3.  Life:  Background Information Needed to Understand It

This chapter is about the strange thing we call ’life.’ 

‘Life’ is what we are. 

We can’t understand ourselves without understanding life.  Since the process of ‘life’ necessarily involves constant change, we can’t really understand it without understanding how these changes take place. 

That is what this chapter is about.

There is a lot of controversy about certain philosophical aspects of life.  People argue about what it means, why it exists on this world, whether it exists on other worlds, and what changes we would have to make to our beliefs if we find it is common.  These are deep questions and we can actually get some pretty good answers from analysis of the thing we call ‘life’ and an understanding of the way it works.  But most of what we know about life is not philosophical.  It is scientific.  This chapter concentrates on these things, the things that evidence tells us.  We need this information as background.  Then, once we have this background, we can go into more detail about what, exactly, ‘life’ is, how it came to exist on Earth, and what it means. 

 

First Evidence of Life

 

The oldest evidence we have for life on Earth goes back to shortly after the Earth formed.  The solar system formed 4.65 billion years ago.  The Earth shortly after that.  Originally, it was nothing but a swirling ball of gas.  It began to cool.  The first rocks began to form, solidify out of molten lava, about 4.4 billion years ago.  We don’t have any actual rocks that formed into formations that became a part of the Earth’s crust that go back this far.  We do, however, have some crystals made if zircon that formed before true rocks condensed.  These crystals contain evidence that tells us it is highly likely that living things already existed even before these crystals were formed. 

To understand this evidence, we need to go a little beyond the scientific understanding that most people get in high school or even early college classes, and understand something called isotopes.  To recap what you learned in high school, the most basic bits of substances on Earth are ‘elements’ can be broken down to ‘atoms.’   Atoms have nuclei at the center and electrons circling.  The nuclei must have positively charged particles called ‘protons.’  They may have neutral particles called ‘neutrons..  Here, we want to focus on the element carbon.  Carbon atoms come in many different isotopes, depending on the number of neutrons in them. 

 

Isotopes are two versions of the same element that have different numbers of neutrons.  The most common isotopes of carbon are carbon 12 and carbon 13.  Both have the same number of protons (6) and electrons (also 6).  That is what identifies them as ‘carbon’ and the way ‘carbon’ is defined.  It is an element with 6 protons and 6 electrons. 

All elements other than hydrogen also have non-charged particles called ‘neutrons.’  Carbon 12 has 6 of them and Carbon 13 has 7.  The neutrons don’t change the way the atom bonds. 

 

The most common isotopes are carbon 12 and carbon 13.  they are mixed together in substances and there is no easy way to separate them.  In most places, the ratio between them is very close to 99:1, meaning that if you take carbon from a rock and test it, you will find it is about 99% carbon 12 and 1% carbon 13.  The global standard for carbon isotope ratios is based on the ratio of these isotopes in a specific type of marine limestone called the Pee Dee Belemnite (PDB). This standard, known as the Vienna Pee Dee Belemnite (VPDB), was established using data from the Pee Dee Formation in South Carolina.

This standard provides a consistent reference point for scientists worldwide when measuring and comparing carbon isotope ratios in various substances, including rocks, organic matter, and atmospheric carbon dioxide. Deviations from this standard can provide valuable information about the source and history of carbon in different materials, including potential biological activity in ancient rocks.

When we examine carbon from living organisms or organic matter derived from them, we find a noteworthy difference in the carbon isotope ratio compared to the PDB standard. Living things, particularly photosynthetic organisms, preferentially incorporate the lighter carbon-12 isotope over carbon-13 during their metabolic processes. This preference results in organic carbon having a higher proportion of carbon-12 relative to carbon-13 than what we find in inorganic sources like limestone.

 

Scientists express this difference using the δ13C (delta-13C) notation, where more negative values indicate a higher proportion of carbon-12. Typically, modern organic matter shows δ13C values ranging from about -20‰ to -30‰ (parts per thousand), with photosynthetic organisms often falling between -25‰ and -30‰. This distinctive isotopic signature allows us to differentiate carbon that has been part of living organisms from inorganic carbon sources. We look at the reason for this shortly, but to illustrate the point, coal is almost pure carbon and it is a ‘fossil fuel’ that has definitely been a part of a living thing.  Coal typically has δ13C values ranging from about -23‰ to -27‰, reflecting its origin as organic material. This marked difference in isotopic composition provides a powerful tool for identifying carbon that has cycled through biological systems, even in ancient rocks where other signs of life may have been erased by time.

