Republicans hate science

The Republican-led government shutdown has also shut down the NSF.

National Science Foundation: Pretty Much Screwed. The NSF is the organization in charge of doling out government dollars to valuable scientific research that could cure fatal diseases, improve quality of life, or create new amazing things. Lest you forget, the MRI machine, voice control, multitouch displays, the internet, GPS, and many, many more advances were funded all or in part by the NSF. This isn’t frivolous. This is important work that will grind to a halt. The NSF will stop making payments to researchers, and government-funded programs the researchers need, like websites and document downloads, will not be operational.

They’ve also sent NASA and all of their active projects off on a vacation.

That now includes the Mars rover Curiosity, which has been shut down, taking a furlough in safe mode like 97 percent (!) of NASA employees. (Safe mode, which Curiosity has gone into for technical glitches before, means it won’t be completely turned off, but won’t be collecting new data, either.) More or less everyone who isn’t working on keeping the International Space Station astronauts safe will be receiving an unexpected vacation.

And have you seen the banner on PubMed?

Due to the lapse in government funding, PubMed is being maintained with minimal staffing. Information will be updated to the extent possible, and the agency will attempt to respond to urgent operational inquiries.

Updates regarding government operating status and resumption of normal operations can be found at http://www.usa.gov.

Thanks, you bastard shit-sucking dumbass Republicans!


Oh, and how about the USDA?

Due to the lapse in federal government funding, this website is not available.

After funding has been restored, please allow some time for this website to become available again.

This is embarrassing.

ransom

“it is time for the genitals of all children to be protected from people with knives and strong religious or cultural beliefs”

Taslima has the news: experts in Sweden, Norway, Finland, Denmark, and Iceland are proposing a complete ban on circumcisions of all types. Unfortunately, it’s a little premature to say it will happen: what we have right now is a group of ombudsmen for children, paediatricians, and paediatric surgeons passing a resolution at a meeting. There is no law yet.

But it certainly makes sense. Hacking up babies’ crotches is perverse and bizarre and unnecessary.

It’s Baturday!

I’m in Austin, Texas this weekend, hanging out with Matt Dillahunty and Beth Presswood, and it’s bats, bats, bats all day long. I’m giving a talk about bat evolution this afternoon (theme: so what if there aren’t many fossils?), and then we’re going on a bat cruise to watch the swarm of Mexican (don’t tell the Republicans) Free Tailed Bats launch themselves into the twilight skies. Also, somewhere in there will be Texas barbecue. I don’t think that will have much bat in it.

While I’m distracted, watch the pretty bats fly.

Satanique!

It has come to pass that we are working with the Stevens Community Humane Society again, which means that they have foisted another hell-beast cat upon us to house.

This is she.

ivy

She is a young beast, all black with a white patch on her chest. She is very curious and there has been a little problem with getting her to sit still — she’s got our whole house to explore so she’s rushing about all the time. She will occasionally jump on me with her claws and bump her head against my chin while making curious throbbing noises — I think it’s the sound of the millstones of Hell grinding souls to a pulp, or something.

We’ve been closing the bedroom doors tightly at night to prevent her nefarious pouncing — I think she has evil plans — but by day, we might have to collude. My cunning brain and her predatory energy…we could take over the world, if one of us doesn’t stab the other in the back.

I am calling her Satanique. The humane society gave her the name Ivy, which you might prefer if you’d rather cloak her true nature. If you’d like to break up our wicked partnership before our plans reach fruition, or if you think you need a partner in crime of your very own, contact the Stevens Community Humane Society. Tell them you want the black-furred agent code-named Ivy that is holed up in the Myers safehouse. They might be able to arrange something.

A philosopher agrees with me

I don’t know whether this is a good thing, or a bad thing, but at least he’s agreeing for a different reason. On the question of whether we’ll someday be able to download brains into a computer, I’ve said no for largely procedural reasons: there is no way to capture the state of all the complex molecules (and the simple ions, either) of the brain in any kind of snapshot, and the excuses of the download proponents are ludicrously ignorant of even the current state of biology. John Wilkins says no for a different and interesting reasons: a simulation (and that’s all a computer version of a person could be) is not the thing itself. The map is not the territory. So even surrendering the idea of a high-fidelity transfer and saying that you’ll just develop a model of a brain doesn’t get you anywhere close to solving the problem of immortalizing “me” in a machine.

Sorry, trans-humanists. I can believe that there can be a post-humanity, but it won’t include us, so I don’t know why you aspire to it. I can sort of imagine an earth transformed by human activities into a warmer, wetter, even more oceanic place that allows more squid to flourish, and it’s even a somewhat attractive future, but it’s not a human transformation.

What are tumor suppressor genes?

I’m trying to raise money for the The Leukemia & Lymphoma Society, and I promised to do a few things if we reached certain goals. I said I’d write a post explaining what tumor suppressor genes are, while wearing a pirate hat and nothing else, if we raised $5000. Shiver me timbers, I did! And it’s cold!

madnakedpirate

If you want more, go to my Light the Night fundraising page and throw money at it. I’ll write about microRNAs and cancer when we hit $7500. Note that we’re also getting matching funds from the Todd Stiefel Foundation, so join in, it’s a good deal.

