Types of Deep Sleep in Animals: Torpor, Hibernation, Estivation and Brumation

In some northern forest, fall is coming to an end. The leaves have fallen, the nights become longer, and a cold winter wind makes its way between the trees. Across the landscape, various animals get ready for the winter using various strategies. Some birds opt to take flight and find warmer places to pass the season, others put on layers of warm winter fur and extra fat, and some retreating into burrows in the ground to pass winter in a deep energy-saving sleep known as hibernation or prolonged torpor. But what if we told you that hibernation isn’t the only time that animals slow down their metabolism to deal with tough conditions? 

What is the difference between torpor, hibernation, estivation and brumation? 

Many of us are familiar with the idea of hibernation, where animals tuck themselves away for the winter and do not emerge until spring, but it is not the only type of “deep sleep” strategy that exists in animals to avoid difficult conditions. In fact, different animals have a range of adaptations that help them to deal with abiotic stress (changes in temperature or precipitation for example) in their environment. One of these strategies is going into a “deep sleep” by slowing down their metabolism and lowering body temperature to conserve energy during certain seasons, or even just different times of the day. 

So what are the different strategies for reducing metabolism in order to survive different stresses? The main four and their most basic definition are as follows:

  • Torpor Physiologically reducing metabolism and body temperature for a period of time. Daily torpor happens every day, usually overnight
  • Hibernation – Prolonged torpor through winter
  • Estivation – Prolonged torpor through hot and dry seasons
  • Brumation – Hypometabolism in ectotherms brought on by the cold (technically not torpor!)

There is also a summary table at the end of this article, but let’s get into a bit more depth on each of these strategies.

Thermoregulation Strategies 

Before breaking down these different deep sleep strategies, it is important to talk a bit about how animals control their body temperature in the first place. 

You have probably heard the terms “warm blooded” and “cold blooded” before, and though these terms can be easier to remember, they are a bit inaccurate.. Why? Well, “cold blooded” animals rely on external temperatures to control their body temperature, BUT, often their body temperature is not cold at all. 

So what should you say instead? 

  • Organisms like mammals that control their body temperature using physiology are called Endothermic (“endo” for inside). 
  • Organisms like reptiles that use the environment and their behavior to help them control their body temperature are called Ectothermic (“ecto” for outside). 

In short, endotherms rely on energy and their metabolism to warm up and cool themselves down. On the other hand ectotherms have to use their behavior, like moving into the sun when they are too cold, or going in the shade or burrowing when they are too hot. 

You can go here for a bit more information on different thermoregulation strategies.  

In order to maintain their body temperature, endotherms use a lot of energy; when conditions are extreme, it ends up being way too much energy. For this reason, torpor is a great coping strategy.

What is Torpor? 

Sometimes called “cold-lethargy.” torpor is a hypometabolic state (very low metabolism) associated with low body temperature. Torpor is used by endothermic animals to save energy, usually in order to survive harsh conditions – such as cold temperatures or lack of food. Daily torpor is distinct from hibernation and estivation, which are considered prolonged torpor. 

What is Daily Torpor? 

Hummingbirds are a great example of daily torpor in animals, going into this deep sleep state every single night. Why? Well hummingbirds have an extremely high metabolism and need to feed every few minutes, so at night they reduce their heart rate and body temperature in order to rest properly. Interestingly, this can also apply to animals that in general have poor diets, such as koala bears and sloths! Last, animals in deserts like cactus mice (Peromyscus eremicus) undergo daily torpor, but to avoid extreme heat during the day!

Now, animals that live in areas with extreme seasons also employ the torpor strategy, but they make it last much longer, for weeks to months at a time even! This in cold regions is known as hibernation. 

What is Hibernation? 

Hibernation is a prolonged state of torpor that animals undergo in the cold. Animals that are true hibernators have physiological mechanisms that help them to slow down their heart rate and lower their body temperature for extended periods of time in order to survive long cold winters. Many rodent’s body temperatures reach almost freezing at this time! An amazing example is the arctic ground squirrel, whose body temperature actually goes below freezing. However, the majority of these hibernating animals must still have a food store, waking up every few weeks or so to eat something, and return to hibernate again until they can wake up properly in spring. 

Bears, which are a popular example of hibernation, are in fact a bit tricky. This is because bears do something a bit different. Bears, unlike rodents, do not slow their metabolism as much, or reduce their body temperature by more than 5-10 degrees. Watch the video below to learn more about how bears hibernate!

Animals that live in places that get extremely hot and/or dry for part of the year also have their own type of prolonged torpor, this is known as Estivation. 

What is Estivation?

Estivation (sometimes spelled aestivation) is a prolonged state of torpor that animals undergo in the heat or during drought.

The mechanism is really similar to hibernation, where organisms use their physiology to slow their metabolism way down and enter a deep sleep, reducing the need for food and especially for water. This happens in places like deserts of course, but it has also been found in marine habitats, where marine animals go more dormant as water temperature is higher and food availability is low. 

One difference here is that for many organisms, the main stressor is the lack of water, not the temperature itself. To help with this many animals have to cover themselves in some kind of mucus and bury themselves away to avoid desiccating. Some frogs and invertebrates like worms will carry out this mucus-y strategy in times out drought. 

Torpor is a great strategy for endothermic organisms, but ectotherms that aren’t actually able to change their body temperature physiologically, they need to do something slightly different. Ectotherms version of hibernation is called brumation. 

What is Brumation

Brumation is also a form of prolonged hypometabolism, but brumation is not torpor. 

Why? Because brumation is a type of hypometabolism undergone by ectothermic animals. These ectotherms simply allow their environment to cool their body down and slow down their metabolism for them. So, there aren’t really many physiological adaptations involved. Unless you get into extreme cases of frogs that freeze almost entirely solid, and have a type of antifreeze in their blood in order to avoid cell death. 

Pros and Cons of Hypometabolism

In nature, every survival strategy has trade-offs – meaning pros and cons. There are many animals that undergo some type of deep sleep, so it is clearly pretty successful, but what are some of the pros and cons? 