 

Carbon samples taken from other rocks (inorganic sources) will have slightly different ratios.  You can look up the numbers in reference books.  If you have something with carbon (like steel) and want to know where the carbon came from (which would tell you where the steel was probably made) you could have it analyzed for the ratio.  You could find which rocks have that ratio and that would tell you where the carbon probably came from.  Although there are differences in natural rocks, they aren’t very great.  The global standard (as discussed above) is pretty close to the ratio found in inorganic rocks everywhere.  

Generally, carbon gets into living things through the process of photosynthesis.  We will look at this process shortly, but lets focus on one particular aspect of it:  photosynthesis has a strong preference for carbon 12.  As a result, any carbon that has been processed through photosynthesis has a dramatically different ratio of carbon 12 to carbon 13 than a natural piece of carbon.  (As noted above, coal has δ13C values ranging from about -23‰ to -27‰).

 

Cyanobacteria:  The First Confirmed Life Forms On Earth

 

In photosynthesis, the energy of the sun is used to split carbon dioxide into carbon and oxygen. The same energy source is used to split water into hydrogen and oxygen. The carbon combines with hydrogen and a few trace other elements to form the proteins, enzymes, collagens, and other substances that living things are made of. The oxygen is left over and released into the environment.

The process of photosynthesis takes place in living organisms. The earliest living things that we know for sure lived on Earth are called 'cyanobacteria.' They use photosynthesis to create their cell structures. Cyanobacteria are crucial in Earth's history as they were among the first organisms to produce oxygen as a byproduct of photosynthesis, dramatically changing Earth's atmosphere.

These bacteria create enzymes that use the energy of the sun to drive the complicated chemical processes described above. As they make new protein molecules, they incorporate them into their own structures, essentially 'growing.' When they grow to a certain point and have everything needed for cell division, they split into two 'daughter' cells that have the same structure as the parent cell.

Of course, the daughter cells are smaller than their parent. But they begin to 'grow' immediately after 'birth' by the same process.

The enzymes needed for photosynthesis are incredibly complex and do not exist in nature outside of living things. These organic enzymes preferentially select the lighter carbon isotope (Carbon-12) over the heavier Carbon-13 when fixing carbon dioxide from the air. This preference results in living organisms having a higher proportion of Carbon-12 in their structures compared to the surrounding environment. When the cyanobacteria dies, its body will still contain this isotopic signature. If the body gets trapped by a cooling crystal, it will have a much lower proportion of Carbon-13, as a percentage of total carbon, than carbon that has never been in a living thing.

Carbon that has been a part of a living thing, say carbon in coal, will therefore have a different isotope composition than carbon that has never been a part of a living thing. The difference is dramatic: carbon in coal tends to have a δ13C value about 25‰ lower than the standard ratio. This means that we can test to determine whether a specific sample of carbon has, at any time in its existence, been a part of a living thing. If it has the standard ratio, it probably hasn't. If it has a 'lower Carbon-13' ratio than the standard, it probably has. (This is a simplification, of course, and there are complicating factors that may create exceptions. But they don't matter for the points here. I am just trying to help you understand how scientists test for 'life' in rocks and other inert materials.)

Scientists have found carbon in certain parts of Australia that is encased in zircon crystals that have been dated to 4.1 billion years old. Since the crystals are this old and haven't been disturbed, the carbon must be at least this old. They tested this carbon and it shows that it has the ratio that we associate with carbon that has been in a living thing. While this carbon isotope signature is consistent with biological processes, it's important to note that some non-biological processes can also produce similar fractionation under certain conditions. Therefore, while this evidence is compelling, it's not conclusive proof of life at 4.1 billion years ago.

Here is a quote from an article in Science that explains it:

 

 

Direct Evidence

 

The encapsulated carbon provides indirect evidence of life going back at least 4.1 billion years.  Some scientists extend this out to 4.4 billion years, although this is highly controversial.  This is pretty significant because it takes us back to a very, very early period in Earth’s history, a period when the surface was still mostly molten lava and a very inhospitable place.  If this carbon was a part of a living thing 4.1 billion years ago, this tells us something very important about early Earth life:  it didn’t require perfect conditions to exist.  It existed in a very inhospitable environment. 

Not everyone accepts the indirect evidence however.  Some people only believe life existed if they can see a fossil of life and can tell, by inspection, that it clearly was alive when it was deposited.  The oldest actual direct evidence we have of life comes from fossils found in the same formations in Western Australia where the zircon crystals were found.  They were dated to 3.65 billion years ago.  The image below shows what they look like:

 

QQQ 13 microbes shapes.

 

What Was Primitive Life Like? 

