Central Dogma of Biology

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For Conversational Biology series – topic POLS

To learn a topic, it is nice to have a central framework upon which to build your “mind map”.  When it comes to biology, my central framework is called “The Central Dogma of Biology”.  To get us started learning about biology, I think it is appropriate to provide this concept for you to use when building your mind map of biology.

If we go back in time to 1956, we would find that Francis Crick was an important figure in biology, particularly molecular biology.  Just a few years earlier, he had looked at Rosalind Franklin’s data and, along with James Watson, had described the structure of deoxyribonucleic acid (DNA).  This was a big deal because biologist were beginning to come to grips with the idea that DNA is the molecule (a type of macromolecule under the umbrella of “nucleic acids”) that stores genetic information.  Prior to this, protein was the top dog in the minds of most scientists.  DNA was considered “boring” and proteins (another type of macromolecule) were considered to be more interesting, so it stood to reason that proteins would have been suspected to be the storage molecule for molecular biology. 

Anyway, back to the central dogma of biology (aka the central dogma of molecular biology).  This concept was proposed by Francis Crick.  His framework can be overly simplified to “DNA is transcribed to RNA and RNA is translated to protein” or, even more simply, “DNA à RNA à protein”, where the arrows are steps that read information of one molecule to create the next molecule in the progression.

Let’s back up a step again.  What’s RNA?  It, like DNA, belongs to the nucleic acid macromolecule class.  It looks a lot like DNA, but it is one oxygen molecule short, so RNA (ribonucleic acid) has a similar name to DNA (deoxyribonucleic acid).  Notice that the difference in the names is “deoxy”, which is a scientific way of saying “lacks an oxygen”.

Francis Crick had one more arrow in his “DNA à RNA à protein” framework and that was a reverse arrow between DNA and RNA (DNA ß RNA).  This left open the possibility that information in the form of RNA could be used to create a new molecule of DNA.  This turns out to be true, so this process is called “reverse transcription” since the process of DNA à RNA is called transcription.

One final point, Crick wisely avoided drawing an arrow from protein back to RNA (RNA ß protein).  When we get to the topic of the genetic code, we will see why “reverse translation” isn’t a thing.

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Preface for writing this series

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For Conversational Biology series

Welcome to Life and Biology’s new blog series called “Conversational Biology”.  There are several reasons that I’m initiating this effort and I wanted to put them up front. 

*Before all that, I have a confession to make.   I am fairly proficient at starting projects and not seeing them through to completion.  This particular project is one that I have considered for quite some time and have finally started.  Time will tell if I stick with it or not.*

My first reason for writing this blog series is that I would like to create a body of work that is approachable for everyone, but goes into college-level depth on all topics in biology.  This is an effort that contrasts with textbooks that are often difficult to wade through or are simply not a pleasure to read.  A collection of books have been written recently that include the F-bomb in their title.  A couple years ago, I had a failed attempt at my “Conversational Biology” goal whereby I started explaining biology with the crudest, most vulgar language I could come up with.  While it was fun to write in such a profane approach, it just didn’t feel authentic.  In another science outreach effort, I created a series of YouTube videos that presented various biological topics in a conversational tone.  That was a far better approach as it felt more authentic to me.  However, the videos (despite their low production value) were time-consuming to create and have thus failed to continue.  I have high hopes that this blog-based approach will be more manageable and yet valuable to the reader.

The second reason for this series is that I turned 40 years old this past year.  If you’re older than 40, you might be able to relate to my experience where I started to do a philosophical examination of my life by reflecting on the “first half” of my life and thinking through what my “second half” of life should look like.  My first 40 years were fairly productive with 20+ years of education, a variety of jobs, and building a family.  At first this made my second half of life seem like it would need to be exhausting to keep up the pace I started. This series of blog posts will be an attempt to conquer one of the biggest stumbling blocks I had up to age 40…writing.  If there is something that grinds me into the ground every time, it’s writing.  Blog posts seem less daunting than writing a book, so I’ve decided that I’m just going to take on blogging as a way of daily-ish writing motivation.  Yesterday was my oldest son’s 13th birthday.  I’m using his milestone as an arbitrary “fork in the road” whereby I take my writing output seriously.  How did I mark the occasion?  I wrote 1415 words!  Very likely this was the highest word count I’ve ever achieved in a single day.  I hope to look back at this and remember how hard writing was until I took it on with full effort.

Enough about me.  My third reason for writing this series is to provide my students with supplementary reading for the courses that I teach at Montana Tech.  Currently, those courses are: Principles of Living Systems (POLS), POLS lab, Discover Biology lab, Introduction to Evolution, Virology, Immunology, and Biotechnology.  I’m always asking students to read the material and then write out the most important concepts as if their parents or non-biology majors were the audience.  The writing professors call this “synthesis”.  I just figured it was a good way of remembering the material.  In fact, when I was a student, I had a habit of daydreaming during my study sessions about how I would teach the topics I was learning about to other people. 

Finally, even though my third reason was based on helping my students in college, I suspect that education is about to go through a major upheaval.  There is so much information available to everyone that can muster a Google search, the high cost of college will soon be viewed as outrageous (assuming the consensus already haven’t put the cost in this category).  Perhaps in the future, advanced degrees will be merit based.  That is, passing a “class” will be based solely on whether the student shows an understanding for that material.  Will college degrees be boiled down to passing tests rather than sitting in lecture halls?  If so, students will still need to learn the material.  Perhaps writing a series of blog posts in a conversational manner to cover all the topics you might come across in current biology courses will be a way of replacing the lecturer of the future.