  • Save energy and water in harsh climates 
  • Need much less food in times of low food availability 
  • Possibly avoid predation while predators have low food availability (but see below)
  • Daily torpor – save energy overnight 


  • It is not possible to wake up quickly from torpor, making animals an easy meal for predators if they get found
  • If the landscape changes while and animal is hibernating underground they might not be able to escape later 
  • Sometimes torpor goes wrong and animals can die 

Overall, this strategy is more beneficial than not, or we wouldn’t see it in so many different animals. Torpor and brumation help animals that live in difficult conditions to save some of their energy waiting for better conditions. 

In Summary 

Here is a table to help you distinguish the 4 types of deep sleep covered on this page!

Humans are not able to hibernate so we need to use other strategies to stay warm during winter. Check our StoneAgeMan winter survival camps if you would like to learn some! 

Aposematism, Müllerian Mimicry, and Batesian Mimicry

Red Flags, United Fronts, and Tricksters

If you are a wild animal, you spend a lot of your time either trying to eat, or avoiding being eaten, and over time many different strategies have evolved to be the best hunter, or the most difficult prey, such as mimicry. 

While many organisms use group defense, camouflage, or behaviors (such as being nocturnal) to avoid being eaten, there are some that have evolved a brave and bold strategy: be poisonous, and make sure everyone knows it – this is called Aposematism. 

Photo by Jelle de Gier

What is Aposematism? 

Aposematism is the term used for poisonous animals – be it reptiles, amphibians, insects – that have a bright coloration that works as a warning signal, or red flag, to potential predators saying, “I either taste really bad or could kill you, don’t eat me!” 

You can think about it kind of like this, if you have ever tried a food and really hated it, or maybe it even made you sick, you are pretty likely to not try that food again, right? Well the same applies for aposematism. A bird might try to eat a bright yellow butterfly, such as a Monarch, then realize how horrible it is, and they are likely to avoid all butterflies that look like that from then on. 

So here is where the interesting piece comes in, there are some animals that have evolved to have similar aposematic patterns and colors, so that once a predator learns not to eat one of them, it won’t eat any of them – it is kind of like a united front against predation and is called Müllerian mimicry. Now, there are also mimics who take advantage of these same colors, but don’t produce any nasty toxins themselves, the tricksters, and this is called Batesian mimicry. Let’s break down these biomimicry basics

A note before we get into it: Nature can be tricky, and most things are found more on a spectrum rather than black and white. In this case the spectrum can be referred to as Batesian-Müllerian mimicry rings, as opposed to two distinct systems, but breaking it down into distinct parts will help us understand the system better.  

What is Müllerian mimicry? 

Müllerian mimicry is when two (or more) poisonous or unpalatable (bad tasting) animals share a similar coloration and/or pattern. The idea is that these two animals form a mutualistic relationship, where they both benefit from sharing a similar look. 

If species A and B for example are Müllerian mimics, and a member of species A is eaten, or maybe just bitten into, the predator is less likely to attack either species A or species B, and vice versa. Now this only really works if the mimics are found in the same place, and predators are able to learn to avoid them. At the end of the day, it is kind of like group or herd defense, but for individuals that don’t have to live together. 

What animals use Müllerian mimicry? 

Thought there are many examples, here are a few examples of Müllerian mimicry: 

Photo by Erin Minuskin
Photo by Joshua J.

What is Batesian Mimicry? 

There are a few tricksters that have managed to take advantage of these colorful warning signs used by aposematic animals, without actually producing any toxin themselves. 

But why is it advantageous to mimic poisonous animals? 

Animals are always trying to avoid being eaten, but toxins are often energetically expensive to produce, so, Batesian mimics have managed to copy the look of other more dangerous animals which helps them to avoid predation, like the mullerian mimics, but without having to be poisonous. 

Now, the mimics aren’t always perfect twins, but we aren’t sure if it is because they look “close enough” for it to still fool predators, or if there are other trade-offs involved making it too difficult for them to look exactly like their poisonous almost-twin. 

Biologists will often refer to this relationship as parasitic, because the Batesian mimic is gaining from its aposematic twin, without giving anything in return. In fact, if a predator eats a Batesian mimic that is palatable, it may attack the actually dangerous species a different time. 

What animals use Batesian Mimicry? 

Here are a few interesting examples of Batesian Mimicry: 

Photo by Dominik Scythe
Photo by Dustin Humes

Recap: What is the difference between Müllerian and Batesian mimicry? 

Müllerian mimicry is when two poisonous or unpalatable animals have similar coloration and patterns while Batesian mimicry is when a non-poisonous animal mimics the patterns or coloration of a poisonous or unpalatable animal without actually producing any toxins themselves. 

The spectrum – Batesian-Müllerian mimicry rings 

So, as mentioned previously, Müllerian vs Batesian mimicry isn’t necessarily black and white, but more of what is called a Batesian-Müllerian mimicry ring. There are a few reasons that make the relationships between these groups more of a spectrum than a “win-win” or “win-lose” etc. Some of the reasons are: 

  • If a Batesian mimic is eaten, this can reduce what we call the “error-cost” that can happen when there are forgetful of naive predators, so the aposematic species doesn’t lose any individuals – known as quasi-Müllerian mimicry
  • Sometimes a Müllerian mimic is less poisonous than the other, so one species is technically gaining more from the relationship, referred to as quasi-Batesian Mimicry 
  • Even within one species, the level of defense produced could vary, so within a species there could be certain individuals gaining more benefits than others! 

So with this being said, just like any interesting theory in Ecology, nothing is 100 percent the rule all of the time!

Overall, we can see here that animals have evolved all kinds of ways to avoid predation. Whether they are truly poisonous or bad tasting, or are just faking it, these bright colors can help them avoid being eaten and carry on to reproduce and help their species continue for another day. 

