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Comment: Sharper angles? (Score 1) 57

What I took from TFA was that it's not the "sharper angles" that add to the power, but the way the fibres stack up as muscles get thicker - greater length of the area where the fibres touch means greater force, as a myosin fibril has lots of 'heads' that provide the force for moving, and where there's too little overlap between actin (the 'inert' structural fibre) and myosin (the active, moving) fibres, only a few heads from one myosin fibre will be able to grip the actin. As they slide towards each other to make the muscle contract, more myosin heads are able to interact with each actin filament at one time and so deliver more power. I'd draw an ASCII diagram, but the junk filters won't let me post it

I'm shocked no one has worked this out until now, but that's the great thing about a lot of discoveries - they look obvious when someone's already made them.

Comment: Re:another hit from technology (biotechnology) (Score 1) 586

by Biotech_is_Godzilla (#43570501) Attached to: Europe Needs Genetically Engineered Crops, Scientists Say

I was talking about golden rice version 1 as I'm ten years out of date. I now see there's a version 2 coming out that's much improved, so good point.

I'm not against GM per se, but depending on the modification it can and should warrant more caution than traditional breeding. It's not just the dangers within one plant (your cucumber example is a single one in a huge history of nothing untoward happening in traditional breeding, though, I'd just point out), it's the fact that this is genetic material that's often from an entirely different kingdom being introduced to a plant, that then has good potential for lateral transfer between different plant species; genetic material that may have unexpected effects.

You're probably right and governments are being overcautious, but it's better to be overcautious than to unleash a super-plant that grows and reproduces like a weed, is resistant to herbicides, sucks all the water out of the soil and is generally an unstoppable pest, for e.g.

Comment: Re:another hit from technology (biotechnology) (Score 1) 586

While classic breeding products (even mutagenesis!) are not tested even though it causes massive uncontrolled genetic changes (e.g. jumping genes get activated).

Mutagenesis is not classical breeding. 'Classical' breeding is extremely well tested. It is a slow process that has been performed for thousands of years and involves selecting traits that already exist in the plants in nature (i.e. that lots of people have already been exposed to) and breeding the plants together to combine traits that you're interested in. Mutagenenis/mutation breeding, on the other hand, started in the 20th century and involves bombarding seeds with radioactivity or treating them with mutagenic drugs which damage their DNA to see if you can come up with new, potentially unnatural, traits by mutating their genes. Don't conflate the two things, it makes your argument meaningless.

There is also no documentation that organic products are healthier in any way. You can find cancerogenic compounds in many organic products (e.g. aflatoxins) and nobody cares about that because it is "organic".

You should get out of your romantic view of nature, nature is dangerous!

What is interesting is that only people who do not understand anything about biology, plant breeding and GMOs are against GMOs.

Nature is dangerous, that much is true. But you're talking about carcinogenic compounds that people have been exposed to in their diets for millions of years, and are well adapted to. It's actually not so much the new, untested carcinogens you should worry about, it's the immunogens - things which may cause an allergic reaction. If you're sticking proteins from bacteria in food, there's every chance that you're going to encourage people to become allergic to that food.

And that's not even to mention the risks of lateral gene transfer between GM and non-GM plants (e.g. crops to weeds). It hasn't been shown to be happening yet, as far as I'm aware, but a lot of biologists are concerned that it could easily happen, considering the much increased tendency of GM plants to outcross, and because there is evidence that lateral gene transfer between plants does happen in the wild. The problem is that it doesn't matter if it's unlikely, it only has to happen once and it won't be easy to undo.

I understand biology very well, thank you, and GM concerns me. The main thing that bothers me is the way people like you say "GM is good"/"GM is bad", without realising that each genetic modification is completely different and you can't predict the consequences of all of them together in one go. You have to do it on a case-by-case basis, and even if we are aiming for low-risk modifications that slightly increase the amount of nutrients in a crop, like golden rice, a lot of testing has to be done to make sure that this doesn't get transferred to other plants/ increase the production of other proteins in the rice/ do something else unpredictable, like make the rice more suceptible to infection by Aspergillus (yay, aflatoxins!).

