real life, Writing

A Writer’s Guide to Lab Equipment: Beakers

I’m surprised that I’ve gotten this far in my scientific blog without talking about beakers (though I have mentioned them in blog posts in the past, I haven’t had a post specifically about beakers).  From what I’ve seen from depictions of scientists in pictures or fiction, beakers are seen as the typical chemistry equipment, though they’re not as distinctive in silhouette as the Erlenmeyer flask or volumetric flask.  Like the other two, they are used to measure and store liquids.  They are definitely less accurate or precise (using the scientific definition I mentioned in a previous post) than the volumetric flask, buret, volumetric pipette, or micropipette.  They’re still ‘read’ the same way, and it can be difficult without a lot of experience to determine the correct volume (I went into more detail about the meniscus in a previous post).

Despite the fact that the accuracy is worse, we tended to have more beakers available, and used them more often, so that, at least, may explain why beakers are considered the essential chemistry accessory.  I find it easier to cause chemical reactions in a beaker, partly because adding the ingredients is easier than through the slim neck of a volumetric flask or an Erlenmeyer flask and partly because mixing was overall easier.  They also came in a number of different sizes, from 5 mL to 5 L, all of which I saw in various school labs.  These two extremes weren’t very common sizes, though—I only saw one of each, though when we were doing microchemistry (chemistry on a small scale with small amounts of ingredients) we used a 15 mL beaker on occasion.  Their popularity is also probably helped by the fact that it’s easy to leave the results of an experiment for another day (assuming it’s not dangerous to leave it around), particularly since the most common size for a beaker (150 mL or 250 mL, at least in our college laboratories) is right around the right size for a watchglass to cover, which helps prevent evaporation.  Unlike volumetric flasks, a number of different volumes can be chosen, though the accuracy is better if the volume is closer to the maximum volume (which impacts what size of beaker is used).  However, just like with the accuracy of the volume contained, the prevention of evaporation is not as thorough as it could be (stoppers for the Erlenmeyer or volumetric flasks exist).

So, beakers would not be appropriate for quantitative chemistry on their own, in which you need accurate measurements of the volume (unless a more accurate pipet or buret is used), and doesn’t work as well when storing the products of the reaction—but, on the other hand, if you’re going for qualitative chemistry, looking for whether the chemicals react or do not react, or a reaction involving color, or even planning to put the product in specific instruments, a beaker is a good choice.  Beakers can, however, be combined with equipment that can be more accurate, hold more volume than your average volumetric piece of equipment, and can easily be combined with a heating mantle, stir bar, or glass stirring rod.

Where was the first place you’d seen a beaker?

real life, Writing

Spotlight on: Tryptophan

I hope those of you that celebrated Thanksgiving had a good one!  I had considered writing a blog post on amino acids before now, and when better to start than discussing tryptophan, a component in turkey?

Tryptophan is an important amino acid needed for human functioning.  I’ve discussed the central dogma before, which involves the one-way pathway from DNA to RNA to protein.  Some amino acids such as Tryptophan can’t be manufactured by the body and have to come from the diet (“essential” amino acids) from foods like turkey, but are incorporated into proteins in the same way.  Tryptophan has abbreviations Trp or W.  Just like a string of nucleotides make up DNA or RNA, individual amino acids make up a protein, which can be written in shorthand using the amino acid abbreviations.  This only indicates primary structure, the sequence of amino acids, not the three-dimensional structure, but even that can be useful for analysis and protein identification.  The codon for tryptophan is UGG in RNA, while the coding strand would be TGG and the template strand would be ACC.  Most other amino acids have multiple codons that code for their inclusion in a protein.

The properties of the amino acids in question determine which amino acids and sequences are used in the protein depending on what the intended purpose of that protein is (remember, structure dictates function in the world of biochemistry).  Amino acids consist of a central (α) carbon, an attached (α) hydrogen, an amino group (NH3+), a carboxyl group (COO) and an R-group or side chain, which is what differentiates amino acids from each other. Tryptophan has a nonpolar side chain, which means it is neither charged (positively or negatively) nor becomes temporarily charged.  The side chain is also aromatic, which means it is a ring structure with alternating double bonds.  Aromatic rings such as benzene are especially stable as the electrons can travel around the ring, spreading out the electronic charge (which is part of what makes it nonpolar).