5 Helpful Note-Taking Tips for Biology Classes

Taking notes is an inevitable part of the studying process especially when it comes to your biology classes. Can you find the same information on Wikipedia? Absolutely. Can you interpret it in the same manner your professor did? Don’t think so. Taking science notes is a kind of art since you deal with both visual and audial information trying to transform it into text (and maybe even sketches). The key is not just being aware of the tips below, but also practice at least 2 of them regularly so that taking biology notes doesn’t make you tremor. 

Note-taking tips:

Prepare for combat!

There are so many note-taking tools – starting from your favorite notebook ending up with not less favorite Evernote. Imagine a brief check-list of items you should bring to your class – pen, pencil, highlighter, markers, or simply a charged laptop. Make sure you didn’t forget to bring review sheets or online notes prepared by your professor (if shared). 

Take care of pre-reading

You’re most likely to know the topic of your lecture – why not glance over the whole chapter in advance? In case you don’t have a textbook, look up essay websites – they have almost every topic you will cover during your course. If you have enough time, you are welcome to write down all the unknown terms, if not – just look at the pictures. Studying biology is all about the visual representation of the theoretical blocks.

Record the lecture

Before the lecture starts, ask permission to record it from your professor. The vast majority of college instructors have nothing against it since they realize the dramatic results of teaching biology in a superfast manner. By the way, there are some applications, which may automatically make a set of notes for you if having the proper format downloaded. Just like your website that writes essays for you, this app may save you lots of time and energy.  

Come up with the creative format 

Even though you may feel a bit skeptical about using colored pencils in your twenties, they may actually contribute a lot to your note-taking process. As you can read from Paperell, most of the students learn faster with the help of visuals. What does it mean? Creating diagrams, highlighting keywords, and drawing schemes may serve a great alternative to writing. Even when planning an essay or generating content for a website, you may come up with its visual version for saving your time and embracing a hidden creative potential. 

Write down the keywords 

Along with the professor speaking, you have to write down the keywords – mainly nouns and adjectives. What can be more obvious, you ask? Most of the students are not able to identify the main points when listening to the speech trying to note each word instead. Therefore, you have to concentrate on the information and analyze it on the spot. The more keywords you have, the easier you can use websites that write papers for you. 

Here is an example of the keywords taken during the “Cell theory” lecture:

  • Theodor Schwann & Matthias Jakob Schleiden – crystallization process (till 1850)
  • Original cell theory: 1. All living organisms… 2. Basic units… 3. Pre-existing cells
  • Remak – cell division – 1852 – binary fission
  • Modern theory: 1, 2, 3 + 4. activity… 5. metabolism & biochemistry… 6. DNA & RNA… 7. similar chemical composition
  • Prokaryotes (nucleus+mitochondria) & eukaryotes (nucleus+plasma membrane)

How to take notes from a textbook?

Some students consider a textbook to be a written analog of what your professor is talking about. In fact, if you’re lucky to use a textbook, you own another precious source of knowledge apart from your offline lectures. 

Textbooks are an amazing tool for learning due to visuals, pictures, and tables they have along with the textual content. You should learn how to interact with your book both during and after the lecture. It’s better to follow the speech and glance at the book from time to time. If you’re allowed to highlight important points right on the textbook pages, don’t miss this unique chance! If not – put the appropriate references to your notebook (e.g., see fig. 2.3, p.534). 

After your notes are ready…

When you’re finished with writing and drawing, you made one more step towards your academic excellence. However, your brain needs to see these notes at least 4 more times to remember at least 60% of this data. Therefore, you have to review everything you’ve been working on, look for possible mistakes, and maybe add something extra you remembered from your lecture. Don’t hesitate to also check some useful sources recommended by your instructor.

At first sight, making notes looks easy. Before we visit our first biology class, we might not even realize how much practice note-taking actually requires. All in all, biology classes wouldn’t be possible without taking notes. Just imagine writing all the tests and quizzes without having memorized the key points from your notebook! Start practicing today and become a note guru.

The Stimulating Science of Animal Enrichment

If you have ever been to a zoo, rehabilitation center, or any other place where wild animals are kept, you have possibly seen animal enrichment taking place and not even realized it. For example, perhaps you have seen the animals interacting with interesting items, playing in pools of water on a hot day, or even being trained to do special tricks; these are all examples of animal enrichment. Believe it or not, there is a careful and scientific process that goes on behind the scenes to deliver the right type of enrichment to each animal in captivity.

What is animal enrichment?

Animal enrichment, also known as environmental or behavioral enrichment, is the process of providing captive animals with some form of stimulation in order to encourage natural behaviors, which helps to improve or maintain their physical and mental health. In a very simple sense, it is giving the animals something to do so that they are happy and healthy. Enrichment can be provided for animals in zoos or rehabilitation centers, laboratories, farms, and even for companion animals, like your cat.

The type of enrichment given to animals should depend on what natural behaviors they normally exhibit in the wild. The intent is to encourage natural behaviors, stimulate curiosity, and to give animals choice and control in their environment Though it may seem simple, giving animals helpful and successful enrichment requires careful research and careful consideration.

What types of animal enrichment are there?

Ideally, animals are given multiple types of enrichment, and the form of enrichment is changed periodically to continue giving them new stimulation. Though they are not mutually exclusive, enrichment can be broken up into five different categories:

    • Social
    • Cognitive
    • Physical habitat
    • Sensory
    • Food

Social enrichment is anything that includes social interactions, often with other live animals. It can include living with conspecifics, which means more of the same species, or other species of animals that can live together peacefully. It could also include people, or even stuffed animals and mirrors to simulate company, or a rival.

Cognitive enrichment is anything new or challenging that will make the animal think, be challenged, or become curious. For example, puzzle feeders, where they must solve a puzzle to obtain their food, brand new food they have never tried, new smells, or even training sessions.

Enrichment of physical habitat is exactly how it sounds: something is added to make their habitat more dynamic, comfortable, and/or fun. Perches for flying and climbing animals, places to hide for insects or prey animals, new dirt for digging or rolling in, etc., are all part of this category.

Sensory enrichment is anything that stimulates an animal’s senses, such as scratch boards, new smells, moving toys, or different sounds.

