Interesting Stuff Thread

recedite

Foot and Mouth virus did get released from a lab in 2007, from a strain which they had collected during a bad outbreak in 1967. They also have some nasty strains of Anthrax in labs around the world (just in case they're ever needed). Not GM I know, but supposedly subject to stringent safety procedures.

BTW this guy is responsible for "the calculations" predicting a Viking apocalypse. Apparently his horn looks a bit like the mythical horn of a Norse god which legend says will sound 100 days before Ragnarrok.
The guy is organising a touristy Viking festival in York on 22nd Feb next, so he has calculated back 100 days from then and blown on his horn. This apparently is guaranteed to trigger a mighty piss-up on 22nd Feb next (but not quite the end of the world).


http://www.jorvik-viking-festival.co.uk/2013/11/the-world-will-end-in-100-days-ragnarok-the-viking-apocalypse-predicted-for-22-february-2014/

Hotblack Desiato

I'd be much more worried about the bugs that are already out there. Global travel makes it easy for a new variant of, say, the flu, to spread rapidly. Flu mutates significantly each year and we've been lucky in recent years in that strains which caused serious illness were not very transmissable human-to-human but mostly only affected people in Asia working directly with pigs or poultry.

Given a new severe strain of the flu, which existing immunity and vaccines don't protect well from, and with strong human-to-human transmission, and we could be looking at many millions of deaths globally with very little we can do about it.

As far as bacteria are concerned, they seem to be evolving resistance faster than we can develop new antibiotics.

Sarky

Most antibiotics come from bacteria evolving new ways to get rid of competitors who evolved such resistance, so they provide the solution to that. Pharmaceutical companies have gotten lazy on stuff that used to be effective, they haven't really come up with anything new in a long, long time. I've worked on bacteria that produce antibiotics that are really effective against a lot of the so-called superbugs. They were only discovered a couple of years ago, but various institutes are well on the way to getting such substances out as working products.

It's an arms race. Bacteria develop resistance, their competitors develop new ways to kill them off. They develop resistance to that, bacteria evolve new antibiotics. That's pretty much how it's been since bacteria first appeared. <shrug>

Turtwig

Speaking of anti-biotics found this a very interesting read.

Many treatments require suppressing the immune system, to help destroy cancer or to keep a transplanted organ viable. That suppression makes people unusually vulnerable to infection. Antibiotics reduce the threat; without them, chemotherapy or radiation treatment would be as dangerous as the cancers they seek to cure. Dr. Michael Bell, who leads an infection-prevention division at the CDC, told me: “We deal with that risk now by loading people up with broad-spectrum antibiotics, sometimes for weeks at a stretch. But if you can’t do that, the decision to treat somebody takes on a different ethical tone. Similarly with transplantation. And severe burns are hugely susceptible to infection. Burn units would have a very, very difficult task keeping people alive.”

Antibiotics are administered prophylactically before operations as major as open-heart surgery and as routine as Caesarean sections and prostate biopsies. Without the drugs, the risks posed by those operations, and the likelihood that physicians would perform them, will change.

Article may have some scare mongering in it. I'm not sure, haven't read too much on it and came across this randomly in stumble upon. Sarklor, in your opinion, is the future for anti-biotics as bleak as painted here, or is it more optimistic?

Sarky

You are just determined to make sure I can't play Planetside 2 tonight, aren't you?

Lots of scaremongering in there all right. Well, from the perspective of this side of the Atlantic, anyway. The US has never managed to get its overuse of antibiotics under control, and most of the numbers are from American industry and health care. Whereas a lot of Europe is working hard on regulating antibiotic use, saving the big ones for important cases and using them sparingly. If the US could sort itself out in that regard, there'd be no need for sensationalism. I suppose if such articles scare people into using antibiotics sensibly, then great. Still, it's not showing us the full picture.

It doesn't really mention the ongoing search for new antibiotics, which is getting an impressive amount of funding. My M.Sc. research project was looking at a particular species of marine bacteria that had been discovered in a sponge off the coast of Galway in 2008. It produces substances that are very good indeed at killing off both MRSA and Clostridium difficile, which are the big players in drug-resistant infections. There were about 20 other species of microbe from that same sponge that produced their own antibiotics. I got to work on one of them after I graduated and the lab hired me for 6 months to continue the work. Same species of bacteria, different strain. It also produced anti-virals and anti-cancer agents. You can find the DNA sequence for that strain here. /shameless plug

I was using fairly new methods to look for antibiotics that didn't require lab work (which is useful for bacteria that are really hard to grow in lab conditions). Y'see, a big chunk of antibiotics are complicated large molecules which require some very specific genetic machinery to produce, and the DNA sequences that contain the genes to make this machinery is easy to spot. And as it turns out, the machinery is extremely modular in nature, being quite a repetitive series of sequences, much like an assembly line. Here are Wiki pages for PKS and NRPS gene clusters which are some of the most important producers of antibiotics. They're quite similar in that they string long chains of molecules together and fold them up in interesting ways, but the machinery that does it is very modular so adding a different group here or causing a bend in the chain there leads to very different drugs with effects on very different organisms. You can also find hybrids of PKS and NRPS clusters for added variety.