Other modifications, like roundup resistance, bother a lot of people as they appreciate that not only could resistance be easily transferred to weeds, it also encourages the use of roundup in larger and larger amounts, which may well have nasty consequences for people eating the crops and giving themselves chronic low-dose exposure to a toxin.

I think a lot of people in this thread have already said some of this, showing that you don't have to be a trained scientist to be aware of the potential issues with GMOs, you just have to have an ounce of sense and to keep yourself informed.

Comment: Re:Simulated vs. Real results (Score 3, Informative) 89

by Biotech_is_Godzilla (#43317575) Attached to: Biological Computer Created at Stanford

Read TFA for the components of this circuit. The DNA part of the circuit is most likely integrated into the cellular genome, so is effectively stationary in the nucleus. The RNA polymerase component is probably the naturally occurring version of the protein that already exists in the cell. RNA polymerase randomly diffuses around in the nucleus, but there's not just one molecule of RNA polymerase around, there's loads of them, and they can all do the same job. With help from other proteins, they bind to sequences in the genomic DNA that mean "make this gene under this condition", and transcribe the DNA into RNA, which then gets made into protein.

The conditions under which RNAP binds and transcribes can be dependent on the cell receiving certain signals from other cells, or a gene may be transcribed 'constitutively', meaning it is always transcribed unless the cell changes state/gets a signal from other cells. That's probably what they're using here - RNAP will transcribe what it can transcribe under all conditions, its just that you change what it's allowed to transcribe (see below). The odds of RNAP hitting the DNA part of the circuit are going to be high, and once they do hit the 'promoter' sequence in the DNA part of the circuit, they will lock onto it and start transcribing. They can't transcribe the interesting bit (the 'signal') unless it has been switched on by the third component of the 'circuit', integrase, which removes (and puts back) the "STOP" control for transcription (by cutting at defined sequences, specific to the integrase, either side of the STOP control).

So the integrase is acting as the gate, and the 'signal' represents electrons flowing to the drain... or whatever. IANACS.

The method of control for these circuits is probably on the level of the whole cell - the researchers will be adding signalling chemicals to the cells that switch on production of / alter the cellular location of the integrase so that it can either do its job or not. The rest of the circuit doesn't have to be directly controlled as it will constitutively do its job.

The potentially interesting bit comes from making the 'signal' that's produced be the chemical signalling molecule that controls expression/localisation of integrase in other cells. The problem they'd then immediately run into is that you can't stop the signalling molecule from also acting on the cell that's generating it, locking it into an "on" state, unless the other cells use a different signalling molecule to control their integrase/ use integrases that act at a different specific defined sequence. They could do that, but it would then be difficult to control the placement of cells containing the different flavours of transistor.

This is all speculation as I haven't got access to the full article, but from the abstract I'm fairly confident that's what these guys have done. It's not about to lead to anything remotely resembling a proper computer any time soon. As I biologist I automatically think of anything associated with 'synthetic biology' as being sensationalist rubbish, and I don't think this is an exception, sadly.

Comment: Re:It's not the academics opinion that really matt (Score 1) 193

by Biotech_is_Godzilla (#43048557) Attached to: The Real Reason Journal Articles Should Be Free

The idea of getting everyone to "decide" a random new open access journal should be high prestige may be a pipe dream, but a top-flight open access journal can spring up overnight, with the right backing. There is a recent example of this in the biosciences, http://www.elifesciences.org, backed by several big funding bodies.

I'm sure it's not much cheaper to publish there than other open access journals, but it aims to be on a par with Nature & Science, and the articles in it look of a similar quality from what I've seen. If enough high-prestige universities and funding bodies back a new open access journal it can go right in at the top...

Comment: Re:Didn't get much out of article... (Score 4, Informative) 67

Actually, the BBC article is very misleading when it comes to pretending that this is an amazing new discovery that this lab has intrepidly worked out from first principles. The head of the lab which produced this paper is a chemist who is big in the field (in that he makes a bunch of drugs that bind G4 DNA, and farms them out to biologists who test them in their cell lines which are defective in DNA repair) but G4 DNA is something that there's a lot of circumstantial biological evidence for.

