Mini “Huzzah!” Moment

It’s always a great moment…
…to see evidence that my students are paying attention in class.

  • The general Beer’s Law equation in the lab manual: Molecule Concentration = Absorbance(at a specific wavelength) * Constant
  • The general Beer’s Law equation I wrote on the board: [molecule]=A??? x constant
  • What several of my students put on the postlab: [molecule]=A??? x constant

There’s nothing really wrong with writing the “book” version, but it was nice to see that my simple version stuck with them.

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Since you asked… Soap!

A student in Principles of Biology asked a question today that I didn’t know the answer to – are phospholipids the molecules in soap that facilitate its ability to dissolve both polar (carbohydrates, nucleic acids, and some proteins) and nonpolar (lipids and some proteins) materials?

The short answer: Nope! Soaps aren’t using any of the 3 major types of lipids, it’s a modified single fatty acid chain.

The longer answer: Sodium salt and potassium salt versions of fatty acids are the main active component of soaps. In fact the process of saponification serves primarily to separate the glycerol backbone from the fatty acid chains. This process results ionized chains in the solution, which then form ionic bonds with Na+ or K+ ions when salts are added to the mixture.

E.g. Sodium oleate: 

Salt form, found in soap

Comes from lipids containing oleic acid

1200px-oleic-acid-based-on-xtal-1997-2d-skeletal

Fatty acid form, found in phospholipids or triglycerides

Cheers for science & research!

 

The book-length answer: 
https://en.wikibooks.org/wiki/Structural_Biochemistry/Lipids/Soap

Nervous? Excited? So is your neighbor.

From freshman to returning grandmother, everyone has to go through that first day of a new class.

I asked my Principles of Biology I students this semester to share “Any concerns that you have about the class” after the first day. Here’s a peek at what y’all said, and some help!

General worries…

  • Finding the textbook – Armstrong bookstore, the textbook broker across from campus, Amazon.com, Chegg.com, Half.ebay.com … Just remember, you’ll need this book again for Biology II. Renting might not actually be the best option.
  • Staying organized / Managing my time – Find someone to help you be accountable. Meet, text, or email each other when you’re supposed to be reading the book/your notes. “This chapter’s killing me… are you doing any better?”
  • Keeping up with notes during lecture – Focus on added explanations that I mention in class. Don’t try to write down every word – outline & use short notes – especially if it’s already on the slide (I post them on the course website for you!).
  • Not sure what/how to read effectively – Don’t highlight everything. Skim the chapter first, looking for unfamiliar ideas. Mark those sections for extra time, and take notes about what you don’t understand.
  • It is a really big class – Well, you have the option to either stand out or blend in, but anyone is welcome to ask questions. There are also more options for who to study with! Also, my office is 50% less intimidating than most professors’ offices. Come by during office hours and ask for help.
  • Memorization – Know the story, memorize the details. Biology is always integrated, so make sure you can put the pieces together. Example: Facts – electrons are negatively charged. The valence shell is involved with bonding. Story – sharing & stealing electrons is the basis for constructing molecules, and the valence structure tells you how an element will bond.
  • This is my first college class / I have first year jitters… / It’s been 10 years since I was in school – Ask questions, and don’t panic. Use D2L/E-classroom to keep an eye on your grades. Ask for help early: Office hours (free…), STEM tutoring (free), Supplemental Instructors (free), making friends (okay, you might buy them lunch sometimes).