So, once you have the DNA sequence for an organism you can feed it into a tool like AntiSMASH (Antibiotics & Secondary Metabolite Analysis SHell), and it'll pick out sections of the sequence that look like they code for antibiotics or similar substances, based on the commonalities most of these genes possess. AntiSMASH in particular is quite nice, as it will even try to predict a chemical structure for the potential antibiotic. Here, the help section of AntiSMASH can explain most of the technical stuff. Suffice to say it uses very clever probabalistic algorithms and cross-referencing with massive databases to tell you which parts of a genome make what most of us would call antibiotics. If you like you can try running some DNA through it yourself, just don't upload a whole genome or it'll take all day and give you so many results you're in danger of breaking the HTML. Tools like the University of Maryland's PKS/NRPS Analyser or the first tool I ever used for this, SBSPKS (Structure Based Sequence analysis for Polyketide Synthases) offer far more detail on those types of gene clusters.

This kind of genome mining is relatively new, and it can show up new avenues for antibiotics from even old well-studied species, never mind the hundreds or thousands of new species and strains being discovered. It also opens up the very real possibility of creating our own antibiotic-producing genetic machinery and inserting it into bacteria to produce it for us. Couple that with our rapidly improving knowledge of how all the genes, proteins and cause-and-effect cascades make an organism tick, and we have a good idea on what metabolic pathways in a bug you need to knock out to kill it.

And that's not even mentioning the research going on with bacteriophages (viruses that infect bacteria). They reproduce and evolve even faster than bacteria do, so they're always one step ahead of their hosts. They are so radically different from the viruses that infect humans that there's just no way they'd be a threat to us. So introduce a bacteriophage to an infection, and watch as the infection dies off to manageable levels, or dies off completely, clean off the wound with some antiseptic and let it heal. It was very big in Russia, but world politics and anti-Soviet sentiment, not to mention all the research being written in Russian means that it's kind of only being rediscovered now.

And then there's the approach of wrapping a drug in artificially synthesised DNA that is coded specifically to look harmless to a bacterial cell, bypasses their defences and releases the payload inside. Still in proof-of-concept stage, as far as I remember, but very promising nonetheless.

We haven't quite cracked this stuff just yet, clinical trials are ongoing for a few of those new drugs, and they take years (and rightly so. You need to be damn sure a drug is safe before anyone will let you sell it) and producing useful quantities of bacteriophage is still hard, but I don't think we have any real cause for worry that humanity will be wiped out by drug resistant bacteria. Give us another few years and we'll have discovered penicillin all over again, several times over, with the ability to KEEP discovering it whenever we need to.

Aaaand it's 11pm. I have to get up at 7 and commute for an hour to get to the lab. Thanks a lot.

[-0-]

Awesome post Sarky.

Sarky

Maybe, but it won't change my k:d ratio or give me back that your of sleep. Jernal hates me and wants me to suffer

pauldla

Sarky wrote: »

Maybe, but it won't change my k:d ratio or give me back that your of sleep. Jernal hates me and wants me to suffer

No, God hates you and wants you to suffer. I'd say Jernal thinks your pretty cool.

Luckily, God does not exist, but Jernal does. Yay cosmos!

robindch

Sarky wrote: »

So introduce a bacteriophage to an infection, and watch as the infection dies off to manageable levels, or dies off completely, clean off the wound with some antiseptic and let it heal. It was very big in Russia, but world politics and anti-Soviet sentiment, not to mention all the research being written in Russian means that it's kind of only being rediscovered now.

I remember reading something years ago about some research center in Georgia, Tblisi probably, which was the FSU's leading authority on bacteriophages. I don't know whatever came of all of that, but the results they were reporting at the time seemed quite impressive, all the more so given the shoestring they were operating on.

Cabaal

Advanced canal network (can be seen on 1960's spy sat photos), hundreds of years before jesus apparently existed

http://www.telegraph.co.uk/earth/environment/archaeology/10470443/Pictured-the-real-site-of-the-Hanging-Gardens-of-Babylon.html

You can watch the doc about this also on 4OD

http://www.channel4.com/programmes/finding-babylons-hanging-garden

The use of the Archamedes' screws 400 years before Archamedes was even born is pretty interesting, the naming of the screw also seems pretty logical.

People named stuff for what it looked like, she makes a very valid point that in hundreds of years from now if you told somebody people had mice on every computer desk it would make no sense what so ever.

