February 2019 – TylerJFord.com

February 26, 2019March 23, 2019

Gene expression

Sketch of a live cell next to a dead cell

In a previous post I discussed how researchers love to use jargon. This field-specific language makes conversation with colleagues easier. It also makes researchers very difficult to understand.

I’ve been trying to avoid using the jargony phrase “gene expression” lately. I find this phrase fascinating because it’s baffling at face value. We express emotions. We use expressions. We can even send express mail. So what the the heck is “gene expression.”

Expressing a gene is probably most like expressing an emotion. When I express emotions (see quick sketches below), I often contort my face to display my mental state. Non-physical information (my mental state) takes on a physical form in the contours of my face.

Sketches of emtions — Physical expressions of emotions

When a cell “expresses a gene,” it reads the instructions in the gene. It then uses these instructions to create cellular parts. Once again, non-physical information takes on a physical form.

Sketches of complex emotions — Complex emotions expressed through drawing.

Emotional expression takes comes in many varieties. Some people draw, compose, or even cook. Similarly, gene expression can change many different cellular attributes. Expressing a gene may cause a cell to change color. Expressing a gene may make a cell move. Expressing a gene may even enable a gene to absorb nutrients. Cells live and die by gene expression!

February 21, 2019

From the BiLOLogy archives: what’s really going on when I do experiments

This is the first post in a series that i’m calling “From the BiLOLOogy archives.” BioLOLogy was a blog that I created in grad school. My intention was to explain papers and lab life through comics. I won’t re-post everything from BiLOLogy, but this series will feature a few pieces I still like. Enjoy!

This post was originally published in October 2014 (my fourth year of graduate school).

The idea for this comic came from a night when a friend of mine drove me to lab so I could do something “really quickly” (nothing ever takes as long as you think it will in a lab).

As you can see in the comic, that night I was doing something biology researchers do all the time. I was taking bacteria that were resistant to a particular antibiotic and putting them on plates containing the antibiotic in addition to some food. In this case, the point of the antibiotic was to make it so only my bacteria could grow on the plate. The antibiotic killed other bacteria, but did not kill the bacteria I was studying because they were resistant to it.

This whole process consisted of little more than putting a bunch of clear liquid onto a plate and spreading that liquid all over the plate. On the face of it, as my friend comments in the comic (and did in real life), it seems like a very uninteresting process. However, this is true of a lot of the experiments I do. Most of my days consist of the following:

1. Mixing different clear liquids together

2. Putting white powders into those liquids

3. Adding slightly more opaque liquids containing bacteria to the clear liquids

4. Putting these mixtures into machines that shake, heat, or cool them. Usually this makes the liquids more opaque

5. Putting these mixtures into machines connected to computers and watching the computers spit out numbers

6. Destroying all the bacteria by mixing them with yet another clear liquid (bleach)

On the face of it, this could be very boring, but I certainly don’t think about it that way… if I did, I would probably quit. Instead, I spend my days thinking about all the things going on that I can’t see.

As you can see in the comic, when they are thrown onto the plate, the bacteria spend their energy destroying the antibiotic (or at least producing proteins that make them immune to it) and growing into colonies with MANY MANY individual cells (the cities in the comic). I then come along and subject the bacteria to a bunch of tests that determine things like how fast they can grow, what molecules they can produce, and how those molecules can be used. While I can only see these things through a bunch of numbers on my computer, they’re still awesome to think about!

February 11, 2019February 11, 2019

Simple things stated in a complex way

While I no longer do laboratory research, I still proudly consider myself a scientist and believe anyone can be a scientist if they have a curious mindset and fuel their actions with critical thinking. Nonetheless, those who consider themselves scientists do often have a few stereotypical quicks. One of these quirks is an infatuation with jargon and making communication more complicated that it needs to be. Part homage, part chastisement, in this blog post I provide examples of the complex ways scientists might say simple things.

*As a side note, the idea for this blog post came from a conversation about linguistics and my first example is the summation of that conversation.

#1
Complex: In many ways, language is shaped by biology and must conform to the shapes and structures of our mouths and airways.

Simple: We avoid saying words that are difficult to pronounce.

#2
Complex: Continued exposure to damaging agents can lead to a series of genetic changes that ultimately enable otherwise quiescent cells to start dividing rapidly and dangerously spread throughout the body.

Simple: Certain types of chemicals and radiation can cause cancer.

#3
Complex: The key to keeping a conversation going is to identify the activities, ideas, and people that excite your conversation partner and work these things into the conversation.

Simple: People like to talk about themselves.

#4
Complex: If your metabolism is predisposed to store excess dietary calories in fatty acids and other macromolecules, you’re more likely to increase your body mass index on a given diet and activity regimen than someone who is predisposed to excrete excess calories.

Simple: Some people gain weight more easily than others.

#5
Complex: It can be easier to associate phenotypic traits in purebred dogs with particular genetic variations because of the level of genetic identity within and between different breeds.

Simple: Dogs are inbred and that can sometimes make their genetics easier to understand.

I should point out that the majority of these aren’t real examples and were just fun to come up with. Feel free to tweet your own whether real or imagined @tyfordfever.

February 5, 2019March 18, 2019

The “properly” anthropomorphized flower

Very often, I anthropomorphize cells and other biological objects in my drawings. I’ve turned bacteria into pirates, phages into bandits, and muscle cells into builders. It is my hope that presenting biological concepts in this way helps you understand and remember them better or helps you think about them in a new way. In this post, I take anthropomorphism to somewhat of an extreme with what I’m calling a “properly” anthropomorphized flower. Reading this post, I hope that you’ll develop a deeper appreciation for what a flower really is as we approach Valentine’s day.

The problem with the smiling flower

Although you can find many cute flower cartoons depicting smiling faces surrounded by petals, it’s a bit odd to compare flowers to faces. You see, while plants can certainly sense many of the things we sense with our eyes, noses, mouths, and ears, they don’t have faces per se. For example, the mouths should be distributed more to the leaves and roots. The leaves “eat” sunlight and carbon dioxide while the roots “eat” other nutrients found in soil and fertilizer (e.g. nitrogen and phosphorous).

When thinking about its biological function, the flower itself is possibly the most lewd thing one could represent as a face. The flower is censored in my drawing because, in reality, flowers house the reproductive organs of many plants. Insofar as a plant’s reproductive organs can be compared to those of humans, single flowers often contain both male and female parts. In fact some flowers can fertilize themselves. In the floral fertilization process, pollen constitutes floral sperm while eggs can be found within the depths of the flower. I find this all very cool but, were I to draw these parts only my anthropomorphized flower, I might turn away some of my audience.

If my drawing didn’t focus too much on the flower’s innards and instead focused on its petals, the censor bar might might not be required after all. This is because you might think of a flower’s petals as gorgeous clothes. These beautiful garments help attract pollinators like bees, much like we use clothes, jewelry, and hairstyles to attract mates when going out on the town (hence the dancing flower below).

A flower that's ready to dance — This flower is ready for a night on the town.

In any case, I hope you’ve found my “properly” anthropomorphized flower enjoyable. With a little more plant know-how, maybe you’ll further appreciate the complexity and life hiding behind the petals you see in your next bouquet!