1, 2, 3, 4, 5, and 6? Extinctions

“Extinction is the rule. Survival is the exception.”
Carl Sagan

An article in Scientific America asked an interesting question, Why Don’t We Hear about More Species Going Extinct? There have been a lot of stories about the planet being in the middle of the 6th mass extinction.  Reports are saying that the rate of extinction is as much a 1000 times normal.  If these articles are correct shouldn’t we see articles in the news about species going extinct?  However, I wonder if people even understand the context of mass extinctions?  If asked, what is a mass extinction, could you answer? 

To understand what a mass extinction is, we need to understand life on earth and the fossil record.  All five existing mass extinctions are in the fossil record.  The first life that appeared were microbes around 3.7 billion years ago.  They lived in a world that was quite different from present-day earth.  The atmosphere was almost devoid of O2 (molecular oxygen) and high in things like methane.  Molecular oxygen is highly reactive and will spontaneously react with any oxidizable compounds present.  The early earth was full of oxidizable compounds, any molecular oxygen that did appear was almost instantly removed by chemical reaction.

About 1.3 billion years later the first cyanobacteria evolved, these were the first photo-synthesizers. Over possibly hundreds of millions of years molecular oxygen produced by the cyanobacteria reacted with compounds in the environment until all the oxidizable compounds were used up.  A great example of this is banded iron deposits.  Only when molecular oxygen reacted with all the oxidizable compounds could molecular oxygen begin to accumulate in the environment. 

After another 1.7 billion years the first multicellular organisms, sponges appeared in the fossil record.  Around 65 million years later a group of multicellular organisms called the Ediacaran Biota joined the sponges on the seafloor.  Most of these organisms disappeared around 541 million years ago.  However, the loss of the Ediacaran Biota is not one of the five mass extinction events.  How much of an evolutionary impact the Ediacaran Biota had on modern multicellular organisms is still an open question.  Most of the Ediacaran Biota had body planes quite different from modern organisms.

The next period is especially important; it started about 541 million years ago and lasted for about 56 million years.  The period is known as the Cambrian.  This period is referred to as the Cambrian explosion because all existing types (phyla) of organisms we see in modern life emerged during this period. The Cambrian explosion is also essential because the diverse number and types of organisms that evolved during the Cambrian explosion form the backdrop for mass extinctions.

The first mass extinction occurred 444 million years ago at the end of the Ordovician period.  During this extinction event, 86% of all species disappeared from the fossil record over about 4.4 million years. Global recovery after the extinction event took about 20 Million years

The Second mass extinction occurred at the end of the late Devonian Period.  The Devonian extinction is the extinction that eliminated the Trilobites.  During this extinction event, 75% of all species disappeared from the fossil record over as much as 25 million years

The third and largest mass extinction occurred at the end of the Permian period 251 million years ago.  During this mass extinction, 96% of all species disappeared from the fossil record over 15 million years.  Research suggests that the Permian mass extinction took 30 million years for full global recovery.

The fourth mass extinction occurred 200 million years ago at the end of the Triassic period.  During this mass extinction, 80% of all species disappeared from the fossil record. The Triassic mass extinction appears to have occurred over an incredibly short period, less than 5000 years.

The fifth mass extinction occurred at the end of the Cretaceous period 66 million years ago.  This extinction is by far the most famous of the mass extinctions because it is the meteor strike that killed the dinosaurs.  During this extinction, 76% of all the spices disappeared from the fossil record.  Research suggests this mass extinction only took 32,000 years.

Now that we have looked at mass extinctions what about regular extinctions.  Normal or background extinction rate is the number of extinctions per million species per year (E/MSY).  Current estimates put the background extinction rate at 0.1 E/MSY.  If the the current extinction rate is 1000 times the background extinction rate, then currently the extinction rate is 100 E/MSY.

The current estimate for the total number of species is 8.9 million.  That means that 890 species are going extinct every year or 2.5 species a day.  So why don’t we hear more about spices going extinct if the extinction rate is that high?  First, the current catalog of identified species is 1.9 million, which means there are currently 7 million species (79%) that are undescribed.  That means 700 of the 890 extinctions a year would be in species that scientists haven’t identified.