Now, getting back to tryptophan and turkey.  Is the tryptophan in turkey responsible for the post-Thanksgiving sleepiness?  Well…maybe.  Some experts say no, while others say it’s more a case of chemical interaction.  First, let’s look at the chemistry of the amino acid tryptophan.  Tryptophan is a precursor to serotonin which is itself a precursor to melatonin which is important in the sleep cycle.  However, tryptophan occurs in other foods, and does not affect the body immediately upon consumption.  There are multiple possible explanations as to the cause of post-Thanksgiving tiredness.  Perhaps the amount of carbohydrates or just sheer amount of calories might allow for easier absorption of tryptophan by the brain.  (Anything getting to the brain is difficult.  The brain is so important that the design of the human body incorporates a number of protections, including the blood-brain barrier.  Good for keeping microbes from getting into your brain; bad for drug delivery.)  On the other hand, perhaps it’s just the sheer number of calories, no tryptophan required.

Have you heard about turkey causing sleepiness?  Do you know what other foods tryptophan is in?

real life, Writing

Of Mice and Men and Lab Rats

Today’s post is a little more biology than usual.  I’ve volunteered for over a year taking care of rodents, though I won’t mention the specific location as I don’t want to misrepresent anything and there is a PR clause.

The first thing you should keep in mind is that you should discard all of your misconceptions about mice and rats from general culture or the Redwall books.  Rats are actually friendlier than mice.  The rat breeders needed socialization (i.e. interaction time with humans) as part of our duties.  No matter how much time I spent with the mice, they didn’t get any friendlier, sniffing my hand and then running, while rats would stay to sniff my hand like a dog and enjoy playing or sitting on my shoulder.

If you’re doing intelligence tests, use rats.  Mice might be interested, but only for food.  They’re not usually curious.  Whenever the mice would do escape attempts, it would be to get away from the humans.  Rats would, on occasion, try it, but would stop to look at everything and come back when they were finished investigating.

Rats and mice often get used for oncology studies (research that involves cancer).  That’s because they develop tumors regularly, unfortunately.  I’ve read that if scientists introduce human cancer cells in a rodent, the tumor will grow.  Rodents may not be the best models for humans in every aspect of science, but in terms of cancer they’re fairly close.

Bedding does have to be changed fairly frequently in order to prevent disease.  Rats need to be given toys to play with or they’ll get bored, and all rodents need something to chew on to keep their teeth trimmed (the teeth will keep growing and become uncomfortable and dangerous otherwise).  The most common disease, other than tumors, which are out of your control, is various respiratory illnesses.  Rodents are very sensitive to dust.  They, like humans cleaning their house, will sneeze if dust gets kicked up, but if it gets too dusty this may cause them to develop a cold.  Many rodents are born with or develop Mycoplasma pulmonis, a bacterium that doesn’t bother the rodent until it is stressed or otherwise has a problem with its immune system.  Humans can develop Mycoplasma, but it’s a different type than Mycoplasma pulmonis, so humans do not catch it from rodents.  If the infection gets out of control, it can cause pneumonia.  Viruses and other bacteria can also cause respiratory infection.  Mice and rodents wake up pretty quickly from a nap and don’t tend to be drowsy, so if they’re lethargic, it means they’re sick.  Really rapid breathing and sneezing that doesn’t go away quickly is an indication of illness rather than allergies.  If there’s ever a red liquid around the rodent’s eyes, it’s a sign of stress—they’re not bleeding from their eyes.  The coat should also be sleek.

Alopecia (hair loss) is fairly common, and, like in humans, unless it’s accompanied by any other symptoms, may be perfectly harmless (if a little embarrassing).  It might be a sign of bullying or stress as well, though, since rodents do groom themselves and rodents attempting to establish dominance might overgroom another rodent to ruin their image.  This is especially possible if there are any nicks to indicate rodent teeth were the culprit.