There’s a basic principle in biological homeostasis (and it’s also true in cybernetics) that for every process that turns something on, you have an anti-process that turns it off. When you look at what’s going on inside the cell, you’ll often get the impression that it’s spinning its wheels — every protein, for instance, is being degraded at about the same rate that it’s being synthesized. The whole cell is in a state of dynamic equilibrium, in which it might look like the concentration of some protein is constant overall, but when you look closely, individual protein molecules are being constantly made, instantly targeted for destruction, and dismantled…only to be nearly instantly replaced by a duplicate. Everything is in a state of flux, and it looks terribly wasteful, but it means that everything is fluid and flexible and the cell is incredibly responsive to subtle cues.

Last time I wrote about oncogenes, genes that are activators of crucial cellular processes like cell division, and I told you that these play a role in cancer by sending faulty signals that switch on uncontrolled cell division. Given the above principle, you might expect that if there are gene products that turn on cell division, there ought to also be gene products that turn off cell division, a kind of anti-oncogene. And there are! They’re called tumor suppressor genes.

While acting in opposition to oncogenes, tumor suppressor genes typically exhibit another difference in behavior that sets them apart. Cancer causing mutations in oncogenes are usually dominant: that is, the mutation doesn’t just knock out the gene, it has to make a hyperactive gene, and just one mutant copy gone rogue is enough to start switching on cellular activity. Tumor suppressor gene mutations tend to be recessive.

You’ve usually got two copies of every gene. A tumor suppressor works to shut down renegade activity, and a cancer-causing mutation in one is most often simply going to be a mutation that destroys the gene — but since you’ve got two copies, it has a backup. Cancer needs to kill both copies of the tumor suppressor to escape from its anti-tumor actions.

The best known tumor suppressor gene is BRCA1, and it exhibits this behavior. BRCA1 is a good gene — it’s working to protect you from breast cancer. For most of us, every cell in our body has two functional copies of BRCA1. It’s like having two cops patrolling the beat, prepared to fight off any cancer threat, and for cancer to succeed, it has to kill off both. Even one left functional can suppress any effort by the cell to go hyperactive and proliferate. A mutation that knocks out one copy is rare, but two mutations that knock out both are even more rare — it follows two-hit kinetics, which means you multiply the probability of the two events together.

You will occasionally hear about someone being at high risk of cancer because they carry a bad allele of BRCA1 — Angeline Jolie was in the news about this recently. What has happened here is that the person was born inheriting one broken copy of the BRCA1 gene — their cells only have one cop on the beat. They aren’t born with cancer — that one copy of BRCA1 is sufficient to keep them safe — but now they are at much higher risk of an accidental mutation taking out their sole protector than if they had two.

Another well known tumor suppressor gene is Rb, the gene that when mutant can lead to retinoblastoma, or cancers of the eye. It also exhibits two hit kinetics, in that familial retinoblastoma is caused by inheritance of one mutant Rb allele, so that all it takes is one mutation later in life to lead to cancer. Sporadic retinoblastoma, that is retinoblastoma without previous examples in the family, is much rarer, because it requires a first somatic mutation and a second mutation later to take out the second copy.

famRb

Having an enabling mutation in one copy at birth so greatly increases the chance of retinoblastoma that afflicted individuals are likely to have bilateral cancers affecting both eyes, while it’s so rare in sporadic cases that it is almost always unilateral, affecting only one eye.

OK, you understand the principle. Last time, I wrote about the oncogene Ras, which, to make it simple switches on the mitotic machinery and promotes cell division. Does it have an anti-gene product that opposes Ras and switches off cell division?

Of course there is. Several actually. One example: recall that I told you that Ras is activated by binding GTP, and deactivated by converting GTP to GDP, and that Ras itself has GTPase activity and therefore works to switch itself off. There are also tumor suppressor proteins that are called GAPs, or GTPase activating proteins, that enhance Ras’s GTPase activity. One of them, called NF1 or Neurofibromin, binds to Ras and elevates its potency as a GTPase approximately 1000-fold — it basically makes Ras ultra-good at shutting down and doing nothing.

nf1gap

Oncogenes and tumor suppressors are the yin and yang of cellular regulation. Cancer cells often contain hyperactive oncogenes, and have shut down tumor suppressors…which suggests that one strategy for treating cancer is to develop inhibitors of oncogenes, and to repair, replace, or elevate expression of tumor suppressors. And that’s a rather pat explanation of some viable general strategies that of course encounter all kinds of additional complexities.


Donovan S, Shannon KM, Bollag G (2002) GTPase activating proteins: critical regulators of intracellular signaling.. Biochim Biophys Acta 1602(1):23-45.

Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646-74.

Weinberg, RA (2014) Biology of Cancer. Garland Science, New York.