You can look at the sequence of DNA (known from the human genome project) and see where G4 structures are likely to form. You can make G4 quadruplexes from short DNA sequences in vitro and do biophysics on them to show how incredibly strongly they interact (hard to boil them apart, and you can measure this happening with a calorimeter). There's also a lot of evidence that G4 quadruplexes are a) necessary as a regulatory/structural feature of chromosomes and b) potentially very dangerous/ deleterious if you take away the proteins which allow cells to replicate across G4-forming sequences properly.

The +5 comments above got a bit confused about why G4 DNA is found in great abundance in cancer cells. The reason for this is difficult to explain quickly, but basically: in a chromosome that's chilling out, and hasn't got much going on, G4-forming guanines are paired with their complementary cytosine residues to make a double helix. They therefore can't and won't form a quadruplex until you do something to them. What allows them to form quadruplexes is the act of DNA replication. In DNA replication the double helix is 'unzipped', forming two single strands of DNA, which are then used to make new strands, complementary to each of the single strands of old DNA.

It's the unzipping into single strands that frees up G4-forming sequences, which can then form a "knot" in the unpaired single strand of DNA by binding "sideways" to each other in the same single strand of DNA (i.e. intramolecularly). Someone above said this 'causes the DNA polymerase to make mistakes in replication'. What's most likely to happen (there's at least 2 strands of evidence for this) is the cell's normal replication machinery cannot deal with the G4, stalls and stops. It then waits around for ages for the G4 to be resolved. This is one cancer link - when the cell can't deal with the knot in a sensible period of time (hours), eventually the replication machinery 'gives up', the replication fork collapses, and you lose and rearrange DNA sequence, causing either massive cell death, or mutations and cancer in the few cells that do survive.

The other link, though, is what the +5 comments were getting confused about above - cancer cells appear to have more of these G4 structures than normal cells. This is in no way surprising at all though - it's not about "having more DNA", or it's about having more replicating DNA. i.e. DNA that's in a single-stranded state, and that can therefore form G4 quadruplexes. Stem cells also show more G4 DNA, as they're replicating, and replicating fast, just like cancer cells.

The 'making G4 drugs' idea comes from the same place that an awful lot of cancer treatments come from - these are fast-growing cells, and are therefore more susceptible to things that disrupt DNA replication, compared to normal cells which aren't replicating (most 'traditional' chemotherapy causes DNA damage, disrupting replication, and the main reason radiotherapy is thought to work is that it also causes DNA damage). If you drastically choke up DNA replication, you get some catastrophic cell death in fast-replicating cells, and if you can make a drug which only affects DNA replication without causing DNA damage, you can get the good effects of chemo without the bad (potential) effects of secondary cancers ten or fifteen years down the line (due to the massive dose of DNA damage you swallowed to catch the cancer, causing more cancer).

Sorry, that was a bit of an essay, but I know the guy who did this work (note the 5th author) and it annoys me that the BBC only pick up on the ridiculously simple stuff, and not the clever but complicated stuff that's been done elsewhere!

Comment: Re:US Metric System (Score 1) 1387

OMG you're right! I buy Sainsbury's milk the whole time, so I hadn't noticed the Cravendale Effect!

On the beer I was talking about beer bought in pubs. I would hope (though I'm probably wrong, what with the ridiculous levels alcohol is taxed at nowadays) that this represents the majority of beer sold in the UK. 440ml is the supermarket standard for lager, but 500ml is pretty much the standard for bottles of real ale. And it's not quite enough. That's why I can't ever have just one!

Comment: Re:US Metric System (Score 1) 1387

250ml, 500ml, 1l, 2l and 4l are typical sales units for dairy products in the UK. And before you say "look, they're using powers of two, metric is all a sham", those particular sizes map quite closely to the old sizes, making it easier for uber-conservative (and ardently anti-European) Britons to accept and understand metric.

Actually, milk is the one example where we don't tend to use metric in the UK - I've got a 2.272 litre (4 pint) bottle in my hand right now... Other dairy products like yoghurt and cream, fair enough, they're metric, but we still haven't let go of imperial measures for milk and beer, because 500ml is not quite enough.

Comment: Re:Kudos (Score 1) 1061

by Biotech_is_Godzilla (#42331583) Attached to: Anonymous Hacks Westboro Baptist Church

Are you kidding me? So if I were to follow you around everywhere you went doing this twenty four/seven you wouldn't want access to legal recourse? There is a point at which constant aggressive targeted pestering becomes an infringement of someones right to live without being driven mad by someone being a dick to them. Anti-harassment laws are there to stop people having to resort to violent means / being bullied into a state of extreme distress when some douchebag decides to make it their life's work to make one other person's life a misery.

