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[inteuniso]

another source for the metal hydrogen if anyone's interested:
https://arstechnica.com/science/2017/01/80-years-late-scientists-finally-turn-hydrogen-into-a-metal/

"Diamond failure," they note, "is the principal limitation for achieving the required pressures to observe SMH," where SMH means "solid metallic hydrogen" rather than "shaking my head."

Clearly we need lonsdaleite anvils.

[Sheb]

Yeah, it's pretty cool that they saw what is basically that in the lab. The amoebas are now dependent on the bacteria being there. Additionally, since they now inhabit a very specific type of amoeba these bacteria might in fact lose the ability to move into "normal" amoebas. I should probably link a source however because the claims are pretty big (1995 paper):

Spoiler: Amoeba symbiosis research (click to show/hide)

https://www.ncbi.nlm.nih.gov/pubmed/14732171

The large, free-living amoebae are inherently phagocytic. They capture, ingest and digest microbes within their phagolysosomes, including those that survive in other cells. One exception is an unidentified strain of Gram-negative, rod-shaped bacteria that spontaneously infected the D strain of Amoeba proteus and came to survive inside them. These bacteria established a stable symbiotic relationship with amoebae that has resulted in phenotypic modulation of the host and mutual dependence for survival.

Well that's just one paper, from googling around it seems that the original paper was in the 1970s and the same people kept researching them up until about 2004, by which point they could report on how the bacteria were switching specific gene expressions in the host on and off deliberately. But obviously what's happening vs knowing specifically how it's happening are two different matters. Obviously in 30 years of symbiosis there's a lot more that would have been going on, but with only one lab doing the research you can only glean so much information.
https://www.ncbi.nlm.nih.gov/pubmed/15537083
After that, the guy researching this retired (he'd been at it since the 1960s).

BTW two independent teams at Harvard and University of Maryland have simultaneously reported the creation of "time crystals" (structures which repeat in both time and space, i.e. the undulate) using very different materials to make them, based on a theory that was recently published:
https://science.slashdot.org/story/17/01/28/2027253/scientist-investigate-a-brand-new-form-of-matter-time-crystals
Obviously this needs to be replicated further, but two completely different teams doing it at the same time, from stuff that is completely different and getting the same result which matches the theory, that in itself ticks the right boxes.

That's pretty sweet, even though it's kinda weird so little people seems to have taken interest in this (his papers have only a handful of citations). Good monday morning reading while my PCRs are running though, thanks!

[scrdest]

I was revising notes and that reminded me to try to get an update on nivolumab.

Two new approvals, week ago for urothelial carcinoma, one on Jan 20th for gastric cancer.

4/270 had lethal side-effect and 17% discontinued due to side-effects, 7/270 had a complete response (clinical->human: all detectable cancer is kill) in the former. CBA to look up data on the gastric cancer trials vOv.

[Reelya]

https://science.slashdot.org/story/17/02/10/2248255/first-gene-drive-in-mammals-could-aid-vast-new-zealand-eradication-plan

Scientists in New Zealand are trying CRISPR genome editing to put a gene in male mice that causes them to only have male children. The idea is to spread these mice and they breed with the other mice, causing a runaway process in which the population runs out of females and crashes. Doing this in mammals is a first, but they're already trying this out with insects such as malaria-carrying mosquitos:
http://www.nature.com/nbt/journal/v34/n1/full/nbt.3439.html

Cane Toads in Australia would also be a great candidate for this sort of thing. They get everywhere, so a few genome-edited males would hop around and once they "infect" a local population of the toads with their male-only germline, then that population would implode, but the excess males would spread out in search of further mates. It's a brilliant strategy.

[Rose]

Children of men?

[Reelya]

I never thought the plot of Children of Men made a whole lot of sense. 20 years of no babies should mean 20 years of steady population decline, yet their was clear population pressure and urban slums developing, with masses of refugees trying to get into the UK.

People stopped working because they don't care because "there's no future" yet they're all desperated for food now. If they're desperate for food, they shouldn't have stopped working now, shouldn't they?

[Eric Blank]

Sounds reasonable, hopefully it works. Wonder if that would work with mosquitoes. Wonder if you could accidentally drive a species to extinction by failing to contain the infected males. Maybe if there was some other marker to identify whether a particular male is affected without having to do genetic testing and which doesn't affect their fitness otherwise. You'd want these affected individuals to be more fit than average to help spread their genes around as much as possible, since once they run out of females the population is done.

[Reelya]

It works by having a copy of CRISPR editing system that's geared to find a specific gene in the host, then "repair" it to match the other copy. Basically the target gene is the one that doesn't have the copy of the CRISPR system in it. So effectively, when you have one CRISPR system in a host, it copies itself to the second chromosome, overwriting a specific gene that you didn't like.

So in other words the gene system makes additional copies of itself that fall outside the normal mendelian genetics system with it's natural selection. That means that the normal ideas about organism fitness don't quite apply in this case, and in fact one of the ideas about doing this in mosquitos involves adding a gene that makes them less fit. Because this system "cheats" at natural selection it can actually drive down the total population fitness as a whole.

[wierd]

It would be interesting to see how that interacts with Wolbachia species in the mosquitos.