Food enrichment involves either new food items, or different ways for the animals to get their food. Food can be presented in a way that encourages foraging behavior, which is the way in which an animal searches for and obtains its food, such as scattering food, putting it inside an item that must be broken open, or maybe even burying it.

What are the steps and considerations for good animal enrichment?

Though simple at first glance, enrichment efforts should be treated like a science, with planning, trial and error, and constant revisions. Second, it is important to stimulate natural behaviors , which you can read about further below.

Essentially, the process looks something like this:

Each program has a slightly different methodology for applying animal enrichment, but the important elements are that they are thought out, planned thoroughly, tested, evaluated, and adjusted accordingly. Animalenrichment.org approaches the process with the acronym SPIDER, an enrichment model of six key steps:

SSetting goals: What natural behaviors should be encouraged?
PPlanning: How to encourage certain behaviors, safety concerns, what materials do we need?
IImplementation: Set a schedule and implement different enrichment types.
DDocumentation: Monitor and document the animals experiencing the enrichment.
EEvaluation: Does it work as planned? Is it safe?
RRe-adjustment: Adjust the implementation accordingly to try to get the best result for the animal.

Each step is applied to each new enrichment that will be introduced to an animal through this program. Though there are small differences, in general, this process will look similar in other programs as well.

Essentially, enrichment needs to be treated as a scientific process. By combining animal behavior studies with other enrichment research, and by testing new methods, we can find what types of enrichment are most effective, and we can find new types of enrichment to introduce in order to ensure the health and happiness of captive animals.

Why is animal enrichment so important?

For the animals

There are plenty of reasons that it is important for us to practice enrichment with captive animals and a wide range of research supports that animal enrichment is indeed beneficial and necessary. It is also important that we encourage natural behaviors in these animals when implementing enrichment programs.

First, if we are going to be keeping animals, it is only ethical to give them the best lives that we can, ensuring that they are stimulated, curious, and don’t become bored and restless. When we keep animals, in zoos for example, we often take away their ability to choose many things, and their need to work in order to survive, which can create an unhealthy level of boredom.

Second, enrichment ends up being crucial for animal’s physical health. Many forms of enrichment encourage physical movement and higher levels of activity, which helps the animals stay in better shape.

Third, the mental health of these animals also benefits greatly from enrichment. Wild animals spend much of their time active, and captive animals can suffer from having “too much free time” and not carrying out normal behaviors that they would in the wild. Giving these animals tasks that they would normally carry out in their natural habitat helps to increase mental health -encouraging natural behaviors that reduce stress and stereotypical pacing, and provide escape mechanisms (if they feel overwhelmed by guest presence or other potentially stressing factors).

Lastly, enrichment, especially when natural behaviors are encouraged, improves mating success, and ends up being crucial to reintroduction programs. Animals that will potentially be released back into the wild need to learn, or continue to practice, the behaviors they would in the wild, such as foraging or interacting in a social group Without these skills, the reintroduction will prove even more difficult than it already is. If you are curious about mating in zoos, check out our polar bear mating video!

For us

Of course, at the heart of animal enrichment is the mental and physical health of the animals, however, it is also great for the guests visiting zoos and rehabilitation centers. Seeing the animals happy, healthy, and active helps to improve guest experience. It also keeps people coming back, which in turn generates more income for the zoos. Said income can be turned into more investment for their enrichment program, or for other important zoo conservation/reintroduction programs. As well, stimulating natural behaviors is important for public education: if zoo animals are behaving more naturally they are better representatives of the species in a wild environment, which delivers more accurate education to the public and better promotes learning and species conservation.

Can animal enrichment be negative for the animals?

If not carried out properly, animal enrichment could be potentially negative for the animals for a few reasons.

First, there are potential safety concerns of adding foreign objects to an enclosure, so careful planning and monitoring is important.

For the optimal mental health of the animals, enrichment should aim to encourage more natural behaviors, and what works for one species would have very different results for another. You could imagine that, for example, adding more individuals to a zebra enclosure could be an excellent social enrichment for zebras, but introducing additional polar bears, who are generally solitary, could have negative and potentially dangerous competition results.

Finally, as London-based NGO Wild Welfare very importantly points out, enrichment is very necessary for happy and healthy animals, but it is not a substitute for substandard care of animals. If animals still have poor habitat conditions, diet, etc., enrichment is not a quick fix. An animal’s basic needs must be provided first and foremost, and attempted enrichment does not cover up poor quality care.

However, when enrichment is treated like the science that it is, for animals that are already well cared for, the result is healthier and happier animals, which is good for them, and even for us!

Who is using animal enrichment?

The great news is that enrichment is beginning to be the norm in zoos, rehabilitation centers, laboratories, veterinary clinics, and even in people’s homes with their pets. Additionally, the caretakers of these animals, and researchers worldwide, are working collectively to better our tools and understanding of this important practice. For a bit of a closer look at the process check out our case study, at the end of the article, with the NC Zoo!

What can we do to help improve animal enrichment?

So hopefully by now we have convinced you that enrichment is important, so how do we help to encourage and improve it?

You can start by visiting zoos and rehabilitation centers that have a clearly demonstrated enrichment program. Entrance fees help these institutions pay for more research and materials to continue and improve their current programs–and you get a nice day at the zoo! If you aren’t sure about your local zoo’s enrichment program, ask them!

Second, you can donate money, materials, or your time as a volunteer to an animal enrichment program near you. Some programs have additionally implemented programs of “repurposing for enrichment,” which repurposes old materials to use with their animals. This is excellent because repurposing not only allows for more variety of materials for the animals, but it reduces wastes, and can lower costs by almost 50% in some cases. For example, the Royal Zoological Society of Scotland lists items online you can donate to repurpose for enrichment. You can check your local zoo’s web page, or contact them, to see what kind of items you could bring to aid in their enrichment programs.

Last, we can not forget about the importance of research for further improving our knowledge of enrichment. You can help by donating or collaborating with research programs, such as The Shape of Enrichment, which is a collaborative group for research on animal enrichment that shares and publishes research, and gives courses and workshops on enrichment.

