Biology - Molecules and Cells


 Terms and Concepts 



CHAPTER 1 - Defining Life




Biology, like virtually all sciences, is a practice, a set of behaviors, done by human beings, which means that some of the "rules and regulations" can be partly understood from the standpoint of general human compulsions.

First, humans like to name / label and categorize things, put them in neat little symbolic boxes, which helps us in our second endeavor.  Humans also like (one could say that they need) to explain how things work.  The science of biology provides one way to explain the world, and what qualifies as a living thing falls into the area of labeling.  It's important to remember that human explanations are always limited by our knowledge at any given time, and that labels and categories are limited by how well real objects squeeze into the constraints we put on them.  Life goes on whether we understand it or not, and living things care not a whit whether they're in one or another of our little labeled boxes.  And, in biology, labels and explanations must be somewhat loose.  For example, a species description of dogs must be broad enough to include all dogs.

You may need to lose a tendency that most students, being human (or so they claim), bring to a biology course - they think that Life always works in the same patterns that you see in humans and other big fuzzy animals.  The sooner you come to the realization that there are lots of other ways of doing things than how it works in people, cats, and horses, the better off you'll be.

Although "life" may seem at first like "art" - "I know it when I see it" - it needs to be better defined for a science to be built around it.  We're going to develop a list of features that can be applied to living things everywhere.  Virtually every biology textbook in existence has a list like this, but if you were to check, you would find that the lists rarely match each other point-for-point;  some things are separated into distinct features, while others may be lumped together.  But if you look closely enough, the categories found here are in those other lists somewhere.




What exactly is a genetic system?  In this instance, it means that living things are able to reproduce in a way that passes features, or at least information about making features, along from a parent to its offspring.  For living things on the planet Earth, this feature is usually based on information stored in Deoxyribonucleic Acid, or DNA.  Genes are made of the material DNA, and this is the basis of the term "genetic."  This molecule holds the code by which proteins are made - and proteins are the workhorse molecules of earthly organisms.

But features can be passed along in non-DNA ways - some features found in your cells are there because they were in your mother's egg cell, and some of your traits and tendencies may be linked to the chemistry that surrounded you in the womb while you developed.   Another type of example would be this book, and all of the sorts of information that can be passed on through learning.  Inheritable traits that are not strictly in our DNA code are called memetic and epigenetic - later, when things like evolution are discussed in terms of passing on traits, this is something to remember:  all that we are, all that we pass on is not just in our DNA codes.  This also opens the door for many of what we might call machines to have this aspect of life - is transferable computer code a genetic system?

Embedded in this feature of Life is reproduction - it's hard to pass traits on to offspring without reproducing. You could probably imagine a living thing that never ages (and, to survive, is really lucky) and never reproduces, but no one has found such a thing.  In our world, living things reproduce, and reproduction falls mostly into two camps:  asexual reproduction, where offspring are genetic copies of the parent (they can be genetic copies yet not to be physical copies, because of how genes work), and sexual reproduction, where offspring are a mix of gene sets from two sources (and which may or may not involve two separate parents).  You might not think so by looking at these definitions, but there is a gray area between these types as well, where copying happens but some mixing is allowed.  As we'll see later, there are advantages to each and disadvantages to each (that is a trend you should be noticing in many kinds of biology pairs, the advantage of one reflects upon the disadvantage of the other).

A side effect of reproduction is growth and development:  without growth, each generation would get progressively smaller beyond their ability to survive;  without development, the next reproduction phase could not be timed properly.  Growth is a fairly simple property, while development can be a simple switch in a cell that says, "Don't divide yet," or the many complicated stages that multicellular organisms go through between one zygote (the very first cell, usually created from the fusion of a sperm and an egg cell) and the next generation's zygote-generating adult.

Epigenetic features, discussed in more detail elsewhere, are temporary modifications of DNA, usually methyl groups "clipped" near genes, that allow the genes to be activated and deactivated;  these can be passed from cell to cell and from parent to offspring in their modified form, although typically most of the clips are stripped off as a preparation for reproduction.

An old biology proverb states that, "An adult is just a zygote's way of making another zygote."  You might have heard a variation:  "A chicken is just an egg's way of making another egg."