There is a project to introduce Wolbachia into the west nile mosquito, but if coupled with a gene-drive to force male phenotype, it could cause strange reactions.

http://www.eliminatedengue.com/our-research/wolbachia

Really, Wolbachia is the *better* approach, because it causes infected females to be self-fertile in most instances. It also forces genotypical male larvae to become female adults, as part of its life cycle. (It can only spread down the insect germline in female hosts, so it disrupts insect pupation and forces female phenotype development.)

[Reelya]

Working out the maths for this (ignoring the gender fixing), there would be "normal" organism AA, and "crispr" organism BB. The special rule is that AA+BB=BB rather than AB. So if AA and BB are half the population each, equally split male and female, then only 1/4 pairings are AA/AA => AA , with the rest leading straight to BB, so it goes from 50% => 75% of the population within a single generation, given equal fitness. As a general rule if the population ratio of the mutant is "n" (out of 1), then the next generation will be n_t+1 1 - (1-n_t)^2), so if the current amount is 0.1 (10%) of the population having BB genes, the next generation will be 1 - 0.81 = 19%, so basically, when it's in low concentrations the prevalence of this gene doubles ever generation, and at high concentrations the prevalence of the unifected basically halves every generation.

But the above assumes equal fitness. I put together a JavaScript to do the numbers, if they're equally fit, then 1% mutants would be 99% in 10 generations, which is an extremely short amount of time. Normally, a mutant of equal fitness wouldn't increase the proportion of organisms with it's genes whatsoever. So how about if the BB's are less fit? Basically since they double their share of the gene pool every generation at the limit of low population, then AAs would have to survive twice as often to stop BBs getting a foothold. As the proportion of mutants rises the needed fitness of the mutants actually drops, they only need 42% fitness to break even with the normal ones at 50% population, and the limit to maintain 100% of the population being mutants approaches 25% fitness at 100%. So even really marginal organisms with this system could permanently take over a population if you seeded enough.

The real advantage of this over the Wolbachia strategy is that this is a self-replicating system whereas the Wolbachia requires you to constantly reseed the infertile males in large numbers. As soon as you stop seeding the infertile males, any residual mosquito population can rebound, and there might be pockets of remaining population that your released mosquitos can't reach.

[wierd]

Wolbachia makes the females self-fertile in many species that have adapted to them.
https://scholar.google.com/scholar?q=wolbachia-induced+parthenogenesis&hl=en&as_sdt=0&as_vis=1&oi=scholart&sa=X&ved=0ahUKEwj7kqOvzIfSAhXEyoMKHUuRAmEQgQMIGDAA


They dont NEED males.

See for instance, wasps, and many species of ant.

Wolbachia puts a VERY strong pressure on the infected organism, and supplies a LOT of biochemical hardware to the organism. Many insect species have become dependent upon their presence, and cannot survive without them.

[Reelya]

The CRISPR based method can pretty much do most of what they want as well. It doesn't need to do gender change - that's just one target application.

This CRISPR gene works by copying itself to any gene that lacks it, attacking one specified "unwanted" gene and carrying a payload along with it. You could use it to deliver anything that you really want. The advantage is that it spreads itself through a population by basically doubling each generation at the low limit and/or halving the non-infected population at the high limit. Exactly what it's delivering is up to the gene engineers.

Similar to walbachia infections, it is self-sustaining as opposed to something you have to keep reapplying. But the risk with walbachia is that it's still possible to have a disease transmitted by a walbachia-infected mosquito. So a disease could adapt to the new host. Also if they do indeed switch to parthanogenesis then future control mechanism which require sexual reproduction to spread them might stop working as a mosquito control mechanism.

[Eric Blank]

My vote is on not only eliminating female mice, but making them all bioluminescent.

[Reelya]

With ears on.

To be honest, I'd like to see the no-daughters gene hack used on feral cats (not to mention rabbits, foxes etc). That would seriously minimize the cat problem here, too. It would also incidentally reduce the number of people's pet cats having girl baby cats and thus kittens. The remainder could then be adopted out and there could be limited breeding to keep up the pet cat population.

https://www.technologyreview.com/s/603533/first-gene-drive-in-mammals-could-aid-vast-new-zealand-eradication-plan/
EDIT: oh and one female environmentalist who totally supported the researchers when they previously used poison to control mice (but eagles and other things also ate the poison), has now publicly dropped support for the group because of the species-specific gene drive tech. And she's also invoked feminism:

Cummings, the environmental lawyer who is also the author of a book critical of GMOs, says she’s also alarmed by the plans to target female mice. “Daughterless anything is a problem,” she says. “The whole ‘eliminate the female’ concept needs to be looked at philosophically and ethically.”

Uhuh, it's "philosophically" the answer because one male can mate with 100 females and have 100 litters of babies. Eliminating males isn't effective. The number of females is the controlling factor.

[wierd]

Reelya, you arent reading the real message there. She feels it is misogynistic to target female mice, despite the science saying it is the proper target, because of her feminism.   (Pure supposition, but I bet she could wax philosophical about how the patriarchy is at fault.)

In more polite and general terms, she has a subjective bias, and thus is not participating in science. ;P