 

We have only tiny amounts of evidence that goes back the full 3.65 billion years. We don’t start to get large amounts of evidence for life on Earth until 3.5 billion years ago.  We find enough evidence to identify the beings themselves.  They were cyanobacteria, a blue-green colored bacteria that is about ½ of a micron across.  (A micron is 1/1000^th of a millimeter).  Cyanobacteria still exist today and have been studied in great detail.  We know a lot about them.  We know they use photosynthesis, described above, to make the carbon and hydrogen that their internal proteins are made of.  This process produces oxygen as a byproduct.  This oxygen goes into the atmosphere. 

In early years, it didn’t stay there very long.  The rocks had minerals like silicon and iron that wanted to oxidize.  As they oxidized, they pulled the oxygen out of the atmosphere.  You can see how strongly many elements attract oxygen by taking some iron filings and setting them outside in moist air.  They will start to rust within days.  The rust is iron oxide.  The oxygen has come from the air. 

The rocks all around us may not look like they contain oxygen, but they do.  About 87% of all of rocks and sand on Earth is silicon dioxide.  This is one atom of silicon and two atoms of oxygen.  The rest consists of other compounds containing oxygen, like bauxite (aluminum oxides) and rust (iron oxide).  When these elements first solidified, they didn’t have as much oxygen as they could hold, so any additional oxygen added to the atmosphere by volcanoes or other processes was absorbed by these ‘oxygen sinks.’  As a result, atmospheric oxygen stayed close to zero until about 2.4 billion years ago (for reasons discussed shortly), even though oxygen was being emitted by volcanoes and the early living things that existed on the planet. 

 

Evidence for as massive explosion of life forms:  The Great Oxygenation Event (GOE)

 

Cyanobacteria takes carbon and hydrogen out of its environment to make the proteins of its own body.  It needs complicated enzymes to do this.  Its body produces the necessary proteins.  It has codes in its DNA that act as blue prints for the proteins.  It also has codes for the proteins that it needs for photosynthesis.  It also has codes that it needs for reproduction.  All these codes together work out to its total ‘geneome’ or DNA profile.  In these bacteria, the DNA profile ranges from  1.6 to 9 million ‘base pairs.’ 

That means that the genetic material (DNA) has this many ‘links’ in that code for the different molecules the bacteria needs to sustain its life processes, conduct photosynthesis, and reproduce.  To get some idea of the complexity of this living thing, consider that if we wrote out the ‘letters’ for the different base pairs on paper in a big list, and printed it out with 12 point font and tiny margins, we would need about 4,500 pages to write out the entire code of one of these microscopic bacteria.   This would generate a pile of printed documents about 15 inches high.  All this is contained in a tiny package:  each cyanobacteria cell is only about ½ of a micron (or 5/10000^th of a millimeter) in size. 

 

The Great Oxygenation Event

 

When a cyanobacteria cell reproduces, it splits into two ‘daughter cells' that have the same DNA as the parent.  The daughters then use sunlight to make more of the molecules they will need to grow into adults and split into new cells themselves.  Under optimal conditions, they can split, doubling the population, in 6 hours.  Again, under optimal conditions, they can go through 30 doublings in 10 days.  If you start with one cyanobacteria (which is only ½ of a micron across), and it doubles in population 30 times, you get more than a billion cyanobacteria. 

This can happen in 10 days. 

All of these bacteria extract carbon dioxide from the air and water from their environment, strip off the carbon and hydrogen to make more of themselves, and release the oxygen into the atmosphere.  Direct evidence shows oxygen production was already taking place 3.5 billion years ago.  Indirect evidence indicates it was already happening 4.1 billion years ago. 

At first, cyanobacteria populations were low so production was low.  But the populations increased and production increased.  The minerals of Earth have an enormous capability to soak up oxygen, as described above.  At first, all of the oxygen produced by these living things went into the rocks.   The silicon became silicon dioxide.  (This material makes up about 87% of the Earth’s crust.)  The iron became iron oxide, the aluminum became aluminum oxide, and all other metals and semiconductors all oxidized.  The atmospheric oxygen didn’t increase, in spite of enormous production by cyanobacteria. 

By 2.4 billion years ago, the rocks had soaked up all of the oxygen they could hold.  The cyanobacteria produced oxygen and it had nowhere to go except into the atmosphere.  Atmospheric oxygen levels on Earth began to increase very rapidly.  This led to the Great Oxygenation Event or GOE. 

 

Life After the GOE

 

Life on Earth is classified into two general categories, prokaryotes and eukaryotes.  Prokaryotes are simple life forms.  Cyanobacteria are in this category.  Eukaryotes are complex life forms.  Humans are in this category. 

