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November 17

Instrumental analysis in the biology department?

So I've never taken a course in biology before, what is the biology equivalent for the chemistry course instrumental analysis? In chemistry, I'm familiar with GC for gases, HPLC for liquids, and UV-vis for liquids and gases and fluorescence for liquids, and flame AA for solid ions. What instrumentation are in biology department, I guess they use a Eliza system. So, suppose I wanted to take a sample of tap water, and what to identity what organisms are in there? What would they use, just a microscope? A microscope can never visually see chemical compounds, but can it work for larger organisms like bacteria and fungi? 2601:249:8200:A640:B03D:42C6:D0C4:CF22 (talk) 05:13, 17 November 2021 (UTC).[reply]

Biology laboratory instruction takes a more incidental approach to the tools needed, usually introducing them with whatever is being taught the same day. For example, pipetting is introduced in the first year, as part of the lab on gel electrophoresis, maybe with a couple of practice runs using water dyed with food coloring. Abductive (reasoning) 05:22, 17 November 2021 (UTC)[reply]
- Automated cell counters are becoming increasingly common. --Jayron 32 13:05, 17 November 2021 (UTC)[reply]

...and are very unreliable in my experience.Fgf10 (talk) 13:57, 17 November 2021 (UTC)[reply]

There is literally a near infinite suite of analysis techniques used in biology, including GC, HPLC and UV-Vis. Biology encompasses a good chunk of the techniques from in chemistry in particular (hence biochemistry), and depending on the field quite a bit of physics too. You could start with the by no means exhaustive Category:Laboratory_techniques. For your example, it depends on what you're after, but you could start with a visible light microscope yes, but these days you'd be more likely to get a more comprehensive answer with PCR Fgf10 (talk) 13:57, 17 November 2021 (UTC)[reply]

Many eukaryotic (animals, plants, fungi, and "protists") organisms could be identified with a simple light microscope, not always to the exact species. In many cases, several species of microorganisms are possible but which exact one is present might make little difference. Bacteria could be identified by culturing on or in various media (gels and broths) to see 1) if it grows at all, 2) how much it grows, 3) what colors and shapes its colonies take up, 4) how it affects the surrounding medium (for example, some bacteria will produce pH changes that interact with indicators in the media to produce color changes). --Khajidha (talk) 16:53, 18 November 2021 (UTC)[reply]

Likely manual methods would be haemocytometry (name is for red blood cells, but the general concept applies to any kind of cell), or for bacteria dilution plating to estimate the number of viable cells. There are also automated techniques which achieve the same results. Blythwood (talk) 01:01, 24 November 2021 (UTC)[reply]

Among numerous examples, including those mentioned above, there's also flow cytometry (which can even be used to sort whole animals, e.g. the worm FACS machine), qPCR (the paper introducing the now-standard approach for analyzing qPCR data has over 100,000 citations), and Hi-C (not the juice). JoelleJay (talk) 05:15, 24 November 2021 (UTC)[reply]

To address the second part of your question, identifying organisms from a sample of tap water, there's a couple things you might do - yes, microscopic examination would be useful in identifying the larger organisms (if any! in treated tap water there's probably not many of these) in your tap water, this could be manual visual qualitative or quantitative identification which would use just a microscope and a taxonomic key, or Automated Species Identification which would require the microscope to be hooked up to a camera and computer. For tap water, though, most of what you would find cannot be identified properly by microscopy. Using DNA Metabarcoding, culturing the organisms on [differential and selective media] or Culturomics would be required to get most of your organisms in tap water identified, and all these techniques come with a host of required equipment - PCR machines, gel rigs & imagers, DNA sequencers, incubators, and so on. A lot of this equipment is so specialized that many biology labs won't have their own (for example, DNA sequencing is so cheaply done, it's easier to send samples off to specialist labs rather than maintain and run your own sequencer in many cases.) Wevets (talk) 15:23, 24 November 2021 (UTC)[reply]