Bear in mind that stalking is a form of harassment. Psychological bullying is a form of harassment. Short of condoning physical violence, how else would you deal with that kind of problem?

Comment: Re:Kudos (Score 1) 1061

by Biotech_is_Godzilla (#42315375) Attached to: Anonymous Hacks Westboro Baptist Church

Actually, harassment is an infringement upon a mourner's rights. It is repetitive behaviour intended to threaten or offend. Just because it's done to different groups of people doesn't make it any less harassment.

In fact, the Patriot Guard Riders mentioned above, who have been at many such events, should be within their rights to take WBC to court armed with the list of names just published and get a restraining order preventing them from going within a half mile of a churchyard or funeral.

That way if they try to pull this crap again they can be (legally) locked up. And hopefully anally raped.

Comment: Re:In defiance of Betteridge's law of headline: ye (Score 1) 333

by Biotech_is_Godzilla (#42301351) Attached to: Will Tablets Kill Off e-Readers?

The Kindle may be book-sized, but the size of a Kindle screen is smaller than a standard (A5?) book page, even that of the touchscreen Kindle. Instead of giving it more screen space and keeping it book-sized, they basically cut off the keyboard and made it a smaller-than-book-page size.

I had a Kindle with a keyboard bought for me as a gift. I would never have bought a Kindle for myself because the screen is irritatingly small. Hopefully now that the 10-inch tablet market is taking off they'll get a clue and release a touch version of the DX (and in the UK) or even better, a book-sized Kindle that's all screen, not the poxy 6-inch piece of crap consumers are subjected to at the moment.

Comment: Re:Balancing potential deaths with real-today ones (Score 1) 130

by Biotech_is_Godzilla (#42258665) Attached to: Altered Immune Cells Help Girl Beat Leukemia

Nope, the treatment does the opposite. There are two main types of lymphocyte involved here, antibody-producing B-cells, and 'killler' T-cells that can directly kill cells. The cancer is formed of B-cells that are proliferating out of control (though there are also normal B-cells about). Researchers remove T-cells from the body, 'arm' the T-cells against B-cells by introducing a new receptor which latches onto a protein on the cell surface of ALL B-cells, then stick them back in the body. They then kill ALL the patient's B-cells, the leukaemia and the normal cells.

It kills the cancer, but also one whole branch of the immune system. The patient is then dependent on getting antibodies injected for the rest of their lives, or they are susceptible to all sorts of disease.

This is a breakthrough, but the cure comes at a large cost as the loss of your B-cells could be permanent (the T-cells may persist in your body forever, continually killing new B-cells). Right now the treatment is a bit like swallowing a spider to catch a fly, but I'm sure they'll find a way to program these T-cells so that they can be treated with a drug and they will self-destruct. The technology exists, and I'm frankly amazed they haven't used it, it's a very small step that could make a huge difference for their patients.

Comment: Re:Polymerase chain reaction (Score 1) 44

by Biotech_is_Godzilla (#42158499) Attached to: First Direct Image of DNA Double Helix

You mean replication fork. "PCR fork" is not a meaningful term. PCR is an artificial way to replicate DNA, and is very different to, and much less complicated than, in vivo (in the cell) DNA replication.

You're right, though, this is not the first time they've visualised DNA. It may be the first time they've visualised it using electron microscopy at a resolution that means you can actually see what its fine structure looks like, instead of it looking like a smooth line, but we already had a good idea what the structure looked like from X-ray crystallography.

X-ray crystallography is an indirect method that gets its data from a massive crystal made of repeated molecules of DNA which is hence in a pretty unnatural state. The question is whether or not this new method is any better. Is the central bit of DNA in any less unnatural a state if it's stuck between 6 other helices, than if it were stuck in the middle of millions? It is possible to make crystals of DNA in the A-form (the ones in this paper are in the A-form, so are the same as what we've already seen from X-ray crystallography) so I'd say that this isn't that exciting a new technique, but this paper is in a pretty high impact journal, so maybe I'm missing something.

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