Aaargh! Physicists!

I read this story with mounting disbelief. Every paragraph had me increasingly aghast. It’s another case of physicists explaining biology badly.

It started dubiously enough. Paul Davies, cosmologist and generally clever fellow, was recruited to help cure cancer, despite, by his own admission, having “no prior knowledge of cancer”.

Two years ago, in a spectacularly enlightened move, the US National Cancer Institute (NCI) decided to enlist the help of physical scientists. The idea was to bring fresh insights from disciplines like physics to help tackle cancer in radical new ways.

Uh, OK…I can agree that fresh insights can sometimes stimulate novel approaches. Cancer is an extraordinarily complex process, but maybe, just maybe, the scientists studying it are so deep in the details that they’re missing some obvious alternative avenue that would be productive to study. I can think of examples; for instance, Judah Folkman’s realization that inhibiting angiogenesis, the process by which cancers recruit a blood supply from healthy tissue, would be a clever way to attack cancers beyond just bashing the cancer cells themselves. But then, Folkman wasn’t ignorant of cancer…he came up with that strategy from a deep understanding of how cancers work.

So I’m doubtful, but prepared to read something that might be new and interesting…and then I read Davies’ suggestion. Gah.

A century ago the German biologist Ernst Haekel pointed out that the stages of embryo development recapitulate the evolutionary history of the animal. Human embryos, for instance, develop, then lose, gills, webbed feet and rudimentary tails, reflecting their ancient aquatic life styles. The genes responsible for these features normally get silenced at a later stage of development, but sometimes the genetic control system malfunctions and babies get born with tails and other ancestral traits. Such anomalous features are called atavisms.

Charles Lineweaver of the Australian National University is, like me, a cosmologist and astrobiologist with a fascination for how cancer fits into the story of life on Earth. Together we developed the theory that cancer tumours are a type of atavism that appears in the adult form when something disrupts the silencing of ancestral genes. The reason that cancer deploys so many formidable survival traits in succession, is, we think, because the ancient genetic toolkit active in the earliest stages of embryogenesis gets switched back on, re-activating the Proterozoic developmental plan for building cell colonies. If you travelled in a time machine back one billion years, you would see many clumps of cells resembling modern cancer tumours.

The implications of our theory, if correct, are profound. Rather than cancers being rogue cells degenerating randomly into genetic chaos, they are better regarded as organised footsoldiers marching to the beat of an ancient drum, recapitulating a billion-year-old lifestyle. As cancer progresses in the body, so more and more of the ancestral core within the genetic toolkit is activated, replaying evolution’s story in reverse sequence. And each step confers a more malignant trait, making the oncologist’s job harder.

I’m almost speechless. I’m almost embarrassed enough for Davies that I don’t want to point out the profound stupidities in that whole line of argument. But then, there’s this vicious little part of my brain that perks up and wants to leap and rend and gnaw and shred. Maybe it’s an atavism.

Please, someone inform Davies that Haeckel was wrong. Recapitulation theory doesn’t work and embryos do not go through the evolutionary stages of their ancestors. We do not develop and then lose gills: we develop generalized branchial structures that subsequently differentiate and specialize. In fish, some of those arches differentiate into gills, but those same arches in us develop into the thyroid gland and miscellaneous cartilagenous and bony structures of the throat and ears.

It’s better to regard embryos as following von Baerian developmental trajectories, proceeding from an initially generalized state to a more refined and specialized state over time. Limbs don’t reflect our ancient aquatic ancestry in utero, instead, limbs develop as initially blobby protrusions and digits develop by later sculpting of the tissue.

Sure, there is an ancestral core of genes and processes deep in metazoan development. But Davies seems to think they’re lurking, silenced, waiting to be switched on and turn the cell into a prehistoric monster. This is not correct. Those ancient genes are active, operating in common developmental processes all over the place. You want to see Proterozoic cell colonies? Look in the bone marrow, at the hematopoietic pathways that produce masses of blood cells. The genes he’s talking about are those involved in mitosis and cell adhesion. They aren’t dinosaurs of the genome that get resurrected by genetic accidents. but the engines of cell proliferation that lose the governors that regulate their controlled expression, and go into runaway mode in cancers.

But even if their model were correct (which is such a silly way to start a paragraph; it’s like announcing, “If the Flintstones were an accurate portrayal of stone age life…”), it doesn’t help. We don’t have tools to manipulate atavisms. We don’t see any genetic circuits that can be called atavistic. The Flintstones might have made record players out of rocks, but that doesn’t imply that the music recording industry can get valuable insights from the show.