Respirator thickness redux

Extending a previous question, I have just received KF-94 respirators for the first time, and they're noticeably thinner than KN-95s, which as I said previously seem to be thinner than N-95s. Imagine Reason (talk) 17:01, 17 November 2021 (UTC)[reply]

Is there something we can help you find references for? --Jayron 32 17:09, 17 November 2021 (UTC)[reply]

I've used lots of different respirators and n95's tend to be thicker. If you are suspicious of your kf94's, there are ways to test them that are borderline feasible for DIY'ers. Basically you spray an aerosol of salt particles through the mask, and use an air quality monitor on the other side to check how many particles get through the filter. There is a guy on youtube who tests various masks that way but I no longer have the url for his channel. Maybe you can find it. These days though, real n95's are plentiful enough that I have not felt a need to mess around with dubious masks. 2602:24A:DE47:B8E0:1B43:29FD:A863:33CA (talk) 06:05, 18 November 2021 (UTC)[reply]

Is it better to boil tap water, then cool it to room temperature?

Hot tap water contains calcium carbonate that regular tap water does not have. So if I boil regular tap water to just below 100 C, then cool it back to room temperature, is it better than using regular tap water?

I know the answer for 2 variables, but I don't know if that is all the variables. For bacteria, yes, and chemicals, mostly yes. Bacteria generally do not have a cardinal temperature of more than 40 C range, (so E. Coli for example, ranges from 8 C to 48 C). Boiling from 25 C to 90 C will definitely destroy/deactivate it. However, tap water, I believe, has more of a chemical problem than a biological problem. I went to the EWG website, and searched for my jurisdiction, to what chemicals are found in my tap water. From that list, only 2 chemicals will be boiled to a gas: chloroform (bp 61 C) and bromodichloromethane (90 C), but will not boil these chemicals: dibromochloromethane (120 C), dichloroacetic acid (194 C), trichloroacetic acid (197 C), and dibromoacetic acid (decomposes 234 C). But, what I don't know is false positives. What if boiling tap water, causes something to decompose, and decomposes to 2 or more, that are more toxic than what it was before, so therefore it should have been left at room temperature? And maybe other factors you guys can think of? Then, for chemicals that are metals found in tap water, of course boiling it then cooling it makes no difference to them. So sounds like there probably is no disadvantage to cooking tap water? I'd also like to know if boiling water can cause 2 chemicals to form combination reactions, and that new product is more toxic and has a even higher boiling point. 2601:249:8200:A640:F9D6:6DF0:48CF:530E (talk) 21:48, 17 November 2021 (UTC).[reply]

I am not sure that it is true that hot tap water contains more calcium carbonate than cold tap water. Calcium carbonate is unusual in that its solubility decreases as the temperature of the water increases. Also, some calcium carbonate in your drinking water us not necessarily bad: no adverse health effects of hard water are known; it may even be beneficial to heart health. Boiling water and then letting it cool back will not appreciably affect the concentration of dissolved salts and other minerals. Boiling the water may kill or deactivate pathogens, but if the concentration of any chemicals poses a health risk, I'd switch to bottled water. --Lambiam 07:29, 18 November 2021 (UTC)[reply]

Any calcium in tap water will be there from the outset and boiling will not alter that. As Lambiam said, the main reason to boil water is to destroy pathogens or because you are making a hot beverage. Your IP address shows you are in the US, where municipal tap water is of high quality, so for the sake of the planet (and your energy bill) I suggest just using the water as supplied and certainly not using bottled water, which is much less environmentally friendly and relatively expensive. Mike Turnbull (talk) 10:56, 18 November 2021 (UTC)[reply]

The drinking water supplied by US municipalities is not necessarily safe coast-to-coast; see e.g. Lead contamination in Washington, D.C., drinking water. --Lambiam 12:10, 18 November 2021 (UTC)[reply]