Case Study: North Carolina Zoo, USA

The NC Zoo is working hard to ensure that their animals remain happy and healthy through their animal enrichment program. Watch this video for a closer look at some of their projects involving chimps, peregrine falcons, polar bears, and even Komodo dragons!

Learn More about Animal Enrichment

The Science of Compost

The practice of composting is becoming more widely used on both small and large scales as we begin to realize its amazing range of benefits. But what is composting, really? And how does one take day-to-day waste and turn it into the “black gold” that is compost?

To start off, let’s be clear, you cannot just throw a big pile of waste together and expect a good compost result. It will decompose, no doubt, but there are ways to optimize it in order to get the most out of your heap!

Before we get into the nitty gritty science, let us take a quick look at something that you probably know: humans produce a lot of waste, and we are wasting it.

With an ever-increasing population, one of the largest human-impact issues worldwide is our waste. We have an overabundance of food waste, sewage, livestock manure, landscaping waste, etc., and we are simultaneously faced with ever-shrinking landfill space, diminishing resources, and detrimental effects of our poor waste disposal. Furthermore, we are wasting that waste. Much of what ends up in a landfill still contains high amounts of nutrients that could be reused.

So how can we reduce this impact and utilize this abundance of unused nutrients? Well, we can do what nature has been doing all along. We can break down and re-use this waste – we can compost. Composting can help to reduce the amount of waste we have and allow us to apply these nutrients back into other systems, such as crop agriculture.

What is compost?

Here is a quick definition, with a breakdown to follow: Compost is crumbly, dark, humus-like material that is the result of the controlled aerobic biodegradation of organic material—or composting.

First, let’s clarify humus-like. Humus ((h)yo͞oməs) is a part of soil that contains recently broken down organic material, such as plants, dead organisms, manure etc. Essentially, it is the part of the soil which contains all the recycled nutrients from a system that can be used again. It generally is a lot darker in color and more moist than the rest of the soil, contains a large amount of nutrients and living organisms, and is a large portion of the topsoil in a natural ecosystem.

Next, what is aerobic biodegradation? Aerobic means that it is a process that happens in the presence of oxygen, and biodegradation is the breakdown of organic materials into their basic elements, and into humic material, by living organisms.

Lastly, why is the word controlled important? Biodegradation of organic material is a natural process, and it occurs without any type of assistance. However, when dealing with concentrated wastes produced by humans, there is a specific process required in order to ensure we produce “good compost,” which will be explained later on.

How does compost happen?

As mentioned above, the process of biodegradation occurs naturally; however, composting is a more controlled process for biodegrading organic waste, where waste isn’t just left to rot in hopes that it will turn into nutrient-rich compost.

Aerobic Biodegradation

The compost process requires oxygen in order to be effective, because the organisms involved are mainly aerobic, meaning they require oxygen to live and therefore to break down substances. These organisms consume and use up the organic material for energy (carbon), to build proteins (nitrogen), and for other cellular processes (phosphorus, sulphur, etc.), and in doing so break down complex organic structures, such as plants and feces, into their more basic elements. During this process they produce the humic-like compost we desire, as well as CO2, heat, and water vapor.

Some anaerobic fermentation—biodegradation without oxygen—is also required in the compost process, especially to break down more durable plant structures, such as lignin (the complex structure that makes up the secondary cell wall of plants and helps them to stay rigid). However, the majority of decomposition must remain aerobic for efficient, rapid composting with minimal odor production.

Organisms Involved in Composting

There are thousands of tiny organisms that are involved in the compost process, including fungi, microbes, actinomycetes (a unique type of bacteria that look like fungi), and invertebrates. The use of earthworms to enhance the compost process is called “vermicomposting.”

The process of decomposition involves a complex food web and a multitude of interactions between these numerous species. As well, different organisms are better at breaking down different elements in a pile of compost. Some organisms are better at the break down of cellulose or hemicellulose (other slightly simpler parts of the plant cell wall), and some for lignin. There are also cases of symbiotic relationships between microorganisms, such as bacteria and fungi, that help to optimize the biodegradation process. Interestingly, there is also a unique population of these microorganisms depending on how long the compost heap has been composting or the thermal phase of the composting process.

Thermal Phases

Compost goes through three distinct thermal phases: the initiation phase (or initial activation phase), the thermophilic phase, and the maturation phase.

The graph below shows these thermal phases of compost. Initially there is a rapid growth of mesophilic (medium-heat loving) microorganisms and some thermophilic (high-heat loving) fungi. During this stage there is rapid consumption of amino acids and a huge growth in microorganism populations, which increase the heat to the point of their own destruction.

Next, there is a dominance of thermophilic microorganisms from all three groups (bacteria, fungi, actinomycetes), though some mesophilic organisms may survive through this phase. The majority of composting occurs during this phase, where the plant wall materials such as cellulose and hemicellulose are broken down. Once the temperature approaches 70 ºC (158 ºF) the compost is sanitized because the pathogens (that affect both plants and humans) are killed. Additionally, this intense heat kills any seeds from unwanted weed plants, making the compost better to use as fertilizer.

Finally, as the resources are depleted and converted by these microorganisms, the process begins to slow and the temperature drops. At this point mesophilic organisms once again thrive, pushing out the majority of thermophiles. Then the compost begins to cool and mature, and BOOM! You have beautiful “black gold” that can be used in other systems as a source of nutrients.

What makes a good compost?

Composting is considered different than natural decomposition because it is normally a carefully controlled environment. There are a number of factors involved in effectively creating and managing a good compost heap that results in desirable compost.

A good compost heap is one in which all of the material is broken down relatively quickly, with reduced odors; is hygienic (has destroyed all pathogens); does not contain viable seeds from weed plants; emits lower greenhouse gases while breaking down; and retains the highest possible amount of nutrients for later use as fertilizer.

In order to maintain this, control of the following variables is key: temperature, moisture, oxygen, chemical and physical composition, and size and shape of the heap. There is an optimum range for each of these elements to produce the most efficient compost.