Cabaal

I weep for our species,

http://www.broadsheet.ie/2013/11/25/can-you-adam-and-eve-it/

Some 40% of DUP activists believe that creationism should be taught in science classes, a Belfast Telegraph survey has found. Creationism is the belief that the world, animals and plants were created “by a supernatural being less than 10,000 years ago”.

Mainstream science holds that the earth is four and a half billion years old and that life evolved from one-celled organisms. Some 50% of DUP respondents believed creationism shouldn’t be taught in science class, with 10% not knowing and 40% believing it should be there as well as, or instead of, mainstream science.

Teaching Adam & Eve as fact, oh your god!

FouxDaFaFa

A ring made from dinosaur bone, gold and meteorite.

Aka, the coolest ring in the world.

(I would have thought that dinosaur bones were all invaluable).

Liamario

Cabaal wrote: »

I weep for our species,

http://www.broadsheet.ie/2013/11/25/can-you-adam-and-eve-it/



Teaching Adam & Eve as fact, oh your god!

Mainstream science holds that the earth is four and a half billion years old

Mainstream science? As opposed to what?

robindch

Liamario wrote: »

Mainstream science? As opposed to what?

As opposed to makey-uppey science?

Delirium

Scientists have found fossil evidence of ancient microbial communities that lived 3.5 billion years ago.

The new fossils, described in the journal Astrobiology, may be among the most ancient fossil life forms ever found.

"This is one of the, or the, oldest fossils ever found. You've got a 3.5-billion-year-old ecosystem," said study co-author Robert Hazen, an earth scientist at the Carnegie Institution for Science in Washington, D.C.

The new find reveals that a scant 1 billion years after Earth's origin, complex microbial communities that clung to sediments along the windswept seashore had already begun harvesting energy from sunlight, rather than the rocks.

Source

Sarky

Saw that a couple of hours ago actually. Fascinating find.

oscarBravo

Shame about the typo in the caption.

recedite

FouxDaFaFa wrote: »

A ring made from dinosaur bone, gold and meteorite.

Aka, the coolest ring in the world.

(I would have thought that dinosaur bones were all invaluable).

Technically the "bone" is more like a stone, being a fossil, so a fossil is a kind of copy anyway. A lot of the "bones" on display in museums are plastic copies of fossils.

Hotblack Desiato

Speaking of fossils - fossilized dino poo.

http://www.bbc.co.uk/news/science-environment-25126333

Giant prehistoric toilet unearthed
By James Morgan
Science reporter, BBC News

Mrs Morgan must be so proud of her little Jimmy :pac:

robindch

Interesting, up to a point - handy list of biblical contradictions:

http://www.skeptically.org/bible/id8.html/

BTW, I gave Popette a copy of The Year of Living Biblically the other day and she didn't throw it back at me. Let's see the response...

kylith

robindch wrote: »

Interesting, up to a point - handy list of biblical contradictions:

http://www.skeptically.org/bible/id8.html/

BTW, I gave Popette a copy of The Year of Living Biblically the other day and she didn't throw it back at me. Let's see the response...

I read that a while back. I'd love to see more Christians live biblically, even for a year, and see how they get on telling female managers to be silent and sacrificing poultry every time they have sex.

recedite

ninja900 wrote: »

Speaking of fossils - fossilized dino poo.

http://www.bbc.co.uk/news/science-environment-25126333

Aaah, a lovely estwing fossil hunting hammer posing photogenically at the edge of the photo. I wonder if anyone will give me one for christmas, so I can add it to my collection of immaculate and rarely used tools?

Obliq

recedite wrote: »

Aaah, a lovely estwing fossil hunting hammer posing photogenically at the edge of the photo. I wonder if anyone will give me one for christmas, so I can add it to my collection of immaculate and rarely used tools?

Ah yes. For the love of your OH's tool fetishes, Christmas is when you attempt to learn basic Norwegian to see if the best hand-forged adze in the world is cheaper from the maker than from the sole EU importer (sadly not, but it would be no fun without the thrill of the chase :rolleyes:).

legspin

recedite wrote: »

Aaah, a lovely estwing fossil hunting hammer posing photogenically at the edge of the photo. I wonder if anyone will give me one for christmas, so I can add it to my collection of immaculate and rarely used tools?

I have had an estwing hammer for 10 years now. Not a geological one but a latt hammer. The single best piece of equipment I have ever owned.

recedite

I had the leather-bound claw hammer for a few years.
Beautifully made and a real work of art, but inevitably it was robbed by some jealous barbarian. Then I got a cheap replacement for a short time until the thin tubular steel shaft kinked over. Now I have the blue handled estwing; not as fancy as the leather one, but better grip and shock absorbency. A really classy and well made tool.

legspin

recedite wrote: »

I had the leather-bound claw hammer for a few years.
Beautifully made and a real work of art, but inevitably it was robbed by some jealous barbarian. Then I got a cheap replacement for a short time until the thin tubular steel shaft kinked over. Now I have the blue handled estwing; not as fancy as the leather one, but better grip and shock absorbency. A really classy and well made tool.