Prior to the GOE, prokaryotes were the only living things on Earth.  They are simple, single-celled organisms lacking a nucleus and other membrane-bound organelles.  They use extremely simple systems to make their energy. 

The oxygenated environment allowed far more complex beings to exist, including the amoeba, molds, fungi, and eventually plants and animals.  All of these complex life forms are called eukaryotes.

Eukaryotic cells are characterized by their membrane-bound nucleus and organelles.  They represent a quantum leap in cellular complexity. The presence of abundant oxygen in the atmosphere allowed for the evolution of mitochondria.  These are organelles that generate energy in all advanced life forms, including humans. 

 

Mitochondria use simple sugars and oxygen to generate energy for use in the life processes.  Their activities are incredibly complex, but here is the bottom line:  They ‘burn’ the sugars (combine them with oxygen) to generate energy.  The energy is then stored in molecule called ATP.  The byproducts of this ‘burning’ are water and carbon dioxide.  Humans and other animals expel the carbon dioxide when we exhale.  We expel the water, along with any excess water that comes from our food and drink, when we urinate or sweat. 

The ATP contains energy eukaryotic ‘bodies’ use to sustain their life processes and reproduce.   Mostly, this energy is turned into electricity (through a complex ‘ion-pumping’ process I won’t go into here).  Your brain and nervous system use electricity to process information.  (Your doctor can monitor the electrical signals with an EEG.)  Your muscles, including your heart muscles, also run on electricity (your doctor can monitor these electrical signals with an EKG). 

Scientists have an extremely detailed understanding of this process.  You can find explanations of it to any level you want on the internet.  The point here is pretty simple however and doesn’t require any understanding of the details to accept:  the advanced life forms that use atmospheric oxygen to metabolize sugars (this includes you) have many structures and capabilities that primitive life forms did not have. 

 

All living things with nuclei in their cells are eukaryotes.  Single celled living things with nuclei are eukaryotes.  All multi cell living things are eukaryotes.  This includes you.  You are far more complex than the simple eukaryotes that began to appear shortly after the GOE, but you are basically the same category of beings. 

 

The Evolution of Sexual Reproduction: A Revolutionary Step in Life's Complexity

 

The emergence of sexual reproduction represents the next quantum leap in the evolution of life on Earth.  This method of reproduction evolved sometime between 1.5 billion years ago and 1.2 billion years ago.  The older figure comes from indirect evidence, specifically from something called the ‘molecular clock.’ 

 

The molecular clock is a technique used in evolutionary biology to estimate the time of divergence between species or the age of certain evolutionary events. Here's a brief overview:

Basic concept: The molecular clock hypothesis suggests that genetic mutations accumulate at a relatively constant rate over time.  Scintists compare DNA or protein sequences between different species, calculate the number of differences between these sequences and use the assumption of a constant mutation rate to estimate the time since their divergence. 

 

The 1.2 billion year figure comes from direct evidence, specifically fossils of the multi-cellular red algae called Bangiomorpha pubescens that reproduces sexually.  

Sexual reproduction involves the combination of genetic material from two parent organisms to create offspring with a unique genetic makeup. This process, introduced several revolutionary advantages:

 

• Genetic Diversity: By mixing genes from two parents, sexual reproduction creates offspring with novel combinations of traits, increasing the overall genetic diversity within a population.
• Rapid Adaptation: With greater genetic diversity, populations can adapt quickly to environmental changes, as beneficial mutations can spread more rapidly through a population.
• Error Correction: Sexual reproduction allows for the repair of damaged DNA and the elimination of harmful mutations through recombination and natural selection.

 

After sex began, evolution accelerated to a breakneck pace.  Living things began to adapt and change at a fantastic pace. 

 

[A short decription of evolution through sexual means here:]

 

 

The chart below lists the ages of the oldest samples of various living things dated so far.  We don’t know exactly when these organisms first appeared on Earth; they may have been here significantly longer than shown.  However, the figures below represent the minimum time we know for certain that these life forms have been on Earth, from direct fossil evidence:

 

 

 

Evolution

 

How did one life form change into another?

In his book ‘On the Origin of Species’ Charles Darwin presents a simple explanation of the process: 

 

 

Over time, beings with advantageous traits replaced those without them.  The basic capabilities of the most capable beings on earth increased steadily, over billions of years.  By 60 million years ago, primates existed—Primates being the ‘family’ that includes humans.  Our ancient ancestors were present in this world 60 million years ago.