Next article: Central Dogma of Biology

Introduction to Discover Biology Lab and BIOMES Chambers

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For Discover Biology Lab

Welcome to Discover Biology Lab.  Each week, I will have a reading assignment for you.  Because there is no textbook requirement for this course, the reading assignments will typically be in the form of blog posts on my Life and Biology website.  There will be quizzes on the material discussed in the reading assignment, so it is in your best interest to read them!

Biology is a world-wide phenomenon.  We are set to discover many different topics of biology in an introductory manner, so covering the whole world is a bit out of the question.  Instead, we will use the concept of ecosystems as our means of discovering biology. 

Now, ecosystem is a bit of a “fuzzy” word because an ecosystem is defined by the person that wants to study it.  Ecosystems are essentially just systems, so we need to think in terms of systems.  What is a system?  A system is a defined area that is either “closed” or “open”.  In a closed system, nothing gets in or out of the defined space.  By “nothing”, I mean matter and energy are confined within the system.  When we learn about calorimetry later in the semester, we will think through the advantages of using a closed system. 

Ecosystems tend to be open.  That is, energy comes into the ecosystem, moves through the system, and then leaves the system.  Same goes with matter.  The ecosystem we will use in the lab this semester is a “BIOMES chamber”.  This chamber is an enclosure that I artificially designed based on the cost-cutting measure of creating two such enclosures from a single sheet of “blue board” (a plywood-sized sheet of Styrofoam that is two inches thick).  The size of the chamber also works well for the 1-foot square light source in the chamber.  Moreover, these chambers can fit beneath the work benches in the teaching lab.

Let’s get back to the idea of the BIOMES chamber.  First off, BIOMES is an acronym for “Biology of Indoor Organismal and Microbial Ecosystem Sustainability.”  Let’s break that down further.  B is for biology, the study of life.  We can have arguments later to discuss what life is.  Next up in the acronym is I for indoor.  Why indoor?  Well, because we live in Butte and the outdoors is a rather cold place most of the year.  Furthermore, we will house our BIOMES chambers within the teaching lab.  OM means organismal and microbial.  By evaluating plant, animals, and single-celled microbes in our BIOMES chambers, we will span a wide range of life forms all in a little box.  Ecosystems have been discussed above, but don’t worry, we’ll talk more about those soon!  Finally, the S stands for sustainability.  Ecosystems devoid of human interference are often sustainable and we will look at concepts behind those ecosystems to create our human-controlled ecosystems.

What are some of the benefits to using BIOMES chambers this semester?  Previously, experiments in the Discover Biology Lab were haphazard and did not overlap from one week to the next.  There was an effort to match the current topic in class with the experimental topic for that week.  However, we will approach the lab portion of this class as a semester-long project.  We will learn about the scientific method and experimental design.  With these tools, we will then create a series of experiments that will address the overarching goal of finding the most efficient method for growing an indoor crop.  Most projects are constrained by time commitment and costs, so we will factor in these concerns as we proceed. 

See you in class!

Introduction to Biotechnology

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Defining Biotechnology.  Biotechnology is the use of biological organisms and processes to produce commercially valuable products.  Many of the earliest biotech products made use of bacteria to produce recombinant proteins.  That is, the bacteria produced human proteins that could be used as therapeutics in humans.  This feat is possible because both humans and bacteria shared a common ancestor.  Remarkably, the genetic information that human cells use to make proteins can be used by bacteria found in human feces. 

Sometimes, the use of bacteria and yeast in the production of foods such as cheese and beer is placed under the umbrella of biotechnology.  However, for our purposes in this class, biotechnology will be limited to the products created using modified genetic information.  For example, the recombinant proteins mentioned above are the result of taking genetic information from human cells and, through the use of numerous molecular biology processes, bringing that information into bacterial cells in the context that these organisms can understand. 

Central Dogma of Biology.  Despite the need to go back in time a couple billion years, humans and bacteria share a common ancestor.  Evolutionary theory as well as the central dogma of biology weave together to allow bacteria to read genetic information derived from human cell to make human proteins.  The central dogma of molecular biology posits that genetic information flows from DNA to RNA to protein. While the “DNA to RNA” step can be reversed, the same is not true for genetic information flowing from the form of protein back to nucleic acids such as DNA and RNA.

Last Universal Common Ancestor.  Of all known living organisms, DNA serves not only as the information that is both passed down from one generation of organisms to the next but also as the source code for proteins using RNA as an intermediate, or messenger, molecule.  This fact implies that the last universal common ancestor (aka LUCA) had a DNA genome.  All organisms since have made use of DNA genomes as well as the genetic code used to decipher the information.  With DNA genomes in all living organisms and a shared used of a genetic code, biotechnology is built on the ability of scientists to use molecular biology tools to edit and modify DNA.  The possible modifications are nearly endless. 

Model organisms. The extent of biodiversity makes it impractical to study all organisms in a laboratory setting.  Instead, representative organisms from the tree of life have been disproportionately studied.  Multiple factors have guided the selection of these “model organisms” including the ease of culturing asexual organisms and breeding sexual organisms.  Biological principles that are determined in model organisms are usually applicable to non-model organisms because of both the central dogma of biology and the concept of LUCA. 

In a positive feedback loop, research of a model organisms incentivizes additional research of that model organism because tools to study the organism are developed in one study that could be used in follow-up studies of that organism.  However, recent improvements in molecular biology and biotechnology methods are reducing the barriers of entry for studying new organisms and, thus, reducing our reliance on any particular model organism.