True, but boiling doesn't remove lead. I believe that the above advice against boiling was meant to imply that US water supplies are generally free from pathogens that boiling water can fix. Other than temporary "boil water" orders that happen when water supplies are contaminated by line breaks and floods due to natural disasters, I am not aware of any widespread cholera outbreaks in the US. The US water supply is generally safe from that sort of thing. --Jayron 32 12:49, 18 November 2021 (UTC)[reply]

Next to the advice against boiling water, there was also a plea to not use bottled water – presumably in reaction to my suggestion to switch to bottled water when the concentration of any chemicals presents a health risk. Such a risk would generally not be mitigated by boiling. --Lambiam 14:37, 18 November 2021 (UTC)[reply]

It is true that carbonate content in municipal water is not detrimental to humans (or at least, not in general; consult your doctor if you have medical issues that make it different for you). However, the OP might well be trying to use that water for some appliance (e.g. a coffeemaker) which does have problems with water hardness. Of course, Lambiam’s answer still stands (any water you get from the tap, hot or cold, comes from a single municipal water pipe, whatever heating-cooling cycles occur at your home are unlikely to affect the carbonate content in any significant direction). Tigraan^{Click here for my talk page ("private" contact)} 14:04, 18 November 2021 (UTC)[reply]

Isn't calcium carbonate found in hot tap water because of the hot-water boiler? If you pour hot tap water and let it stand still, you will see it is cloudy/foggy, compared to cold tap water that is clear. That foggy substance is calcium carbonate. Anyways, I just look at the decomposition reaction article and saw solids will have a decomposition point in place of a melting point. What about for liquids? Can there be liquids that have a decomposition point in place of a boiling point? 2601:249:8200:A640:F9D6:6DF0:48CF:530E (talk) 14:14, 18 November 2021 (UTC).[reply]

Certainly their are. But not water or calcium carbonate; the cloudiness is not because new calcium carbonate is being created out of thin air; it is merely becoming more visible because it is precipitating very slightly at the higher temperature, heating and cooling water with calcium carbonate in it does not change the amount of calcium carbonate; to remove it you would need to use some sort of water softener. --Jayron 32 14:21, 18 November 2021 (UTC)[reply]

There will generally be an equilibrium when using a boiler: as much calcium carbonate flows out as flows in. The build-up of limescale in the vessel, mainly calcium carbonate deposit, means that actually less flows out than flows in, although the difference is truly minute. --Lambiam 14:37, 18 November 2021 (UTC)[reply]

Okay, I checked my notes. Says calcium carbonate is formed from calcium ions and bicarbonate ions when heated. But this is irreversible in the sense that cooling it, will not decompose it, cooling it will just keep it as a solid. 2601:249:8200:A640:F9D6:6DF0:48CF:530E (talk) 15:03, 18 November 2021 (UTC).[reply]

Quite possible, Carbonate equilibrium is complex, in solution there will always be an equilibrium between CO₂, CO₃^2-, HCO₃^- and H₂CO₃, the exact ratios are dependant on things like temperature, pH, and other dissolved ions. The only one of those that significantly precipitates with Ca²⁺ would be CO₃^2-. Indeed, if I were to fathom a guess, the formation of cloudiness at high temperatures is probably largely due to the increase in CO₃^2- ions due mainly to the increased solubility of carbon dioxide at those higher temperatures; ~~as hot water absorbs more carbon dioxide from the air~~, more carbonate ions form, causing more calcium ions to precipitate out as calcium carbonate. --Jayron 32 15:14, 18 November 2021 (UTC)[reply]

Actually for your last part, gases are more soluble in colder water than hot water, and I don't believe CO2 is an exception. So boiling water will cause CO2(aq) to part into a gas, or from the HCO3-. 2601:249:8200:A640:F9D6:6DF0:48CF:530E (talk) 16:26, 18 November 2021 (UTC).[reply]

You're correct, of course. Mea culpa. --Jayron 32 11:55, 19 November 2021 (UTC)[reply]