However, in general, a good compost heap simply has a good mix of materials (woody, dry material and rich, organic material; 2:1 dry to green material is the best!), is kept moist, is aerated, and is maintained at a size and shape that is sufficient for the process to occur but is not so big as to stop oxygen from reaching the center. You can also break down your materials to smaller sizes for more surface area and fast break down.

Now, depending on the scale of composting, the exact numbers and the amount of work needed to maintain these elements varies, but here is the scientific breakdown of a good compost heap…

Variable Ideal range Why It’s important How to maintain
Temperature >40 – 65 ºC (104 – 149 ºF) during thermophilic phase
->70 ºC (158 ºF) to sanitize
-Temperature reflects the metabolism of the decomposers.
-Decomposers live and operate best in a certain range of temperatures: too cold and they cannot live, too hot and they die.
-Largely self-regulated by the organisms.
-Water content.
-Size/shape of heap.
-Mechanical turning and/or ventilation.
Moisture 45 – 60% by weight -The organisms involved in biodegradation require water to survive.
-Water content helps to control temperature.
-Too much water means not enough oxygen.
-Keep in a container/area where it does not receive too much rainfall, or where moisture is held in, depending on the region.
– May have to add water (lots of evaporation)
Oxygen 5% oxygen at least -Aerobic biodegradation: decomposers require oxygen to survive and to carry out the composting process. -Ensure heap is not too large.
-Mechanically turn compost frequently.
-Infrastructure (like tubing) allowing oxygen to penetrate the heap.
Nutrients (C:N P,S, and more) High organic content.
C:N = 20-25:1 but 50:1 can work
-Will drastically alter time it takes to break down.
-Decomposers require different levels of these nutrients in order to survive, thrive, and decompose.
-A variety of substrate.
-Good mix of rich organics (food waste) and “bulking agents” (poultry manure, straw, wood chips, bark, leaves etc. to maintain ratio)
-More bulking agents than organics.
Size of Particles (difficult to measure) -Need small enough particles for good amount of surface area to volume ratio that is easier to break down.
-Particles that are too small do not allow for aeration.
– A good mix of different composting material.
Porosity of Substrate 35-50% -Too low and there is no oxygen; too high and temperature remains too low. -Bulking agents
-Use of fungi or earthworms to increase porosity
pH 5.5-8 (best below 7.5) – Each type of decomposer functions best at a certain pH and may die at the extremes. – Addition of fungi, urea, P, Fe, S etc. can alter pH.
-Proper water content helps maintain good pH.
Size and Shape of Heap In a non-insulated container = Min. of ~3.8 L(10 gallons).
Larger amounts =more mixing.
-Large enough to avoid rapid heat and water loss
-Small enough to allow for aeration
Monitor your other parameters and compost success and adjust accordingly.

Why should we compost?

Composting has a lot of benefits and very few downsides. First, compost reduces the amount of waste that goes to the landfill or gets incinerated and re-uses valuable nutrients that would have otherwise gone to waste. Food waste is a huge problem worldwide and throwing out a big portion of the food produced is a lot of wasted energy.

Second, compost can also be used as a safer, cheaper, and more environmentally friendly alternative to synthetic fertilizer in agriculture or in your home garden. Compost material is also better than using raw manure because the heat generated during the process kills dangerous pathogens and seeds from unwanted plants.

Third, composting can be extremely beneficial to human health and economy. If done properly, the composting process kills harmful pathogens and can help reduce human health hazards caused by waste; which is especially problematic in areas of the world with high population densities and/or low resources to deal with waste. Composting can also lead to job production and a means to remediate soils in a cost-effective manner.

Last, compost is lighter and has less volume than raw waste, which means we need fewer vehicles to move it, an environmental and economic benefit. Once the compost is produced it can be moved long distances, from areas of high nutrients—where we have lots of livestock, for example—to areas with nutrient-poor agricultural soils. As well, compost can be used in land reclamation and soil restoration projects.

Just like any method of waste management there are possible downsides to composting. If compost is improperly managed there can be issues with odor, methane production, and heavy metal build up in the final compost. However, if compost is managed properly these risks are greatly reduced. Unfortunately, well-managed compost may still have problems, such as greenhouse gas emissions during decomposition and the land/infrastructure needed for the process. On the contrary, waste that is left untreated also emits greenhouse gases and can produce harmful leachate that can seep into precious water sources. As well, the land space used for compost can be reused again and again once the compost is removed and used, whereas landfill spaces stay relatively full. Essentially, any costs associated with composting are generally outweighed by the benefits.

Compost on a Small Scale

The great thing about composting is that just about anyone can do it. There was a lot of science explaining “perfect compost conditions” in this article, but as long as you maintain a good mix of ingredients, a bit of moisture, and ensure your compost is aerated, you can re-use your own home waste in your garden, on indoor plants, or even give it to your neighbors. In doing so, you can help reduce what goes into a landfill and use fewer artificial fertilizers, reducing your environmental impact and saving you a little money!

Compost on a Large Scale

Compost on a large scale is becoming more and more popular as we realize the benefits of composting sewage, food waste, manure, and more. Cities, towns, and farms worldwide have increased the effort of composting on a large scale, and hopefully the trend continues.

Research on compost optimization improves every day, especially on how we can better implement large-scale compost and continue to reduce the waste that ends up in our landfills. Our knowledge of the optimization/addition of organisms involved in compost, how to best aerate compost at low cost, and what is the best way to obtain that perfect mix of materials continually increases and soon we will hopefully be composting and re-using almost all of the waste that we produce. The below photo is composting at the North Carolina Zoo

Case Study: The North Carolina Zoo and Compost

A good example of compost on a large scale is the composting process that takes place at the North Carolina Zoo in Asheboro, NC. At the NC Zoo, they process 2000 tons of compost every year! They manage to compost a huge percentage of the waste from the zoo, including manure from their large grazing animals. In fact, the main ingredients in their compost are rhino and elephant manure, and there is a lot of it. Check out the video to see the process from start to finish.