The second problem is that even with identified species, it is often difficult to know if a species has gone extinct.  The International Union for Conservation of Nature (IUCN) maintains the Red List of critically endangered species.  One of the categories is Possibly Extinct (PE) based on the last time anyone saw an organism.  For example, no one has seen the San Quintin Kangaroo Rat in 33 years, no one has seen the Yangtze River Dolphin in 17 years, and no one has seen the Dwarf Hutia in 82 years.  It is likely that these three spices, along with several others, are extinct.

However, not being seen is not good enough to classify a species extinct.  After all, the Coelacanth was thought to be extinct for 65 million years until a fisherman caught one in 1938.  For a species to be declared extinct, a thorough and focused search must be made for the organism to declare it extinct.  These types of searches require time, personnel, and money.  Therefore, searches don’t often happen.  So with the exceptions of particular cases, like Martha the last Carrier pigeon who died on September 1, 1914, most species go extinct with a whimper, not a bang.

We don’t hear more about species going extinct because even knowing extinctions are occurring, in many cases, we don’t know about them.   Returning to the question of what is a mass extinction, and could there be a 6th happening?

Use the five existing mass extinctions as examples a simple definition of a mass extinction is an event where 75% or more of the existing species become extinct within a short (less than 30 million years) time.  Using the current estimated number of spices, and the current estimated rate of extinction we can calculate how long it will take to reach the 75% mark the answer is 7500 years. Since 7500 years is less than 30 million years, we could be on course for a 6th mass extinction.  However, as Doug Erwin says we are not in the middle of the 6th mass extinction.  If we were in the middle of a mass extinction like Dr. Erwin said cascade failures would already have started in the ecosystem and there would be anything we could do.  However, that is good news we still have time to do something.

What we need is an accurate count of extinct species.  So, do you have a class that could do fieldwork?  There is probably a critically endangered species near you.  Maybe you will even be lucky, and you will find the species then you can help with a plan to save it.

Thanks for Listening to My Musings
The Teaching Cyborg

The Raven Paradox and Science

“Anything that thinks logically can be fooled by something else that thinks at least as logically as it does.”
Douglas Adams, Mostly Harmless

The democratization of knowledge is a tremendous and empowering idea. The internet plays a huge role in this democratization. The growth and expansion of the Internet are almost unfathomable. The growth of online video is an example of this. In the early stages of the Internet, one small picture could slow your website to a crawl. Now we’re watching 4K YouTube videos at 60 frames per second.

You can find almost anything on YouTube. Need to paint a room in your house there’s a video for that. Want to listen to your favorite band they probably have a channel. Want to know how to build an electric guitar there is a playlist for that. There are even channels focused primarily on teaching science. Some of my favorites are Dianna Cowern’s Physics Girl, Derek Muller’s Veritasium, Michael Stevens’s Vsauce, and Brady Haran’s Numberphile.

However, there are also other channels on YouTube presenting pseudoscience or even outright falsehoods. Did you know that the Flat Earth Society has its own YouTube channel? (No, I’m not linking to it!) As much as we might like the idea of deleting them if we support an open and free Internet and the democratization of knowledge we can’t.

Fortunately, a lot of them are easy to spot. However, what about videos that make a mistake or fall into a logic trap. What about videos recommended by YouTube? Does a YouTube recommendation increase the validity of a video?

The other day a video popped up in my YouTube recommendation feed the title intrigued me “The Raven Paradox (An Issue with the Scientific Method)” the video is by a channel TritoxHD which is a channel about “science, theory, and history!” The video concludes that scientists shouldn’t make overly broad generalizations.

The video centers around the Raven Paradox, which is an argument in inductive reasoning first presented by Carl Gustav Hempel and how it impacts on the scientific method. The raven paradox is interesting from a logical standpoint. The paradox is dependent on logical equivalents from a logical point of view; all A’s are B’s is equal to if not B then not A.

The paradox uses these two statements.