Hopefully, you have enjoyed your little look into the world of biology.  How realistic are depictions of rodents you have seen?

real life, Writing

A Writer’s Guide to Lab Equipment: Test Tubes

laboratory test tubes
Photo by Chokniti Khongchum on

You have, no doubt, seen test tubes before.  My mom was watching one of the baking shows the other day, and one of the bakers was assigned to depicting a scientist.  They chose to make test tubes (without the test tube rack or a stand and clamp, which would make it clearer that the depiction wasn’t of pens, figure animal balloons, or any other elongated object).  (The baker also erroneously called them beakers.  Hopefully, having read this blog post, you will not make the same mistake if you were likely to do so before!)  Test tubes, for me, aren’t very symbolic of scientists.  Interestingly enough, I would probably imagine PPE (Personal Protective Equipment), such as a lab coat or, more ubiquitous and important, goggles, instead.  As that would be difficult to create for a cake, though, my next go-to would be an Erlenmeyer Flask, as we used them often and they have a very distinctive image.

In my experience, test tubes are mostly used, in biochemistry and biology, not in chemistry.  Part of this might be due to the fact that, for the most part, in chemistry we were not using small or micro amounts of chemicals, and most test tubes do not hold a lot of liquid.  Test tubes are used to store or mix liquids or solids.  Many of these are made of glass, and the most likely lab equipment to get broken (we had more broken test tubes than any other glass piece of equipment in our laboratory classes).  Some are made of plastic, however, for the chemicals that interact badly with glass or to limit the number of broken test tubes and glass clean-up with chemicals is a pain.

Great care has to be taken as most gloves in laboratories are easily cut by glass shards.  A brush and dustpan are used, and there’s usually a spill kit (often using a base) in case an acid was still in the glass when it broke and it needs to be neutralized.  (The danger of breaking glassware exists for other glass equipment such as Erlenmeyer flasks and beakers, but we broke only a couple over my time at school.  Maybe the fact that they are bigger makes it easier to be aware of where they are?  Also, it’s a lot easier not to break them while cleaning, since it can be a lot harder to get small deposits out of test tubes and it’s pretty easy to get a bit too forceful when cleaning them.)

The danger of breaking is part of why a test tube rack is required, though we mostly used old wooden ones.  A stand with a clamp is also often used.  I’ve seen a really large test tube, and there’s a variety available from suppliers such as Fisher Scientific, but most are the standard laboratory size.  They are perfect for most centrifuges, though.  I’ll do a post on centrifuges later, but the short version is that they’re another way to separate a solid, possibly produced by a reaction, from the liquid.  I will note that test tubes are mostly used in the medical science field for phlebotomy (the testing of blood), partially because centrifugation is required often.

To you, what is the iconic piece of lab equipment?

real life, Writing

Science Gone Wrong: So You Still Wanna Write a Mad Scientist?

This time, I’ve got one last October Scare post for you.  Remember where I said unethical experimentation isn’t very common?  There are exceptions, unfortunately.  Most of these involve government okay, or were carried out by corporations.  War serves as a particularly nasty excuse to use our fellow humans as guinea pigs, but that isn’t the only cause.  You can find all sorts of examples by searching.  The IRB (Institutional Review Board) was only established in 1966.  Before that point, there wasn’t established oversight required to sign off on every experiment.  Rules for submitting your desired research are stringent, and I’ve heard a lot of people complain about how difficult it is, but the IRB often suggests changes rather than outright rejecting applications (you definitely need to submit early in case of desired rewrites), and it prevents atrocities (or some scientist not thinking through all the consequences of their work).  It can certainly be said of many scientists that there are difficulties seeing the forest for the trees.  Approaching a subject creatively, or from a different angle, can be difficult, which is why having an outside perspective or talking the work over with other scientists working on the same objectives can be very helpful.  Experiments like these led to the realization that a process like the IRB would be required to better protect volunteers (and those who have been volunteered, such as prison inmates).

I’m going to focus on two experiments that are still taught in psychology classes, both as insights into the human mind and as examples of ethically problematic experiments.  The IRB would not have allowed these to be conducted, and the scientific community would probably have condemned them as well.  One was not expected to get as bad as it was; the other is an excellent real-life example of an unethical scientist.