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Basic Types of Cells

The Four Main Types of Cells

Even though there are several hundred cell types in the body, all of them can be grouped into just four main categories, or tissues. This makes them easier to understand.

These four main tissues are formed from:

  1. Epithelial Cells. These cells are tightly attached to one another. They cover over the interior of hollow organs, like blood vessels or digestive organs, or else form the surface of things, like the skin. There are dozens of types of epithelial cells. Without epithelial cells, you would have no skin to protect your body from injury and would have no stomach to digest your food!
  2. Nerve Cells. These cells are specialized for communication. They send signals from the brain to muscles and glands that control their functions. They also receive sensory information from the skin, the eyes, and the ears, and send this information to the brain. There are dozens of varieties of nerve cells in the body, each with their own shapes and functions. You would have no consciousness or control over your body without nerve cells.
  3. Muscle Cells. These cells are specialized for contraction. Without muscle cells, you would not be able to move! There are three kinds of muscle cells. They pull and tug on bones and tendons to produce motion. They also form the thick outer walls of hollow organs, like blood vessels and digestive organs, and can contract to regulate the diameter of these hollow organs.
  4. Connective Tissue Cells. These cells provide structural strength to the body and also defend against foreign invaders like bacteria. Two types of cells—fibroblasts and fat cells—are native to connective tissue. Other cells migrate into connective tissue from the bloodstream to fight diseases. Special types of connective tissue—cartilage and bone—are designed to be stronger and more rigid than most connective tissues.

Structure of the Cell Nucleus

Nuclear Envelope

The nucleus is surrounded by a barrier, formed by two membranes, called the nuclear envelope. This barrier separates the contents of the nucleus from the cytoplasm. However, molecules can still move between the nucleus and the cytoplasm because the nuclear envelope is pierced by hundreds of hollow structures called nuclear pores that allow traffic between the cytoplasm and nucleus. The nuclear pores are suspended in a framework found on the inside of the nuclear envelope. This framework, composed of lamin proteins, governs the overall shape of the nucleus. If the lamin proteins change their function, this causes the nuclear envelope to change its shape or to even disappear, as occurs during cell division! These features help explain why cell nuclei look so different in different types of cells.


Chromosomes are the most important parts of the cell nucleus. Each chromosome has two components: 1) an axis formed by protein fibers, and 2) long loops of a molecule called DNA that hang off of the chromosome’s axis. There are 46 chromosomes in each human cell. Each chromosome is plastered onto the interior of the nuclear envelope in its own special place. Information on the DNA is used to control the function of the cell. This information is copied onto other molecules (messenger RNA molecules) and sent to the cytoplasm of the cell. In the cytoplasm, this information is used to make the proteins that operate the cell machinery.

How, exactly, is this done?


DNA is partly composed of thousands of sugar molecules, all linked together into long strands by molecules of phosphate. The name of each sugar molecule is deoxyribose. The molecules of phosphate that join the sugars together are very acidic. Thus, DNA represents an acidic molecule found in the nucleus that contains deoxyribose. In other words, DNA is deoxyribonucleic acid.

Attached to each deoxyribose sugar in each strand of DNA are 4 types of molecules called nucleotides, or bases. These bases are called adenine (A), cytosine (C), guanine (G), and thymidine (T). The sequence of bases found on the strands of sugars, which can be thousands of bases long, represents a coded form of information that is used to control the cell. The encoded information on the DNA is called a gene, and there are about 20,000 active genes in human chromosomes. How is the information in the DNA of a gene used?

The sequence of bases on the DNA is copied onto a similar molecule called messenger ribonucleic acid (mRNA). Then, the mRNA travels through the nuclear pores into the cytoplasm. In the cytoplasm, tiny machines called ribosomes use the information on the mRNA to link together hundreds of amino acids into long chains. A long chain of amino acids is called a protein. Proteins are the building blocks of the cell. They can form rigid structures inside the cell, which help organize its structure. Alternatively, they can form enzymes that accelerate chemical reactions and provide the cell with energy.

Structures of the Cell Cytoplasm


Microtubles are long, straight, hollow structures formed by lots of protein subunits called tubulin proteins. They function as sort of a railroad track system within cells. This allows for the transport of various structures from one part of the cytoplasm to another. During cell division, two sets of chromosomes ride along this railroad track system to reach opposite ends of the cell.

Rough Endoplasmic Reticulum (rER)

Microtubules pass through numerous other structures in the cytoplasm. One structure—a mass of flattened membranes called the rough endoplasmic reticulum (rER)—is specialized to make proteins. Tiny, dark-staining machines called ribosomes are embedded in the membranes of the rER. These ribosomes use the information on messenger RNA to make proteins. Once the proteins have been made, they are packaged in hollow bubbles called vesicles. These protein-filled vesicles also ride along microtubules to reach another stack of membranes called the Golgi apparatus. Proteins are modified within the Golgi apparatus to achieve their final form, and then ride in another vesicle to their final destinations. They can be inserted into the cell membrane, or else can be exported into the watery environment around the cell.


Mitochondria are small, oval-shaped structures that generate energy for the cell. They do this by slowly combining nutrient molecules (fats, sugars) with oxygen; in other words, they “burn” these molecules. When a portion of the cell runs out of energy, mitochondria travel on microtubules to this part of a cell. To provide energy, mitochondria produce an energy-rich molecule called ATP, which powers many of the processes carried out by cell machinery.

Cell Membrane

The cell membrane is a thin film of oil and proteins. While it is an excellent water-proof barrier, it is not very strong and is always in danger of being punctured, like a soap bubble. To prevent this, filaments of a protein called actin are placed just beneath the cell membrane. Actin filaments form a thick, rubbery mat called a gel that reinforces the cell membrane. Also, other proteins called spectrin filaments form an interconnected meshwork on the inside of the cell membrane. If the function of these filaments is altered, this can produce dramatic changes in the overall shape of the cell.

Proteins in the cell membrane can have numerous functions. Some of these proteins form hollow, barrel-shaped structures called transporters. These allow for the entry or exit of small molecules like sugars or water from the cell. Other proteins called receptor proteins react to the presence of signaling molecules like hormones that attach to the outside of the cell membrane.