  1. All ravens are black.
  2. Something is not black; then it is not a raven.

Since these two statements are logically equivalent observing one is support for the other. As an example, the flower in my front yard is pink, this flower is not black, and it is not Raven, so this pink flower supports all ravens are black. If you are like most people, your response was just “WHAT!” The idea that dissimilar things can be used to prove each other is where the paradox comes from how can an observation of a flower have anything to do with ravens. Fred Leavitt does an excellent job of explaining how this works in his article Resolving Hempel’s Raven Paradox in Philosophy Now; my interest is in the description of the scientific method.

How does The Raven Paradox relate to the scientific method? Our YouTuber and others have suggested that many if not most hypotheses are of the format all A’s are B’s. In this case, the YouTuber makes his first mistake when he takes All ravens are black as a hypothesis.  The video states that the hypothesis is the first step in the scientific method, this is not true.

I like to think of the scientific method is a cycle that we can enter from any point, so there isn’t a first step. However, if you think of the scientific method linearly the first step is to ask a question.

Two representations of the Scientific Method one circular the other liner.
Two representations of the Scientific Method one circular the other liner.

Following in the raven example the question would be “Is there a trait that all ravens share?” Then you’d go out and observe ravens. This step is necessary because a hypothesis is a prediction based on observation. So, if you need observations to make a hypothesis, the hypothesis can’t be the first step. Our YouTube author even states that a hypothesis is a prediction based on observation.

An important thing to know about the hypothesis all ravens are black is that while very rare there are white (albino) or cream (leucistic) colored ravens.

Modified from Raven by Marcin Klapczynski, licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.
Modified from Raven by Marcin Klapczynski, licensed under the Creative Commons Attribution-Share Alike 3.0 Unported license.

The argument concerning the paradox is twofold one, to “prove” the hypothesis you must observe every single raven, I’ll come back to this latter. Two, you can observe hundreds even thousands of ravens and never see a white raven and therefore conclude that all ravens are black incorrectly.

Let’s suppose you examine 50 ravens and they were all blacks you come up with the hypothesis all ravens are black. You then go out and examined 5000 ravens, and they are all black. What is the problem, while we don’t know the exact numbers there are 4 or fewer albino ravens worldwide out of a total population of 16 million. That means that your probability of seeing an albino raven is 0.000025%. 

Beyond the small chance of seeing a white raven, there is another problem with the approach. Observing Ravens to see if they are black is an experiment that is designed to prove the hypothesis.  Specifically observing 5000 black Ravens is a result that is consistent with the hypothesis, this type of research doesn’t provide any information on alternative hypotheses.

With science, supporting or consistent data is of a lower value. Experiments that focus on disproving a hypothesis always have a higher value. They have a higher value because they eliminate alternative ideas which strengthen the validity of the remaining hypothesis. Additionally, a hypothesis is only scientific if it can be disproven.  Which means if you try to disprove a hypothesis and can’t the likely hood that the hypothesis is pointing at something real is stronger.

Let’s briefly get back to the issue of testability, since all ravens are black requires an examination of all ravens something that is impossible the hypothesis is untestable and is therefore not a scientific hypothesis. 

In the end, this the video uses the Raven Paradox to say that scientists can overreach and should be careful of generalizations. However, this argument is problematic because it is dependent on the definition of a hypothesis which is not complete.  The hypothesis all ravens are black is not a valid hypothesis. The author states a hypothesis is a prediction based on observations. I would say a prediction that is consistent with observations. Additionally, a hypothesis must be testable. Lastly, a hypothesis must be falsable or able to be proven incorrect to be a scientific hypothesis.

While I would like to see the YouTube logarithm not suggest things that are incomplete or oversimplified beyond usefulness, I suspect that will not happen.  Like I have stated before we need to focus on teaching students how to evaluate information.  I suspect most of the problems with the video come from things being oversimplified. As Einstein said, “Simplify everything as much as possible but no further.” Concerning basic education, I think we’ve taken the scientific method further. We tend towards being very simplistic in how we present the scientific method. We need to do a better job of teaching the basics if our students don’t know the foundation how can we hope to teach them the specifics.

