Origin of
Life
Lecture notes ©Bob Field 2005
This is a draft summary of an emerging and
highly complex subject by a physicist who is self-taught.
Check the writings of my expert references before quoting my work extensively.
People puzzle over the origin of life. The job of science is to provide plausible natural explanations for natural phenomena. Here is my plausible explanation for the origin of life: Once upon a time, long, long ago, a self replicating molecule inevitably and spontaneously formed in a rich prebiotic soup of naturally occurring organic molecules. “From so simple a beginning”, natural selection produced the first primitive living cells, among whose descendents was the Last Universal Common Ancestor, the mother of all life on Earth. The rest is history – natural history!
What do we mean by the last common ancestor? All living things are related to a common ancestor, a long gone cell that shared many attributes with modern living cells. No matter which of the five kingdoms you belong to, bacteria, algae, fungus, plant, or animal, the cell is the building block of life. All cells are descended from cells. The natural selection of molecules is the essence of the origin and evolution of life. Most people understand that evolution is the result of chance variations in DNA molecules that provided advantages for descendents in particular environments, descent with modification. But natural selection of molecules began before life began and is the origin of life.
How do simple molecules evolve naturally into complex living cells? My answer is: When energy flows, simple building blocks form complex materials and processes – naturally! How much power does the Sun generate per pound compared to us? Our metabolism produces at least 100 watts or about one watt per pound. The Sun – being less complex and less highly evolved – produces about one watt per five tons. Surprised? That’s because the Sun is extremely hot and heavy and its opacity and poor conductivity trap most of its energy for millions of years and thermonuclear fusion proceeds slowly for billions of years.
The origin of life involves two steps: Complex molecules form and evolve and then simple proto-cells form and evolve. The third step is evolution; namely, complex cells evolve and diversify. But before we can start you need to know the answer to one question: What do cells do?
Cells store, exchange, and transform matter, energy, and information. In order to understand life, you have to understand the structure and functions of four types of molecules: carbohydrates, fats, proteins, nucleic acids like ATP and DNA. Carbohydrates and proteins are building blocks of body structure. The cell membranes that isolate molecules from the external environment are made of fatty materials. The primary energy carrier is ATP, which is closely related to the building blocks of DNA and RNA, the information molecules. The primary function of RNA is to join amino acids to make proteins which are enzymes that facilitate most other biochemical processes in cells including turning simple sugars into complex carbohydrates like cellulose.
You are all familiar with producers, consumers, and decomposers. One way or another, they all acquire energy for use in cellular processes like metabolism which includes photosynthesis, respiration, glycolysis and more.
How does a sea otter resemble bacteria? Their cells have DNA composed of four nucleic acids, proteins made out of 20 amino acids, a fatty lipid membrane enclosure, and many related metabolic processes.
Modern cells are chemical factories: complex, highly efficient, self-replicating. Cells store and release energy to build up and break down biomolecules and perform many other specialized functions. Eukaryote cells have a nucleus and specialized organelles for digestion, respiration, and protein production, all packaged within a complex membrane. Complex molecules are assembled from simpler molecular building blocks. Complex metabolic processes are assembled from simpler metabolic building blocks. Molecular and metabolic complexity, efficiency, and precision evolve from diversity and natural selection. Let’s begin our oversimplification of molecular cell biology and biochemistry!
If you look at a bacteria cell, it is much simpler than the cells of higher life forms with all their specialized compartments. But they seem to move about purposefully. Contrary to what people believed a century ago, cells are not animated by vital spirits and do not violate the laws of thermodynamics. They obey the same physical laws that inanimate matter follows.
What are the building blocks of molecules? Hydrogen, helium, oxygen, carbon, and nitrogen are the most abundant elements in the universe as a result of thermonuclear fusion in stars. Although helium is chemically inert, the other four are the most common elements in the composition of every living thing, generally comprising 99% of the atoms. The atomic composition of a mammal, bacteria, and comet are remarkably similar. Add two more elements, sulfur and phosphorus, and you get CHONSP. With these six elements, you can make all of the water, oxygen, carbon dioxide, carbohydrates, proteins, fats, and nuclei acids in every living cell on Earth! And much more.
Many common molecules are made exclusively from CHONSP, especially biologically important ones. Methane and water can form new molecules because of the special properties of carbon with its tetrahedral bonding possibilities. CHONSP molecules are abundant in space: 100 tons per year of interplanetary dust particles land on Earth. That is 100 million tons per million years or much more early in the Earth’s history. Look closely and what you find is that the molecules of life have many variations on a few themes.
The common sugar glucose is a building block of carbohydrates. Glucose supplies energy to make ATP. Photosynthesis makes glucose from carbon dioxide and water. Respiration liberates energy by oxidizing glucose into carbon dioxide and water. Fructose is an isomer of glucose, it has the same atoms: C6H12O6. Table sugar forms when glucose and fructose are joined. Simple sugar building blocks combine to form carbohydrates when water is squeezed out – table sugar and cellulose for examples. Another sugar, ribose, C5H10O5, is a building block of ATP, RNA, and other nucleotides. If you remove an oxygen atom, you get deoxyribose, the sugar in DNA nucleotides. RNA has a code based on four nucleic acids, AUGC, whereas DNA uses a slightly different code, ATGC. The same set of nucleic acids is common to all living cells.