Epithelial Cells

Varieties of Epithelia

Epithelial cells are specialized to stick tightly to one another. These cells line the interior of hollow organs or cover over surfaces like the skin. There are dozens of types of epithelial cells in the body. Each cell can have one of three shapes:

  • flat (squamous)
  • cube-shaped (cuboidal)
  • tall (columnar)

Also, an epithelium can be only one cell layer thick (a simple epithelium) or many layers thick (a stratified epithelium).

Simple Squamous Epithelia

A single layer of thin, flattened epithelial cells lines the interior of blood vessels. They provide a slick surface that promotes a smooth flow of blood cells through the vessel. These lining cells can be surrounded by smooth muscle cells, which form a thick, contractile wall for a blood vessel. If these flat cells become detached from the lining of a blood vessel, harmful chemicals (cholesterol) can enter the wall of the vessel and cause it to become thickened. This condition is called atherosclerosis, or “hardening of the arteries.” Atherosclerosis can reduce the diameter of blood vessels and slow the passage of blood through the vessel. In the brain, this can cause damage to brain cells (a stroke). In the heart, reduced blood flow can damage heart muscle and cause a heart attack. So these cells play important roles in fighting diseases.

Simple Columnar Epithelia

Simple columnar epithelial cells are found lining the interior of the small intestine. An important job that they fulfill is to transport nutrients from food into the connective tissue beneath the epithelium, so that they can be absorbed into the bloodstream.

Control of the Shape of Epithelial Cells

Why do some epithelial cells have a flat shape, and others have a columnar shape? Part of the answer to this question is a layer of a protein that forms an interconnected meshwork on the interior of the cell membrane. This protein, called spectrin, regulates the overall shape of a cell.

Stratified Squamous Epithelia

Stratified squamous epithelial cells are found covering the lining of the lips and tongue or providing the covering for the skin. There are many layers of cells in this epithelium. Cells at the bottom of the epithelium are rounded in shape. These basal stem cells constantly divide to produce 1) exact copies of themselves and 2) flatter cells that migrate towards the top of the epithelium. When the cells reach the top of the epithelium, they can be worn away and thus often need to be replaced by newer cells.

What causes the appearance of so many layers of cells in a stratified epithelium? Recent study has shown that a protein called P63 is responsible. This protein stimulates the basal stem cells to divide. If P63 is inactivated, the body cannot produce a stratified epithelium. In experiments with P63 in developing mice, it has been shown that such mice will develop a skin that is only one cell thick! Such a skin cannot perform its protective job, and the mice would not survive. So, a stratified epithelium has a vital function.

Pseudostratified Columnar Epithelia

Two types of cells are present in a pseudostratified columnar epithelium: 1) round-looking basal stem cells, which continually divide, and 2) taller, columnar cells that resemble tiny cylinders. This type of epithelium is found within the lungs and trachea. The top of each columnar cell is decorated with tall filaments called cilia. These cilia beat in synchrony with each other and propel mucus out of the lungs and towards the throat. The function of this mucus is to trap particles and other inhaled material so that they don’t enter the lungs. Cilia move the mucus towards the mouse and esophagus, so it can be swallowed and destroyed in the stomach.

Nerve Cells

Parts of Nerve Cells

All nerve cells have three parts:

  1. a portion of cytoplasm immediately surrounding the cell nucleus, which is called the cell soma
  2. multiple processes that extend from the cell soma, which are called dendrites
  3. a single, thinner process called an axon

Cell Soma

The cell soma of a nerve cell has several characteristic features. The cell nucleus of a neuron is typically very large, spherical, and light-staining. Also, it contains an unusually prominent, dark-staining dot called a nucleolus. The cytoplasm of a nerve cell also has many dark-staining patches, which we know represent an unusually abundant rough endoplasmic reticulum (or rough ER). As it turns out, it is no accident that all of these features are found in nerve cells somas, because they all are related to each other.

A pale-staining nucleus signifies that the DNA and the chromosomes are unusually active. Many genes in nerve cells are active, and many types of mRNA molecules are being produced. For this to happen, the DNA and chromosomes must be spread out, or dispersed, so that cell machinery can read the information on the DNA. Dispersed DNA stains lightly.

To produce proteins from the information on the mRNA, many extra ribosomes are needed. The nucleolus functions as a factory for the creation of ribosomes, so it makes sense that it is unusually large in nerve cells. When the ribosomes leave the nucleus and enter the cytoplasm, they attach to membranes of the rough ER, which are correspondingly very abundant.

Other cells in the body have an appearance different from that of nerve cells. If such cells have a small, dark-staining nucleus, a small nucleolus, and very little rough endoplasmic reticulum, this means that they have few active genes and produce only a small amount of mRNA molecules. So, you can tell a lot about the activity of genes in a cell simply by looking at the cell.


Dendrites carry information from other nerve cells towards the cell soma, in the form of altering electrical voltages. The pattern of dendrites extending from the soma differs greatly between different types of nerve cells and makes the activity of nerve cells different from one another in different parts of the nervous system. Most nerve cells are found within the brain, although fewer numbers of nerve cells can be found in the walls of the intestines, near glands that they control. The nerve cells of the cortex of the brain have unusually large numbers of dendrites.

Axons and Synaptic Boutons

Axons end as small, button-shaped structures called synaptic boutons. Synapses attach to target cells such as other neurons, muscle cells, or glands. Each synapse contains many bubbles, or vesicles, that contain chemicals called neurotransmitters. When an electrical impulse reaches the synapse, it causes membrane pores called calcium channels to open. This causes calcium atoms to rush into the cytoplasm of the synapse. Calcium binds to a protein called synaptotagmin. This protein, in turn, then interacts with other proteins called snare proteins, which bring synaptic vesicles close to the cell membrane. When these vesicles fuse with the cell membrane, they release their chemical contents into the environment. These chemicals bind to receptors on the target cell’s membrane, they stimulate the target cell to change its function.