Thanks for Listening to My Musings
The Teaching Cyborg

Tell Me a Story

“A story has no beginning or end: arbitrarily one chooses that moment of experience from which to look back or from which to look ahead.”
Graham Greene

Story it’s an interesting word like so many words in English it has many meanings.  If you look in the Mariam Webster’s Dictionary, the word story has 18 definitions if you include the sub-definitions.  We use story a lot in the sciences.

How do I know when my research is ready for publication?  You’re ready for publication when you can tell a story.  How will I know when I’m prepared to write my dissertation?  You’re prepared to write your dissertation when you can write a complete story. The answer to many a question is when you can tell a story.

A lady telling a gripping story to young women and children. Mezzotint by V. Green, 1785, after J. Opie. Credit: Wellcome Collection, CC BY
A lady telling a gripping story to young women and children. Mezzotint by V. Green, 1785, after J. Opie. Credit: Wellcome Collection, CC BY

Why a story?  A story is a very efficient way to teach something.  A properly constructed story helps us understand what is going on by logically presenting information and highlighting the links and connections between separate facts and events.  There is even a word for this storification in the paper Storification in History education: A mobile game in and about medieval Amsterdam the authors talk about the advantages of storytelling in History,

“In History education, narrative can be argued to be very useful to overcome fragmentation of the knowledge of historical characters and events, by relating these with meaningful connections of temporality and sequence (storification).” (Computers & Educations Vol 52, Issue 2, February 2009, p449.)

Storification also makes sense in regards to working and short-term memory.  Working memory and short-term memory are transient; permanent information storage takes place in long-term memory.  However, they are both critical to the establishment of long-term memory.  Information enters the memory system through Short-term memory, and processing and connections happen in working memory.

Unlike long-term memory, both short-term and working memory have limits on their capacity.   Recent work suggests that the size of working memory is 3 – 5 items.  For example, I could reasonably be expected to memorize a list of letters; H, C, L, I, and Z. I know some of you were going to say seven items as in the magical number seven, I break down the changes in our understanding of working memory in another blog post, you can read about it here.

However, we can quickly see a problem with 3-5 items; I can also remember a sentence, “All the world’s a stage” this sentence has 18 characters 19 if I count the apostrophe. I can hold this sentence in short-term memory.  I can remember these 18 characters due to a process called chunking coined by George Miller in his paper The Magical Number Seven, Plus or Minus Two Some Limits on Our Capacity for Processing Information.  Miller describes it as “By organizing the stimulus input simultaneously into several dimensions and successively into a sequence of chunks, we manage to break (or at least stretch) this informational bottleneck.” (Psychology Review Vol. 101, No. 2 p351)

In our example’s words are chunks; specifically, each word is a list of letters that have a specific meaning.  If I were to present that list of letters to you in a different way as zilch, it would be much easier to remember. Chunking is the same idea behind storification or storytelling; you are organizing the information into related chunks to make it easier for the mind to remember and digest.

With all the complicated information in a scientific paper, A story is a perfect format to present new scientific knowledge.  A scientific paper starts with an abstract which gives an overview. Then the paper has an introduction which places the new information in context with the old. Then we show the experiments (in the order that explains the information the best. not necessarily chronologically). Lastly, there is a summary that reiterates the new information in context with the old and what directions the research could go next.

A faculty advisor of mine once described writing a science paper as tell them what you are going to tell them, tell it to them, then tell them what you told them.  That might seem a bit excessive, in fact, I once had a non-science faculty member after hearing this triple approach to paper writing say, “what are scientists stupid?”  I think it’s a smart strategy, after all, have you ever had a teacher tell you how many times you need to hear something to commit it to memory? (I always heard it was three)

There is one thing I find quite strange about storytelling in science education.  It seems to me that helping students make connections and tie information together is the most important in the earliest stages of education — for instance, the steps of education that use textbooks.  However, the writing of most current science textbooks presents information as separate chunks.