Oh, well, I shouldn’t be so negative. I’m alienating possible sources of work here. I understand the physicists have encountered some peculiar results lately. Have they considered bringing in a biologist consultant with no prior knowledge of particle physics? I have some interesting ideas that might explain their anomalies, based on my casual understanding of phlogiston theory and ætheric humours.

My cunning plan has worked!

In my talk at the Society for Developmental Biology, I encouraged more scientists to take advantage of the internet to share science with the public. Someone fell for it! Saori Haigo has started a blog, and she even explains why.

I’ve started this blog because I believe I have a social responsibility as a professional scientist to communicate science openly to the people. I will blog about what I think are important topics in the biological and biomedical sciences and explore the value, current issues, and realistic expectations of what we gain from doing research on that topic. In addition, I’ll explore how science is done, share with you why I think the research I’m working on is of interest and worth funding by taxpayers, give you a taste of what my daily activities entail, and share the latest cutting edge research published in science journals. All in layman’s terms, so you can follow too.

I hope through my posts you will come to appreciate the value of academic science and learn about a world which may seem ‘foreign’ to you. And also to learn something neat along the way. Enjoy!

So go browse already. It’s a brand new blog, but she’s already got some interesting stuff, including spinning eggs.

Coming attractions

I have a couple of promising events that don’t have firm dates yet, but you might want to keep your eyes open for them in the near future.

  • The paperwork for Rock Beyond Belief has been resubmitted, and with any luck they might be able to pull off an atheist event at Fort Bragg after all.

  • What are you doing next spring? You might want to think about visiting Washington DC for the big Reason Rally. Several of the big atheist organizations are coordinating for a massive rally on the mall. Everyone must show up! We will all demand a secular nation NOW!

Changes, one way or another

I have news. Scienceblogs is going to be folded into a new organization sometime soon — basically, we’ve been bought. I can’t discuss all of the details just yet, but let’s just say it is a prestigious national magazine with a healthy bottom line that will do us a lot of good. There are certainly some advantages: like I said, prestigious, and there’s also a commitment to up-to-date technology and migrating to better blogging software. There’s also an agreement that the range of topics I discuss here, including the strong dissent from religion and the atheism and the anti-creationism stuff, are acceptable subjects. So that’s the happy part of the story.

The worrisome bit: there are standards and practices to follow, which is not a bad thing in and of itself, but I do not want my peculiar voice to be compromised. That’s why I’m in this thing in the first place, to be able to express myself as I want when I want. So we’re in the delicate negotiation phase, trying to find agreements on form that don’t infringe on content, that will allow me to say any damn thing I want but maybe will require me to take an extra moment to review my articles with more cool deliberation before clicking that ‘submit’ button.

It is entirely possible that we won’t be able to find that position that is acceptable to both sides of our discussion, in which case I’ll cheerfully move on to an independent server and keep on keeping on right there. I’ll be thinking about the pluses and cons for a while.

I said “both sides,” but there are actually three sides: me, the hosting organization, and you the readers. How would you react if, for instance, profanity filters went up on the comments? Right now, it’s a real free-for-all in the comments, but I do clean up spam, ban certain elements that have demonstrated their trollishness, and will occasionally swoop in and erase comments that reveal personal information or contain nothing but bigoted raving. Would you leave if some automated software converted certain four-letter words to euphemisms, or if comments containing such words were held up until you edited them to meet the standards? What limits to expression would you accept?

These are trade-offs, so another interesting question is, what would persuade you that some limits to language are acceptable? Are there features that you think it would be worth demanding (say, user editing, or just faster performance, or free ponies with every comment) that you’d like to demand for the price of watching your potty-mouths a little more? We’re negotiating, you know — they make requests, we make requests — so tell me what’s most important to you.

I sure haven’t signed any contract with this organization yet, so it’s still entirely possible that I’ll just fly off my own way. Your input will be a factor, so speak up here, and I’ll listen. No matter what, though, things will not be the same, and there will be changes coming this summer.

Order soon!

The latest special t-shirt from woot is this one:

i-91a6e5800d6852f9dd30e9a95b4ee958-wootshirt.jpeg

I don’t think they’ll last long so you better get your order in fast.

Woot seems to track their sales stats closely; I wonder if there is a significant preference for cephalopods on shirts over, say, flowers or trios of wolves or something.