Information worries…

  • Making the best grade that I can / Making an A – Shoot for the stars, and at least you’ll land on the moon. Read the study guides along with the textbook chapter, so that you know what the most important topics will be. Always aim for that A, and back up that ambition with solid, productive work.
  • I might not catch on as fast as other students – Positive thinking + Positive action = Positive results. Reality check might be that you need to ask for help: Office hours (free…), STEM tutoring (free), Supplemental Instructors (free), making friends (okay, you might buy them lunch sometimes).
  • Not learning as quickly as I did in high school – Find out how you learn. Does it help if you draw everything? Do you need music in the background while you study? Take notes in class. Answer the questions at the end of the chapter – I’m not going to assign them like your teacher used to, but it will help you learn if you do them.
  • Have I forgotten my high school biology? – Maybe so, but don’t panic. Khan academy might be helpful, or CrashCourse. I post extra videos and activities that will give you another run through of many of the crucial topics. Send me an email or stop by during office hours.
  • Worried about the topics that I struggled with last time – Don’t psych yourself out, psych yourself up! You are going to knock them out of the park this time, because you are planning ahead, asking for help, and working hard. Remember to still study for the topics that you understood well, as it’s easy to forget the basics. What’s the mitochondrion do again?
  • This class will be a lot of work / will be difficult – Maybe so, but you can plan ahead. Do the assignments, be prepared, and find out why/how you answered wrong when it happens. This class is designed to prepare you for amazing upper level courses – such as parasitology, applied microbiology, environmental chemistry…
  • The comprehensive final exam – Study Guides on D2L are already posted! Come to office hours and review exams I-IV after they are graded so that you understand why/how/when you chose the incorrect answers.

It helps to remember that you’re all in this boat together, even if your seats (your lives/backgrounds) are different!


Featured image: Science scarf and epic purple shirt – cool things from my mother-in-law and mom, both of whom love that I’m a college professor.

New Semester, New Technique?

Humans love stories, but get bogged down by information.

“Shrimp wisely divide their time between eating, hiding from predators, and finding mates.”

“Shrimp respond to variable changes in their environment in order to optimize their caloric intake while minimizing predation risk and maximizing reproduction.”

Let’s be honest – it’s much simpler to understand the first sentence, but as scientists we’re expected to write the second sentence. The content is basically the same, although the details are variable.

Why do readers relate to the first version?
1 – less jargon (technical language)
2 – intuitive phrasing that connects the main ideas

Why is the first version problematic?
1 – less information, fewer details
2 – teleological (the shrimp has goals)

In teaching, can we reconcile the two? Can we use stories to help our students build mental models of the topics?

In an attempt to utilize one of the ideas that we discussed in our faculty reading round-table last semester, I am incorporating the idea of narrative sensemaking, or storied truths, into my biology lectures. The idea is to use sensible, intuitive stories to understand realistic, complex, patterns in the real world.

Good stories don’t just have to come from fantastical imaginings, rooted in the mythos of our ancestors. Scientific facts don’t have to be clinical and hyper-accurate in order to be useful. Just like a good teaching model, we can incorporate the best parts of both.

Why am I doing this?

Students are often frustrated by exam questions that require critical thinking skills, and say they are “too hard” or “not based on the lecture.” I am hypothesizing (Yep, I’m a scientist – I do this all the time.) that part of this problem is a mental disconnect from the material.  Many of the extra study materials that I direct my students to use are youtube videos (Hello, CrashCourse) or activities that have a clear, succinct, and entertaining story – they are more likely to mentally interact with the information more intuitively than if I were to simply remind them to “review section 7.3 in the textbook”.

Understanding connections is key to successfully studying increasingly complex topics in science, not simply rote memorization. Without the ability to think on their feet, analyze available information, and reach sound conclusions, they also are not productive, scientifically literate citizens. They can’t make connections if they don’t understand how the story works in the first place.

How am I going to do this?

I’m adding “What’s the story?” pieces to my existing lectures, in an effort to regularly remind students of the larger picture. My goal is to create 1-2 sentence story bits that aren’t just summary, but illustrate the narrative thread running through the past few topics for the section of material that we’ve just discussed.

For example, Chapter 1 of our Campbell Biology textbook discusses overall themes in biology. The first topic is the basic properties of life vs. non-life, moving on to where it is found. What’s the story? Life has adapted to deal with a wide variety of conditions.

What are the results?

I’ll let you know!