Like I have said in previous blog posts the reason for writing the modern textbook as independent chunks are so we can use the textbook in any class and any order. However, if we want textbooks to be as useful as possible shouldn’t they be written as a story?  We should write the textbook so that we group information into meaningful chunks, we should write the textbook so that we present information in ways that reinforce the relationships and dependencies between new information and preexisting knowledge.

What do you think is the lack of storytelling harming modern textbooks?  Has our desire to produce textbooks (commercial and open source) that can be used in as many different classes as possible hurting the usability of the modern textbook?  Can we create textbooks that are storified or would they be unusable in current courses?  However, if a storified textbook helps the students learn and if we can’t use them in current courses is the problem with the textbook or the course?

Thanks for Listing to My Musings

The Teaching Cyborg

But I Thought I Knew That!

“We are infected by our own misunderstanding of how our own minds work.”
Kevin Kelly

 

Over the last several decades we have learned a lot about teaching and learning.  One of the most critical things with regards to education is the addition of new information to memory. The storage of new information in memory and our understanding of that information is dependent on what we already know. According to Jean Piaget’s Cognitive theory, three critical components of learning depend on preexisting knowledge Equilibrium, Assimilation, and Accommodation.

In Piaget’s modal assimilation occurs when the new information matches a learner’s preexisting views and without changing can be incorporated into their view.  Accommodation happens when new knowledge conflicts with the learner’s preexisting view of the world, in this case, the student’s view must change to incorporate the new knowledge.  Equilibrium is the condition where most new knowledge can be dealt with by the students existing view.

In simpler terms, preexisting knowledge can either help or hinder a student’s learning.  If the preexisting knowledge aligns with the existing knowledge, it helps, when the current information does not align with existing knowledge it hinders.

PriorKnowledge_Combined Files-1

Modified From: Exploring Research-based Principles of Learning and Their Connection to Teaching, Dr. Susan Ambrose

Since no student is a blank slate, they will always have a view based on their own life experiences.  When a student learns something that does not fit their view, either their view must change (accommodation), or the new information is altered to fit their view (incorrect assimilation).

In modern education, we call these incorrect views a misconception.  To overcome misconception so that accommodation can occur students must actively acknowledge their misconceptions.  These misconceptions can be especially impactful in science education where many of the ideas taught can’t be touched or physically observed.

In chemistry, we teach students about atoms and molecules, which are too small to see or feel. In astronomy, we teach students that the earth is orbiting around the sun at 67,000 miles per hour.  However, do we feel that speed on the surface of the planet?

Beyond misconceptions derived from observations, students can also acquire misconceptions from language.  In the field of genetics, a common misconception is: A dominant mutation is the most likely one to be found in the population. This misconception likely comes from the word dominant which has six definitions according to the Marian-Webster dictionary.

Dominant

  1. a: commanding, controlling, or prevailing over all others the dominant culture
    b: very important, powerful, or successful a dominant theme a dominant industry the team’s dominant performance
  2. overlooking and commanding from a superior position a dominant hill
  3. of, relating to, or exerting ecological or genetic dominance dominant genes dominant and recessive traits
  4. biology: being the one of a pair of bodily structures that is the more effective or predominant in action dominant eye used her dominant hand
  5. music: the fifth tone of a major or minor scale (see scale entry six sense 2)
  6. a: genetics: a character or factor that exerts genetic dominance (see dominance sense 1b)
    b: ecology: any of one or more kinds of organism (such as a species) in an ecological community that exerts a controlling influence on the environment and thereby largely determines what other kinds of organisms are present dominant conifers
    c: sociology: an individual having a controlling, prevailing, or powerful position in a social hierarchy: a dominant (see dominant entry one sense 1) individual in a social hierarchy

Most of the definitions have to do with importance, power, and control, which is likely why students think a dominant mutation is the most likely one to be found in a population.  However, there is another genetic term for the most common allele in a population, wild-type.  In genetics the term dominant must always be used about something else, for example, the phenotype of the dominant allele B is expressed instead of allele b.

I have always preferred to use the five-terms established by Hermann Muller to classify the specific types of genetic mutations over general terms like dominant and recessive.  Regardless of the words used, the students need to understand that we are discussing mutations that change the function of genes which has nothing to do with a mutation’s frequency in a population.