Both parts of this term are important - dynamic refers to how living things are always changing as their internal chemistries use resources, convert energies, and produce wastes (this chemistry is known as metabolism)units refers to how living things exist as individuals, separate entities with particular needs.  We have looked at the internal dynamism of enzymes and pathways, and the energy-transforming systems of photosynthesis and respiration - these, in some form or another, are universal in living things.

An image showing some metabolic pathways in a liver cell.

Internally, living things are a storm of interactive atoms and molecules, not themselves considered alive, whose complex relationships, involving energy and particle transfers, make up the activity of life on its tiniest level.  This is a good example of science as reductionism:  the expectation that any large activity can be totally understood if you understand how all of its tiny pieces work.  Again, being human makes us feel in our guts that all of the little labeled components must add up to the whole, even though biology commonly exhibits what are called emergent properties that appear when several complex systems produce effects that don't seem to be simply a product of the pieces.   Anyone familiar with computers has seen examples in those complex systems as well - behaviors that can't easily be explained by knowing how each piece of software works by itself.  Of course, computer people and biologists are often sure that even emergent properties can be reduced to understandable components, and they may be right.  It is essential to have a good understanding of molecular issues as a foundation for most biological fields, but the basic mindset of biologists does not tend to match that of chemists.

More on reductionism.


Emergent properties are a philosophical concept.

The units of life begin on the small level (much bigger than molecules, though) with cells, contained bags of many atoms and molecules, dissolved in water, sealed inside a lipid-based membrane that allows a large degree of control over what enters and leaves.  Organisms can be just one single cell (the vast majority of living individuals on Earth are unicellular, made up of only one cell), or they can be a collection of cells that divide up duties (multicellular organisms).  In keeping with the odd reality of the world, there are also unicellular colonial organisms made up of individuals that are technically "independent" but virtually cannot exist without others in the colony - this "colonial" term applies to collections of unicellular organisms, but also multicellular species such as ants, and even people.  Unicellular colonials are somewhat intermediate between unicellular and multicellular organisms.

Image of a unicellular colonial eukaryote, Volvox.




Living things, as stated before, are dynamic as their internal chemistries use resources, convert energies, and produce wastes.  These changes cannot be sustained in a locked chamber with no connection to the world around them.  Organisms must pick up materials, release materials, and try to avoid circumstances that would kill them, either from immediate threats (such as something trying to consume them, or a toxin, or potentially-harmful germ) or long-term needs (examples would be finding needed resources, or preventing its own wastes from poisoning it).  These needs require the ability to pick up cues from the environment and respond to them, something that can be very simple, as some molecule-based "switches" are, or as complex as the information to absorb and process and the responses you produce every minute (Hello, you are responding, right...?).

Sensory molecules at work (abstract).

Using the same proteins for different senses.

Evolution of sensory signalling (blog post).

The level of interaction may depend upon the "size" of the environment being discussed ("environment" is a very flexible word).  Each cell exists in an immediate locale of atoms and molecules, usually in a water-based soup.  Individuals exist in microenvironments that are just their immediate surroundings and fit into ecosystems that include, in theory at least, all of the factors in the world that influence them and which they influence.  Not surprisingly, any practical discussion requires limits be imposed when studying any particular ecosystem. 

Tumors evolve in their own microenvironments.

Microenvironment and antibiotic resistance.

Ecosystems have niches, kind of like functional "slots" into which types of organisms fit - for example, most earthly ecosystems have a niche or niches for Top Predator(s), defined by factors including available prey but also territory and water availability.  This is another area where biology is reductionist, assuming that the workings of any ecosystem can be understood and predicted by a knowledge of all the "pertinent" niches;  this is also another area where emergent properties can be very inconvenient.

Image of warbler niches.

Niches and invasive species.




Biological evolution is a change in type over time.  It connects back to that human compulsion to label and categorize things, combined with a knowledge of how the world of the past was different than todays world.  All sorts of things can evolve, so this may be the feature of Life found most often in things that are not alive.  In living things, evolution happens to populations, groups of related organisms, over time - changes happen to the "average" until the definition of the group doesn't quite fit anymore.