Featured image: Stalactites and stalagmites at Carlsbad Caverns (July 2016)

Nightingale Woman

“Nightingale Woman” was a poem by Tarbolde, written in 1996 on the Canopus Planet. It was said to be one of the most passionate love sonnets of its time. An excerpt of the sonnet from page 387 is all that is known from Star Trek lore (the first two lines).

MacHuginn, Cleric of Deneir, completed the sonnet, writing it for his love, the kenku Karrakaniin.


My love has wings – slender, feathered things,
With grace in upswept curves and tapered tips.
In every beat she strikes a chord that rings
As true as cherished words from readied lips.

My love’s dark eyes are quick, and undismayed
To pierce the shadowed veil of deepening night.
Oh, smould’ring gaze of moonlit thoughts betrayed
By sable feathers limned in silver light.

My lover’s mind takes flight, she claims my eyes,
As wingtips brush with whispered, promised, notes.
Each silken touch, a slow caress, gives rise
To fierce, enchanted cries from joyous throats.

Her slender curves my upswept wings now trace –
Stars gasp to watch our shimmering embrace.


featured image: one of MacHuginn’s feather darts

The Artist

Being an artist can mean many different things.

For me, being an artist means that I draw, paint, play several musical instruments, photograph weird things, and occasionally sculpt clay, wood, metal, and leather. Although I actually did take university courses in drawing and sculpture at Dartmouth and in high school, much of what I know comes from self-study and working in the Claflin Jewelry Studio while I was a student.

Am I a great artist? Nope, but I’m not bad. I enjoy spending a lot of time on a piece, so that dedication usually shows through in the final product. Short, quick things are a bane, though. Why? Because I don’t draw/paint/sculpt often enough. I don’t practice flute regularly, and haven’t set a regular schedule for learning harp yet.

Even though I may not produce much art in any form, part of what I enjoy most about being an artist is being able to truly appreciate and be inspired by the work of others. To be capable of looking at someone’s painting and work out how they might have planned and executed the work, or to understand how impressive a musical performance is (or isn’t). I’m often inspired by history (Hello, Society for Creative Anachronism!) and fictional characters and places, in addition to the constant inspiration that is provided by the natural world. When I do create something worth sharing, I usually post it on DeviantArt, but I don’t photo-dump on there like some people tend to. It takes a pretty impressive or well-planned shot for me to put it on DeviantArt.

harper_unfinished_by_myrddinderwydd

The Harper, Deth

Deth from Riddle of Stars by Patricia Mckillip
Drawn in high school, based on an illustration in the edition of the book that our library had. Never really finished.

machuginn_s_feather_darts_by_myrddinderwydd-dawyz05

MacHuginn’s Feather Darts

A sketch during a Dungeons and Dragons session last year – my character MacHuginn (one of the characters in Divergent Paths) commissioned a smith in ?? to make him a few dozen metal-tipped darts out of his feathers. He also uses them for making his own quills!

leather_bracer_finished_by_myrddinderwydd-d9kx95v

My leather archery bracer, tooled leather.

Cameron taught me leatherworking last year, and I made a bracer so that I’d tear up my arm less while shooting. Since I have an Irish persona in the SCA and love Celtic knotwork, I ended up with this painstakingly time consuming piece!

claddagh_ring_by_myrddinderwydd

Claddagh ring, cast in silver. Terrible photo…

Much of my earlier work I don’t have photos of, since camera phones weren’t as common then and I wasn’t as interested in photography either. This Claddagh ring was carved in wax by hand, then molded and cast in silver in the Claflin Jewelry Studio at Dartmouth. Unfortunately, Cameron lost it several years ago… So no luck on taking a better photo.

I can take good photos though! These are from our road trip out west in July 2016. We had the Nikon 5300 with us, and had a great time visiting family and roaming around in parks, reservations, and fishing.


featured image: Raven ring, another Dungeons and Dragons sketch for MacHuginn (2016)

Healthy Eating Plate

Sometimes simpler is better.

Eat real foods, avoid hidden calories (such as sugary drinks), and exercise so that your body actually uses the calories that you consumed.