Another common genetic misconception is that all mutations are harmful.  At the DNA level, a mutation is simply a change to the DNA, a lot of mutations do not affect.  As an example, if a mutation occurred in a coding region, there is a good chance it will not change the final product.  If the mutation occurred in the third position of the alanine codon GCT and became GCC, it would still code for alanine, in fact, all four GCx codons GCT, GCC, GCA, and GCG code for alanine. That means any change in the third position of this triplet will not affect the protein formed. There are a lot of other misconceptions in genetics, but that is a discussion for another day.

When it comes to helping students deal with their misconceptions, it can help to try and understand where the misconceptions came from, and what might be influencing them.  As a faculty member once said, “If you want to understand what a student is thinking, ask them.”  If a student does not comprehend new information, it might be because of previous notions.  Learning what the student’s assumptions are and how the assumptions are interfering with the students learning will only make you a better teacher.

 

Thanks for Listening To my Musings

The Teaching Cyborg

Clear and Obvious Facts

“There is nothing more deceptive than an obvious fact.”
Arthur Conan Doyle, The Boscombe Valley Mystery

 

I have watched or been a student in a lot of biology classes over the years.  I sometimes think we take a lot for granted when we teach students. Not only in biology but in many of the STEM fields. We have the advantage of teaching science on the shoulders of all the greats that came before us.  Sometimes I think we forget how long it took to answer questions and just how smart the people that figure them out were. Also, we forget how fast things change, in biology we have something called The Central Dogma. Simply it states that DNA goes to RNA goes to protein. It’s as simple as that; we know proteins are not made directly from DNA and RNA is not made from proteins.

The funny thing about The Central Dogma’s place in modern biology is that it’s relatively new. We’ve been studying biology for a long time; Van Leeuwenhoek discovered single-cell organisms in 1670,  Hooke coined the term cell in 1665.  Macromolecules came later; Proteins in 1838, DNA in 1869, and RNA between 1890 and 1950, RNA was initially thought to be the same as DNA. However, we didn’t know whether DNA or proteins were the sources of genetic inheritance until 1952. We didn’t know the structure of DNA until 1953. Meselson and Stahl published the proof of semi-conservative replication of DNA in 1958.

In 2018 most of The Central Dogma is less than 70 years old. There are a substantial number of people alive that are older than The Central Dogma. This information is only old because of the speed at which biology has been progressing over the last century.

When teaching facts In STEM education we often run into a severe problem, students can often give us the “correct” answer on a test.  However, if you dig a little deeper, they don’t understand what that answer means.

I have often thought that teaching biology (or any STEM field) through an understanding of the foundational experiments would help students understand the facts. Imagine going through these experiments; What was the question?, Why did they do this?, Why didn’t they do that?, What do the results show?, and What do they do next?. Teaching these experiments to students would explain not only what we know but why we know it.

Let’s look at a couple of examples. We know that DNA is the molecule responsible for genetic inheritance. How do we know? For many years scientists thought proteins had to be the source of genetic inheritance because DNA was just too simple.  In 1952 Alfred Hershey and Martha Chase conducted an experiment that provided some of the most persuasive evidence that DNA was the source of genetic inheritance.

Hershey and Chase use T2 bacteriophage for their experiment, T2 phage reproduced by infecting a bacterial cell. The bacterial cell produces new phage that would be released when the cell lysed. While the mechanism of T2 phage reproductions was not known, the process required the transfer of “genetic material” from the phage to the bacteria. The T2 phage is composed of two components a protein shell and DNA core. The researchers needed to determine what part of the T2 phage entered the bacterial cell.

The researchers needed a way to label proteins and DNA independently of each other.  Two atoms helped sulfur and phosphorus. Proteins use sulfur while DNA does not. DNA uses phosphorus while proteins do not. They grew phage with radioactive sulfur or radioactive phosphorus. These radioactive phages infected cells, after infection, the phage and cells were separated, and the location of the radioactivity was determined.