The current best explanation for a lot of how evolution works is based upon the Theory of Evolution by Natural Selection, developed and written down originally by Charles Darwin and Alfred Russel Wallace in 1858, with many adjustments and additions by many people since.  Generally, "disagreement" in scientific circles with this theory involves a dispute about how much Natural Selection influences evolution compared to other factors, not whether the basic ideas are accurate.  A comparable theory might be the Theory of Gravity - scientists might disagree on the details of how gravity works, but no one suggests that gravity doesn't exist.

What is Evolution by Natural Selection?  Sometimes nicknamed "Survival of the Fittest," it would be more appropriate to call it "Reproduction by the Fittest."  Simply put, since more detail will appear later, in any given group of organisms, there will be some features, genetically passable to offspring as different allele combinations, that directly affect the chance that each individual has of living to reproductive age and then successfully reproducing - who manages to live long enough to make little ones?  As a general trend, each generation of offspring, in its gene pool of total alleles, will shift ratios toward those alleles the parents had that are advantageous to their environment, that produced the features which helped their forebears survive.  The important detail to include here is that environments change over time and location - what was a good feature in one environment may not be so good elsewhere or elsewhen - and these changes in environment (the "Nature" part of Natural Selection) influence (the "Selection" part) which individuals likely will live long enough to reproduce and what alleles preferentially wind up in the offspring.  Over time, depending on an organism's suitability to the new environment, new features and combinations of features (called adaptations, a confusing term that does not always mean the same thing even to biologists) may spread through the population, significantly changing the gene pool as a whole until the basic "type," or species (there will be a more particular definition of this term later) has changed enough from the "type" of its ancestors that it needs to be relabeled.

Evolution is not an "ever upward movement toward perfection," although that is what it often is portrayed as;  species don't get better at anything other than fitting the environment of their time, which could always change.  There is no target, no progress, no ultimate peak at humans (our brand of intelligence may not be a great adaptation, since it comes with a long list of self-extinction threats from our own meddling, including but not limited to making our own planet inhospitable to us), and not everything evolves at the same rate, partly because the rate at which environments change varies considerably from place to place (even pieces within environments vary), partly because some forms are more flexible and require little change for a new environment (think of humans - when faced with a new environment, we largely change the environment to suit us, a good thing on a small scale but a possible problem at larger scales), and partly due to how long generations last.  Organisms that reproduce quickly also can evolve quickly if need be.


Viruses - are They Alive?


After defining the traits of living things, it should be made clear that there are things in this world that act alive but maybe don't hit the entire checklist of necessary features.  Modern computerized construction robots (especially ones used to build more robots) can present an interesting debate, but the question of viruses is an old one.

Viruses are extremely tiny things, well above molecular size but smaller than the smallest cells.  The basic structure of viruses varies widely and often is not cellular - many have protein casings rather than membranes.  They float around the world, ejected from the last host cell, like set mousetraps, primed to become active only if they make contact with the right surface molecule of another potential host cell.  That is one of the problems:  free of a host, they seem completely inactive, with no metabolism of any kind.  Inside a host, their metabolism is totally focused on turning the cell into a factory to make more viruses, which will eventually be released fully-formed and "set" to infect the next cell - there is no growth and development in a virus, only construction.  Viral diseases are hard to cure with drugs because viruses lack vulnerability - no working chemistry to interfere with when free, and when they are active, they use borrowed cell chemistry, where interference could kill regular uninfected cells.  Only the fact that in some viruses, some of the chemistry is unlike what a normal cell uses, gives drug designers possible targets to poison.

Put these features together - no metabolism in the free form, no growth, no development, often no cell form - and it's not surprising that many biologists refuse to consider viruses as living things.  Some do consider them alive - after all, they do reproduce and evolve, and they do interact with the environment inside a cell in some ways (that's a gray area that can support either side in the debate).

It may be useful to remember one important fact - no virus in the world cares whether we put it on a "living" or "unliving" list.

Introduction to viruses.



Image of some viruses.



Webpage about human immunodeficiency virus (HIV).



Video about viruses.



Are viruses alive?


Terms and Concepts

In the order they were covered.

Genetic Systems  
Memetic and Epigenetic Features  
Asexual Reproduction  
Sexual Reproduction  
Growth and Development  
Emergent Properties  
Interaction with Surroundings  
Theory of Evolution by Natural Selection  



General Biology 2 - Molecules and Cells

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