ETs ‘seeding’ humanity on earth? How is it that such apparently primitive peoples had in-depth accurate knowledge of constellations such as Sirius – which cannot be seen with the naked eye – several thousand years ago?

It is in my knowing that originally, a group of spiritually and technologically advanced ETs seeded humanity with the apparently ‘benevolent intent’ of mankind becoming ‘custodians’ of Mother Earth and working to live in balance with her. That’s why so many of the original tribal cultures such as the North American Indians, The Mayans, The African Dogon, The Tibetans and the Australian Aborigines all lived largely in harmony with the earth and at balance with nature.

I love that phrase, “It is in my knowing.” So meaningless, so pompous, so vacuous. You also get a taste of that benign assumption that any alien intervention was friendly in intent, and that “tribal cultures” are one with the Earth Mother. No, these cultures had relatively small population sizes and so did not impose any stresses on their environment that the environment could not handle, but give ’em a chance, and they could overwhelm a place just about as well as Europeans — look at Easter Island, for instance. We are all of us just people.

But that optimism also hides some profound ignorance and some nasty racism. On the ignorance side, this passage is about as annoyingly stupid as anything I’ve heard from creationists:

When Official Science delved deeper [into the question of why humans have 46 chromosomes while other apes have 48], it realised that the reason we have two less, is because the second and third chromosomes have been fused into one. It tries to explain this by saying such a mutation could happen naturally and points to other evidence in nature such as butterflies. Indeed such spontaneous mutation can happen, but what they’re not saying (and quietly brushing under the carpet), is that although this ‘mutation’ offers no natural evolutionary advantage whatsoever, it appears in EVERY SINGLE HUMAN!

How could that be? This fusing of the chromosomes is not what makes us human, and it does not offer any ‘natural’ evolutionary advantage (I’ll return to this in a moment). Yet we all have the mutation? If we supposedly evolved from Hominoids (like Neanderthal) and this mutation offers no advantage, then you’d expect to see some humans with 48 chromosomes and some with 46, but not ALL with 46!

But when you delve deeper into the chromosome story it gets even more curious. Each chromosome has three parts to it: both ends and a middle. Now in eight of the other human chromosomes, there has been an inversion of the middle part – it’s been ‘spun around’. Again, these inversions offer no natural evolutionary advantage – they don’t change the genetic material – yet ALL eight supposed ‘mutations’ appear in ALL humans.

Now you don’t need to be a mathematician to know, that the odds for all nine mutations to happen spontaneously, where no natural evolutionary advantage was gained, and for that to happen to both the original human male and female, at exactly the same time, and in exactly the same place, and for them to breed and produce the entire human offspring is so unlikely, the odds are literally zillions to one!

“Literally zillions to one!” Heh.

Just look at that raging typological thinking, though. This person apparently can’t grasp the idea of long, slow periods of gradual change in relatively neutral properties: it all had to happen all at once. Zing! All at once, all of the differences between humans and chimpanzees had to occur.

And here’s the underlying nastiness. This same post includes the video below with no qualification. It’s a smug little conversation between two racist assholes of the genus Newageius concluding that human races are soooo different that they must have been independently transplanted to earth from different alien worlds.

If you don’t want to listen to the whole awful thing (and I don’t blame you), here’s a representative comment from youtube that nicely illustrates what we’re dealing with.

My studies have actually yielded the idea that there are four basic structures that the Multi-racial structures evolve from: Africans, Asians, Europeans and Native Americans. These will coencide with the colors of the Medicine Wheel being Black, White, Yellow and Red. As with paint in art, you can derive many colors from four basic colors. Cells Are solar systems. We’re making all of this harder than it has to be. Chakra Systems. LOOK for crying out loud.

I can’t possibly address all of this bullshit in one hour; I also don’t assume that most of the audience agrees with this particular brand of lunacy. So I’m going to be giving a very simplified introduction to the human genome and properties of the human population that show that we are entirely children of Earth. Baby steps. Basics first. We’ll see how it goes.

A shame

Ken Ham is very proud to have spent a half-million dollars to buy a genuine, rare allosaur skeleton, which will now be locked up in a non-research institution and used to gull the rubes. It’s all part of their grand plan to pretend to be a scientific institution, while doing everything in their power to corrupt the public understanding of science.

What a shame.

And of course they’re going to use it to lie to visitors. Here’s what Andrew Snelling, their pet pseudoscientist, says about it.

As a geologist, Dr. Snelling added that unlike the way most of the Morrison Formation bones had been found scattered and mixed, the intact skeleton of this allosaur is testimony to extremely rapid burial, which is a confirmation of the global catastrophe of a Flood a few thousand years ago.

Lovely logic. Because the bones this one example were unscattered, it somehow supports their claim that it was killed 4000 years ago in a global flood. What? There’s nothing in the distribution of the bones that can be said to support a particular age for the specimen, and even if it were killed in a flood, floods do happen — it says nothing about a global catastrophe.

And if unmixed bones equal Recent Global Flood, what does it say that they admit that “most of the Morrison Formation bones had been found scattered and mixed”?

The rest of the press release is revealing in that it mentions that money for this grand exhibit, and another half-million dollars, came from one family — one very, very rich family — with far more money than sense. Just another demonstration that being an idiot does not interfere with the process of getting rich.

Friday Cephalopod: Wonderporn!

Oooh, those glossy thick pages. The bright colors that pop. The action shots. The extreme closeups. I admit it: I have an addiction to aquarist magazines. You’ve gotta check out CORAL: the reef & marine aquarium magazine, especially this issue, the one with the big bold feature on “WRASSES”. Turn to page 70. Oooh, baby. Wonderpus action, with the camera right up in the sweet spot.

Insertion! Hooah!

insertion

Money shot. Mmmm.

moneyshot

Was it good for you, too?