HealthyEatingPlate

Professors Disappear at the end of the Semester.

Well, at least I do. It’s been a very busy past 2 months, and I’ve been busy even amongst the grading and teaching too. What have I been doing? Earth Day March for Science, visiting family, cheering on spring blossoms.

Being science-y.

And being nerd-y. How? Dungeons and Dragons, of course. Can’t go wrong with the classics. My current character is a Norse skald (bard) from ~800 CE, and we somehow managed to sail from Midgard to Vanaheim – magic is much cooler there, but there are were-beasts, and two moons. I’ve been playing a lot of Dragon Age: Inquisition and Origins, especially since I turned in final grades. Solas and Blackwall are two of my favorite characters, and I’ve started writing a Solas + Inquisitor fan-fiction “A Long Hunt” to show my love for it. Later chapters of the fanfic will definitely be NSFW.

Being nerd-y

What am I up to next? I’m teaching future K-5 teachers how to “Do Science” in the course Earth and Life Science for Early Childhood Education Majors, so I’m preparing materials for starting June 5th.

Food for Thought – And Eating.

A discussion of biodiversity and the role of fungi as decomposers turned into a chat about “expired” bread today, and afterward (while making a sandwich with “expired” bread) I decided that they could probably benefit from a little bit more concrete advice to back up our discussion. One of the students asked how they [the bacteria and fungi] got to the food after you put it in the refrigerator. We talked about what preservatives are and the balance between safe consumption and preventing organisms from growing in the food, and about the fact that the fungal spores and bacteria are in the air and on the surfaces all around us. After a few incredulous looks after discussing moldy bread, I threw up my hands and gave in. “Look, I couldn’t tell you just how many products in my fridge right now are past their printed dates, and they are perfectly safe and good to eat. There are plenty of other foods that don’t have expiration dates on them either because – for example – it’s just a raw carrot.”

This is what I shared with them after class, and is generally my guide for why I continue to buy short-dated products and tear moldy bits off of bread and eat the rest.


Since I wouldn’t want to provide advice without evidence… a bit more information about so-called “expiration dates” on perishable products such as bread. 

My version: The dates are advice from the manufacturer and/or a regulation agency, and their purposes are two-fold: Sell products that you are pleased with, and reduce the chance of you from being harmed by the product. Use dates as guidelines for how fresh a product is so that you can plan to use the food within an appropriate amount of time. The dates are more likely to be indicative of food quality and how quickly it should be sold, and is not a deadline for using the product.

IMAG0007

Evidence: Bread with a March 01 “Sell-by” date, which was slightly dry but still delicious and not the slightest bit moldy. 

Learn about food safety, especially the types of foods that tend to develop harmful bacteria or fungi that are likely to be hazardous to your health. And you should always know how to handle your food safely! Safe cooking is just as essential as safe storage. Keep in mind however, that all of this information from the USDA below is based on customs and policies in the US and is general advice covering a range of foods and people, and additionally does not always reflect the rest of the world.

Use good judgement, and know your own body. I have a strong immune system from years of living in the country on a farm and I have an in-depth working knowledge of how organisms live and survive, so I’m likely to make good decisions about the safety of my food. If you don’t exercise good judgement, there will often be consequences – just as there were for our early human ancestors 2,000,000 years ago (Yes, 2 million years ago).


Info from the USDA about labeling: https://www.fsis.usda.gov/wps/portal/fsis/topics/food-safety-education/get-answers/food-safety-fact-sheets/food-labeling/food-product-dating/food-product-dating 

Are Dates for Food Safety or Quality?
Manufacturers provide dating to help consumers and retailers decide when food is of best quality. Except for infant formula, dates are not an indicator of the product’s safety and are not required by Federal law.

How do Manufacturers Determine Quality Dates?
Factors including the length of time and the temperature at which a food is held during distribution and offered for sale, the characteristics of the food, and the type of packaging will affect how long a product will be of optimum quality. Manufacturers and retailers will consider these factors when determining the date for which the product will be of best quality.