They found the radioactive DNA was always with the bacteria (Figure 1B) while none of the radioactive protein was with the bacteria (Figure 1A). They also showed that radioactive DNA could get incorporated into the bacterial DNA. While other scientists conducted additional experiments, this experiment showed it was the DNA, which carried the genetic information.

Cartoon depiction of the Hershey Chase Experiment
Hershey Chase Experiment, Derived from Hershey Chase experiment.png by Thomasione from Wikimedia Commons

Your students can probably (we hope) tell you that DNA replicates semiconservatively.  However, if you asked them to prove semiconservative replication of DNA, could they do it? Without looking up the Meselson and Stahl experiment. In the late 1950s when Matthew Meselson and Franklin Stahl conducted their research, we already knew the structure of DNA. It was immediately clear from the structure that DNA could serve as a template for its replication.

Early on there were three competing models for DNA replication; conservative replication (Figure 2A), semiconservative replication (Figure 2B), and dispersive replication (Figure 2C). The differences in these models can be described based on where the new and old DNA strands are after replication. In conservative replication after one round, you end up with one DNA molecule composed entirely of new DNA and one molecule composed entirely of old DNA. After two rounds of replication, you now have three new DNA molecules and one old DNA molecule. In semiconservative replication after the first round, you get two molecules that both contain one new and one old strand of DNA. After two rounds you get two molecules composed entirely of new DNA and two molecules composed of one new and one old strand. In disrupted replication, the DNA molecule was cut every ten base pairs on alternating strands, and then new DNA would fill in the gaps. After one round you get molecules that are 50-50 old versus new DNA. After two rounds of replication, you get four strands that would have somewhere between 50-50 and 75-25 new versus old DNA.

Cartoon representation of 3 different modes of DNA replication tested in the Meselson and Stahl Experiment.
3 different modes of DNA replication, Dertived from DNAreplicationModes.png by Adenosine from Wikimedia Commons.

The beauty of these models is that if you can follow the new and the old DNA you can distinguish between all models. Meselson and Stahl marked new and old DNA with nitrogen isotopes specifically N14 and N15 these isotopes differ by one neutron. Which turns out is enough to separate DNA by density in a cesium chloride gradient.

They grew bacteria on media which contained N15 then allowed the cells to grow on media containing N14 for 0, 1, or 2 cycles of replication. The DNA was then isolated from the cells and density was used to separate the DNA molecules.  After zero rounds of replication, there was a single band lower than cells grown only on N14 (Figure 3 N15 0). After one round of DNA replication, there was a single band between the N15 and N14 bands (Figure 3 N15 1). This result ruled out conservative replication since conservative replication should have produced one heavy (N15) and one light (N14) band. However, both semiconservative and disrupted replication should produce 50-50 molecules at round one. After two rounds of replication, we get two band’s one at the 50-50 spot the second at the light (N14) position (Figure 3 N15 3). This position of bands is what you’d expect from semiconservative replication but not dispersive replication. Dispersive replication would have produced a band between the 50-50 and the N14 band. Therefore, DNA replicated semiconservative.

Cartoon representation of the Results from the Meselson Stahl Experiment.
Meselson Stahl Experiment, Derived from Meselson-stahl_experiment_diagram_en.svg: LadyofHats, Wikimedia Commons

Even if you don’t need this experiment to teach your students how semiconservative replication works, the Meselson and Stahl experiment is often referred to as one of the most elegant experiments ever conducted in biology and is worth studying to learning experimental design.

Up until these experiments were conducted the information that we teach as clear and obvious facts was up for debate. While we probably can’t go over every single fundamental experiment in enough details, so our students understand them, because of the total amount of material we need to cover, foundational experiments can be useful. If there’s a topic that your students are having trouble grasping maybe take the students through the experiments that demonstrated the facts. Perhaps the solution is a one-credit recitation that covers the experiments in conjunction with the lector.  That might solve all our problems (shakes head ruefully).  One last thought, if students are having trouble grasping that clear and obvious fact maybe stop and ask if it is clear and obvious?

 

Thanks for listening to my musings

The teaching cyborg