Wikipedia:Reference desk/Archives/Science/2015 November 12

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November 12

Basic DNA sequence alignment problem

I need some bioinformatics advice. I have two sets of seven DNA sequencing results from PCR fragments cloned into pGEM-T plasmid. Because the PCR amplicons can be incorporated into the plasmid in either of two directions, I've no way of knowing which are forward and which are reverse without trying to align each one individually in MegAlign (software from the pretty crappy suite available to me). There must be a quicker way to check alignments in both directions automatically though, right? --129.215.47.59 (talk) 12:53, 12 November 2015 (UTC)

Yegods! There were better tools 20 years ago. I'd suggest: a) concatenate all the sequences into a text file (put some N's or something between them so you can see the gaps so you don't have to look up the lengths); b) do a dot plot (bioinformatics) against the plasmid sequence and/or itself. There are various public servers that will do dot plots. Wnt (talk) 14:21, 12 November 2015 (UTC)

Zoom creep

Zoom creep is an effect in zoom lenses for cameras, exhibited when gravity causes movement in whatever device is responsible for adjusting the zoom of the lens. I was tempted to put it into Category:Effects of gravitation, because it's indeed an article "describing observable effects of gravitation", but everything else in the category is related to astrophysics. Is this still a good category for this article, or should I avoid it? Nyttend (talk) 14:31, 12 November 2015 (UTC)

Well, should the category contain BASE jumping, Cliff diving, bungie jumping, pachinko, foot injury from dropping a heavy weight on it, committing suicide by jumping off a bridge... ? I'm thinking no. Wnt (talk) 15:12, 12 November 2015 (UTC)

I guess this is one of the rare situations where I actually agree with WP:DEFINING; it's not particularly relevant to those, but it is here. All of those articles are people taking advantage of gravity for a purpose because nothing else can compare, not a problem specifically caused by gravity, and the intro says "Zoom creep is a phenomenon in zoom lenses where the angle of view of the lens changes when gravity is allowed to freely act on it". Since gravity is the focus of the lead here, but not mentioned in the others (or in jumper (suicide)), I see it differently. I'm just curious whether RD users familiar with this kind of subject would find (or expect others to find) its inclusion rather confusing. Nyttend (talk) 16:00, 12 November 2015 (UTC)

I think this category, "effects of gravitation," is not a particularly useful one for readers.

I agree that you could add zoom creep to the category. You would be totally justified if you included zoom creep in that category; by the same logic, we have articles on hundreds of other phenomena that are also effects of gravity.

But, do readers go searching for information in this fashion? The category just isn't an efficient way to represent organized information on a topic. It's sort of an indiscriminate collection of eclectic articles. There are broad articles on topics of physics; there are articles on geology; there are articles on specific events and experiments... but a reader who lands on the category page doesn't really get a coherent picture of how all these articles fit together. If the only criteria for inclusion in a category was that the item isn't technically not in the category... well, we could also create categories for all sorts of other physically-accurate descriptions: "things that reflect visible light," "things that have mass..."

These descriptions, while completely true of many subjects, are not useful ways to organize our encyclopedia for consumption by human readers. If the intent is to semantically mark the article for consumption by machines or software tools - well, there are better ways to do that, too.

I would expect to find "lens creep" in a category about photography - or camera equipment - or a category about gears, even. I would not expect this article to show up if I was reading about gravity at large.

Part of me wants to say that the category should be totally eliminated; or refactored so that it has better topical specificity.

For these reasons, I think that you should not add the article to the category, even though I agree that zoom creep is actually an "effect due to gravity."

Nimur (talk) 16:39, 12 November 2015 (UTC)

What are the other better ways to currently add semantic marking to articles on WP? I mean not considering the article itself, but a type of metadata, as the categories are. I semantic markup was an important value to our categories, independent of human browsing, but maybe I'm missing something. SemanticMantis (talk) 20:16, 12 November 2015 (UTC)

"Zoom creep" would be a good name for a member of the paparazzi. :-) 17:15, 12 November 2015 (UTC)

Drone attacks on killer bees (and vice versa)

Killer bees are known for attacking anything that vibrates and makes noise. Are they prone to attack drone aircraft?

Has anyone made a drone aircraft that is sturdy enough to not be destroyed by a killer bee swarm in mid-attack?

Can such a drone reliably sense when it has been attacked, and scan for where killer bee colonies are present?

If the drone narrows in on where a hive is located, how many of the killer bees will kill themselves trying to attack it?

I'm picturing a drone that scans an area; if attacked by killer bees, it scans more intensively, hones in on the hive, lets them kill as many of themselves as want to, then perhaps even determines the location and sprays insecticide on what is left. Can you do this?

An entirely different drone project: has anyone tried to make honeybee drones (European or African, I don't know...) that are exceptionally attractive (or otherwise successful) in mating with killer bees, that are sterile, carry parasites, genetically dilute, or otherwise neutralize the would-be colony? Wnt (talk) 19:50, 12 November 2015 (UTC)

How do you think a swarm of bees is going to hurt a drone? Drones don't feel pain, and stings won't do anything to a plastic shell. Conceivably enough could get squooshed and gum up the propellers, but I'm not seeing that as too likely. Part of what makes them more aggressive than ordinary European honeybees is that the alarm pheromone elicits different (and greater) responses at the same concentration, due to differential gene expression [1]. Also alarm pheromone induces analgesics that operate on opioid receptors [2], so they won't be feeling any pain. They will pretty much keep attacking stuff as long as the alarm pheromone is above threshold levels. I think getting squished may well release more alarm pheromones, but I can't easily find a ref to support that. The only robot bee that interacts with real bees that I know of is this rig [3] that can communicate via the bee dance and tell real bees where to go. As for a seek and destroy drone - sure, why not? The only really hard part in my mind would be distinguishing Africanized bees from any other insect that may defensively swarm an intruder. These things look and act a lot like regular old A. mellifera, with defensive aggression being the only main difference. SemanticMantis (talk) 20:33, 12 November 2015 (UTC)

If enough bees attacked the drone, would the weight of the bees eventually drag it to the ground? (A thought - The drone could perhaps detect the swarm using a thermal camera and some pattern-recognition software)DrChrissy ^(talk) 20:43, 12 November 2015 (UTC)

Oh wait, do you mean drones as in male bees for the second part? Sort of like what Oxitec is trying with mosquitoes? No, pretty sure that also won't work, virgin queens mate with a lot of males on their nuptial flight - [4]. So sterility and dilution won't matter, and I don't know know of any bee parasites that are spread through sex - mostly those spread through a hive, not via meetings in the air. Actually, one theory is that polyandry helps mitigate the effects of parasites and disease on social insects [5] SemanticMantis (talk) 20:43, 12 November 2015 (UTC)

Ok, I found a few viruses that can spread through sex [6] [7]. But the last thing I'd want to do is release viruses that can hurt regular domestic bees, they're having a tough time these days anyway. SemanticMantis (talk) 20:48, 12 November 2015 (UTC)