For example, sausage formulated with certain ingredients used to preserve the quality of the product or fresh beef packaged in a modified atmosphere packaging system that helps ensure that the product will stay fresh for as long as possible. These products will typically maintain product quality for a longer period of time because of how the products are formulated or packaged.

The quality of perishable products may deteriorate after the date passes, however, such products should still be safe if handled properly. Consumers must evaluate the quality of the product prior to its consumption to determine if the product shows signs of spoilage.

Food Safety Tips from the USDA: https://www.fsis.usda.gov/wps/portal/fsis/topics/food-safety-education/get-answers/food-safety-fact-sheets/safe-food-handling/basics-for-handling-food-safely/ct_index 


Featured image: Perfectly safe, delicious bread that was discounted 3 weeks ago because of the March 1st sell-by date. 

The Scientist

Scientists don’t think the same way as your average person.

What does that mean? Well, it means that we’ve trained our minds to use a particular set of skills that many people don’t understand or actively avoid using. Often those who pursue science have natural tendencies toward curiosity and information, and a quicker grasp of numerical analysis than others, but not always. Many of us are simply passionate enough about science to buckle down and learn the mindset that a scientist needs.

One skill is the ability to objectively analyze information.

We don’t just nod approvingly, our minds latch onto bits and pieces of everything that comes our way. From behavioral patterns to mathematical models, we are surrounded by information that is often raw and complex. Information alone doesn’t do anything for us, it isn’t good, or bad, or helpful – it exists, with that existence having inherent value and potential. Scientists are the ones who use that potential, those who look for the reality of what is truly there instead of just skimming the surface.

This skill comes in two flavors, and not everyone likes both equally.

First, there is the ability to dig deeper and deeper into the minute details. Taxonomists, chemists, and molecular biologists are examples of those who use this skill extensively. They need the attention to detail, the patience, and the dedication to catalog all  of the differences between two species, or to analyze thousands of samples of DNA looking for a matching sequence across taxa. Often, this is described as a reductionist analysis of the world. Application of objective analysis in this way leads us to further understanding of precisely how things work and what they are.

Second, there is the ability to analyze patterns and interactions at the scale of whole systems. Ecologists, sociologists, and climatologists are examples of those who use this skill extensively. These scientists need to integrate information from a variety of sources and find out how everything fits together, how individuals and parameters are connected, and determine the consequences of a series of changes. They are often dealing directly with the emergent properties of a system, rather than with the individual cogs in the machine. Application of objective analysis in this way results in a better comprehension of what happens and why it can happen again.

A second skill is the willingness to step back from our beliefs.

Scientists rely on evidence. We search for evidence, analyze our evidence in the form of data, build our models out of pieces of evidence, and sometimes change the world by finding evidence to support new ideas about the world. Yes, new ideas about the world. The importance of this skill is that every good scientist inherently understands that they are actively seeking to determine if they are wrong. We make the absolute best hypotheses possible, that logically could be right and are based on the most complete information at the time. And then we set out and dedicate ourselves to finding the truth.

Falsifiable hypotheses, experimental controls, and large sample sizes are all tools that we use to try to find the truth. And yet all of those tools are useless indeed if we ignore the result of their dedicated application. What happens when we are wrong? First, we determine just how much we can trust that answer. Did we collect reliable information? What might have gone wrong? This is also where statistics comes into play. Second, we accept it and determine the consequences. We know nothing – we seek everything. In reality, what this means is that we do change our minds sometimes (We thought the world was flat until evidence indicated otherwise, remember?). Additionally we end up accepting contradictions as an inherent part of reality.

Perhaps the evidence didn’t support my hypothesis because I don’t know enough to write the correct hypothesis yet.

socrates1

“I know that I am intelligent, because I know that I know nothing.” -Socrates


Why? What is it about these two skills that often sets scientists apart?