Have been very lucky with mine. It is unusual enough in work that everyone knows it's mine and any time I have misplaced it, it has come back to me.

sephir0th

Sarky wrote: »

AntiSMASH in particular is quite nice, as it will even try to predict a chemical structure for the potential antibiotic. Here, the help section of AntiSMASH can explain most of the technical stuff. Suffice to say it uses very clever probabalistic algorithms and cross-referencing with massive databases to tell you which parts of a genome make what most of us would call antibiotics.

How far away are we from computing an antibiotic with a high degree of certainty (I guess it can't be deterministic)? And if we can do that, I assume we could synthesize (is that the right word?) the antibiotic, or perhaps we can already do that.

Sarky

sephir0th wrote: »

How far away are we from computing an antibiotic with a high degree of certainty (I guess it can't be deterministic)? And if we can do that, I assume we could synthesize (is that the right word?) the antibiotic, or perhaps we can already do that.

Still a ways off, but closer than you might think. It is actually quite deterministic; all the genes that make a specific antibiotic are usually found next to each other, and often in the order in which their end product is assembled. A bioinformatician that knows their chemistry can look at a set of genes and work out exactly what proteins they code for, and then work out pretty much exactly what those proteins with eachother. The computer prediction isn't able to account for everything. The individual groups that are added to the chain of an antibiotic can be modified before and after they're added by other genes, which aren't always easy to link to the main set of genes. The result is the end product may have a significantly different shape, or contain bits we hadn't thought of. Often the DNA assembly contains gaps in the sequences that make antibiotics, as they're long and repetitive and putting them back together is like assembling one of those jigsaws of a picture of a plate of means, and some of the pieces are perfect fits in several gaps but there is still only one 'correct' place to put them. Gaps confuse prediction software. You can fill them in with bits from similar species, but there's always a chance that something unique was there instead of a sequence we already knew. Lot of human work still involved in getting the full picture.

Still, something like AntiSMASH does a good job at predicting the backbone of the chemical, so you'd know what most of it was made of and you'd have a number very close to its weight, which are very important when you're trying to isolate a single molecule to have a look at its structure via electron microscopy or HPLC or whatever. I'm no biochemist but I worked with one for about 6 months on this subject. You'd have to ask someone else about the nitty-gritty of synthesising new drugs.

My guess is that it'd be easiest to modify existing genes that do most of the work, pop them into E. Coli or another easy to grow species and let them mass produce it.

sephir0th

Thanks for the detailed explanation. With regards the determinism, I was getting at the fact we do not have a complete computational model of the entire biological systems in the body, or even know if certain environmental factors could thwart gene expression and the effectiveness of the antibiotic - but, I'm probably being a little cynical here. In probabilistic terms, I guess we can be assured that the antibiotic will work with a high degree of certainty.

I still assume that the ultimate goal in bioinformatics is a complete computational representation of the human body and all it's interactions. In a sense we could build a body from a DNA sequence and experiment with it.

Sarky

sephir0th wrote: »

Thanks for the detailed explanation. With regards the determinism, I was getting at the fact we do not have a complete computational model of the entire biological systems in the body...

Not yet, but some day. We've got a couple of small microorganisms modelled quite well at this stage, and a few of the subsystems of humans like the inflammosome and gut metagenome are coming along nicely, all of which were a pretty big job. We're still figuring out the fine details of humans. But that's pretty much just a matter of time, storage space and processing power.

or even know if certain environmental factors could thwart gene expression and the effectiveness of the antibiotic - but, I'm probably being a little cynical here. In probabilistic terms, I guess we can be assured that the antibiotic will work with a high degree of certainty.

A high degree indeed. Clinical trials help determine any factors that might limit effectiveness. So do professional chemists- when they see the chemical structure of a drug they can work out a huge number of chemicals that would interact with it. Some antibiotics look very similar to anti-booze, for example, and based in that they'd know that if you took alcohol with them, you're going to be vomiting yourself inside-out.

I still assume that the ultimate goal in bioinformatics is a complete computational representation of the human body and all it's interactions. In a sense we could build a body from a DNA sequence and experiment with it.

Well I imagine it's the goal of people interested in humans. I'm way more interested in bacteria myself, and I suppose a detailed human model would be handy for working our how it'd react to infection, but I'd see that as an added bonus to modelling how the wee beasties work. Plenty of botanists more interested in a working model of their favourite plant. Depends on your particular interests really. Handy thing about science on that level though is that information is information, regardless of species everything works pretty much the same so specializing is less important. I imagine it's how a cross-platform language like Java feels...