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real life, science developments, Writing

Making Your Own Genetic Abomination

…Or not.  Fact is, we don’t exactly have the tools to do this unless you’re doing it from scratch, and even then creating the exact creature you want is a little difficult.  For one thing, we still have yet to figure out what all the genes do, never mind the epigenetics, even if we have sequenced the entire human genome.  You could string together a DNA sequence, like what they (probably) did for GloFish or genetically modified organism (GMO) plants, but unless you know what all the DNA does, you won’t know for sure if you’re accidentally interrupting an important gene with your foreign implant.  Only for a few model organisms do we have the entire genome sequenced, and even then we don’t always know the purpose of every gene (E. coli is an exception, as there aren’t a ton of genes).

A quick primer on DNA and how it’s used in the body is important here, since gene editing will involve a lot of that.  DNA is essentially a language spelled, in humans, with only four letters—A and T, G and C.  These are nucleotides that pair together as mentioned before.  For example, if you have a DNA sequence that reads AGGTGC then its counterpart (on the second strand) would be TCCACG.  One strand is the coding strand, the one that is “read” for the message, while the other one is used both for stability (two strands woven together is stronger than one) and to duplicate the message.  The RNA template needs to be identical to the coding strand, aside from the fact that RNA has U (uracil) instead of T (thymine), so it needs to match up with the noncoding strand.  If the previous example had the first sequence as the coding strand, then the RNA template would match up with the noncoding strand (TCCACG) and would be AGGUGC.  From there, each group of three nucleotides forms a codon, which usually codes for a specific amino acid (but may also mean ‘stop’, in which case another amino acid is not added on the end).  In our example, AGG would code for arginine, and UGC would code for cysteine.  Genes generally code for specific proteins (which are made by chains of amino acids), beginning with a start codon and ending with a stop codon.

Most of our tools for adding genes are a little difficult to use.  CRISPR is one example (though it’s properly called CRISPR-Cas9, but it’s easy to call it CRISPR).  CRISPR/Cas9 is a system discovered and coopted from bacteria, so it’s natural.  The bacteria actually use it to protect themselves from things such as viruses or other unwanted DNA elements.  CRISPR is actually the target—a sequence of nucleotides that the actual gene editor, Cas9, edits.  Cas9 cuts the gene at a (chosen) particular location.  The scientist creates a guide sequence of DNA for the ‘editor’ to search for.  The problem is that the sequence generally has to be fairly short to be usable, but that also opens up the possibility of it being very unspecific.  In the English language, if you wanted to insert letters in every instance of the word “there”, you could design a sequence that cuts at every instance where ‘th’ appears next to ‘e’, but you’ll also get cuts every time ‘the’ appears as well.  When you hear about off-target effects, this is what they’re referring to.  With work, scientists have managed to find alternative gene editors that are less prone to off-target effects, but even they’re a little problematic.  It’s part of why gene therapy has taken so long to be approved by the FDA.  A different system has to be used to insert a gene after the cut has been made, which is what makes the difference between editing and modification.  Scientists often use the organism’s natural gene repair system, providing a gene sequence to add, to do that part of it.

Plants and bacteria are easier to edit due to the way their genome works—plants often end up with multiple copies of genes, and bacteria are DNA hoarders and often pick up random DNA fragments from the environment.  In contrast, humans are much more complex and we don’t understand all of the DNA.  In addition to the difficulties, there are laws against gene editing in humans for non-necessary medical reasons.  The censure against a Chinese scientist who did so is a good example of a mad scientist ignoring international agreements and individual laws and getting in trouble with the scientific (and legal, and world) community as a result.  Other laws also limit the uses of gene editing (or modification).

The easiest gene editing method is the one used by Mendel—selectively breeding plants or animals to get the result you want.  There’s a long history of humans doing that, creating all the varieties of oranges or apples, for example, or the various dog breeds.  Other methods, such as the specific technique used to make the patented GloFish, are probably kept a secret to protect the patent.

In the future, perhaps you could create your mad scientist scorpion birds, or a dragon, or something along those lines, but as of now, we don’t know enough about genes or designing an entire genome of something larger than a bacteria to do something like that—for the most part, we just make pets glow, figure out the function of genes by snipping pieces of them so they stop functioning, and change the DNA of crops.

What is the most outrageous gene editing stories that you have heard, and do you know if they are based in real life?