One reason, in my opinion, is that humans have a deep desire for the status that comes with being right. James Gee discusses our desire for social status and the need to support our “family” in his book The Anti-Education Era, and these are traits that do help us survive. We are inherently social animals, and being wrong can, quite frankly, sometimes have devastating consequences. Not only do we want to be right, we also want to be with others who are right because of the direct and indirect benefits we gain.

Consider this: “Do you want to rely on someone who says that they might be wrong?”

This is the kind of mental construct that exists to some degree in all social organisms, and it developed entirely outside of (and prior to) the construction of formal scientific methodology. It is a Darwinian safety mechanism that has been built over time because bad decisions have consequences – often death. The result is that most people tend to hesitate in following someone that has been wrong in the past.

Consider this: “Can you trust someone who refuses to admit that they could be wrong?”

Aye, there’s the rub. We are also aware of our own fallibility. Since we are capable of being wrong, there is always the possibility that we are at this moment, actually and truly wrong. This understanding of ourselves and others logically leads to skepticism that also benefits our survival, and someone who refuses to accept this possibility can (and should) seem insane and untrustworthy.

The Conundrum: A need to be skeptical of both those who state that they can be wrong, and of those who state that they cannot be wrong. 

Thus we see how trust in scientists is so easily lost, and how people can so easily be misled. We see why scientists rarely become celebrities, and why bad ideas that don’t kill you can spread like wildfire.

A second reason is the fear of the unknown, resulting in the construction of explanations independent of evidence. This is based in part on the concept of “mental comfort stories”discussed by Gee, as he illustrates how much our happiness and contentment about the state of our lives often relies on not challenging these comfort stories. Effectively, humans often reap benefits from ignoring evidence that contradicts their long-held beliefs.

Consider this: You (most likely) hold some beliefs for which you have no supporting evidence, besides tradition. Holding to those beliefs hasn’t killed you, and probably makes you happy and accepted by your community. 

So, what is wrong with this situation? You benefit from the mental comfort story (perhaps about god) and no one is harmed, right? Well, that is only true until you encounter a community that doesn’t hold those same beliefs. Then, those unsubstantiated claims might very well cause people in both groups to die, and will at least make people unhappy and unacceptable to the opposite community. Who is wrong? Is there any way to tell? No, because the ideas weren’t based on evidence in the first place – they were based on what comforted people, made them accepted and content with the world around them.

Consider this: You are shown evidence that contradicts your beliefs (perhaps about ethnicity/race), and you refuse to alter those long-held beliefs. Although you are happy that you’ve upheld your beliefs, the consequences can be major – losing your job, failing a class, being arrested because of your actions.

Well, you now have 2 good reasons to change this particular belief, but if you’re like most people, you won’t. The evidence indicates that your belief is wrong, and there are negative consequences to holding your belief. Perhaps you decide to split the difference – to not act on your belief in a way that causes problems such as being fired, but it will still make you unhappy. Or you decide to deal with the consequences so that you can remain happy and accepted by your chosen “family.”

The Conundrum: Some beliefs cannot always be conclusively shown to be right or wrong, and the resulting conflicts can be devastating. Other beliefs can be demonstrably wrong, and upholding them in the face of evidence can also be catastrophic.

What is the scientist’s solution (and Gee’s)? Use the skills of a scientist – objective analysis of reliable evidence & an open mind.

Evaluate your ideas with evidence whenever possible. Do not continue to hold beliefs that are conclusively false. Not only is this illogical, it will eventually have consequences for you and/or your society.

Build and use your mental comfort stories when there is no way to find the truth – but be open-minded. Other people with varying perspectives can hold ideas that are different from your own, and you should allow them that to retain right so long as it does not cause you harm. If it does, then you have the ability of any organism to make decisions that benefit your survival. You should feel free to try to convince them that you are right, but understand that typically neither of you has any evidence, and both ideas may be equally valid.


A social community for researchers, mostly scientists: ResearchGate


featured image: A grass shrimp (Palaemonetes pugio)