Speaking of which, nucleic acids are building blocks for energy and information in ATP, RNA, and DNA. Nucleotides are combinations of nucleic acids, ribose sugar, and inorganic phosphate. Monophosphates like cAMP relay signals within a cell. Triphosphates other than ATP transport energy for transfer RNAs (GTP), membrane synthesis (CTP), and sugar synthesis (UTP). They all release energy by losing a phosphate and forming a diphosphate. They are recycled to ATP when energy is provided in the presence of phosphate. Of course, this oversimplified like everything else in our plausible natural explanation. Once nucleotide building blocks are formed, they can be combined to form RNA and DNA polymer chains, again when water is squeezed out. When the polynucleotide chains are complete, RNA spontaneously assumes a helical shape and DNA forms a double helix. DNA replicates itself (with help) before cell division.
Many amino acids are readily made from simple molecules by adding energy. Amino acids are building blocks of proteins that function as enzymes and structures. The same set of 20 amino acids are common to all living cells and all proteins have the same chemical backbone with H and OH on the ends. These amino acids are a very small subset of all possible amino acids. Squeezing the water out is called condensation polymerization or dehydration condensation and is the universal method of forming polymers including synthetics like plastic. Of course the challenge in cells is to remove water from molecules that are immersed in water – that is why catalysts are so important. Aside from the occasional self-replication, DNA’s primary function is transcription of RNA. RNA’s primary function is translation into proteins.
Ribosomes synthesize proteins by translation crawling along a molecule of messenger RNA (mRNA) that attracts matching transfer RNAs (tRNAs) that are attached to corresponding amino acids. Ribosomes reuse tRNA and mRNA. Some of the 20 amino acids are represented by more than one of the 64 triplet codons. Once the chain is complete and leaves the ribosome, the protein spontaneously folds itself into a complex structure that determines its functions. In the end it is all about structures built from building blocks. Catalysts are vital to many processes: proteins help produce complex molecules. Modern cellular processes are highly regulated and involve many molecules and processes.
Messenger RNA provides the message (transcribed from a section of a DNA molecule) to link amino acids into proteins. How does a computer “design” its own software? How does information evolve in DNA? There are many processes including duplication, deletion, and insertion of nucleotides that ultimately change the sequence of amino acids and the regulation of other important cellular processes.
With this understanding of cellular composition and functions, you are now ready to imagine a lifeless prebiotic environment with a wealth of organic molecules. In an energy rich environment, many combinations of prebiotic molecules form and break down constantly. Some molecules replicate due to catalytic effects of a clay or metallic substrate or a fatty membrane. Some molecules expedite chemical reactions including molecular synthesis. Molecules that encourage replication outcompete others for energy and raw materials.
Where and when did molecular evolution occur? There may have been many places on Earth long ago, but in this competitive world, there may be no place where primitive prebiotic molecules could gain a foothold. That is why it is so hard to imagine the circumstances that led to the origin of life. In a primitive world, slight advantages were sufficient to produce dramatic changes in the abundance of key molecules.
Which self-replicating molecules came first? As we have seen, we live in what we might call the DNA+RNA+Protein World. Since the last common ancestor of this world is too complex to have been closely related to the first cells formed, something simpler must have preceded us. Most likely we were preceded by the RNA+Protein World, in which the functions of DNA were performed less efficiently by its close relative RNA, which no longer self-replicates like DNA.
Even this had a simpler predecessor, which is commonly believed to be an RNA World with no proteins or DNA, in which RNA also serves as a less efficient catalyst for other processes that now rely on proteins. Recall that efficiency becomes important when you have fierce competitors, but may not be critical to survival in a less complex world. RNA is believed to be the first polymer in our biochemical heritage and interesting enough is made from nucleotides that are important for signaling and for energy transport, functions that would have been beneficial early on.
However RNA is hard to form spontaneously because ribose is not naturally highly abundant, so RNA World is probably not the very first living world. There is no surviving historical record of early biochemistry in previous worlds because molecules do not leave fossil remains, but scientists speculate that something simpler came earlier. They have proposed several candidates including Peptide (PNA) World, Thioester World, and Clay World. In order to evaluate these ideas and identify the most plausible natural biochemical pathway from molecules to protocells, a great deal of experimentation and analysis will be required. This challenge will probably take a number of decades, especially considering that it is not considered a national priority.
When the final analysis is complete, some scientists anticipate that we will realize that molecular and metabolic evolution may be relatively simple and rapid, in time frames of thousands or millions of years rather than hundreds of millions of years. That would suggest that life evolves readily throughout the universe; perhaps there are trillions of advanced civilizations scattered among the galaxies.
Chance affects the diversity and abundance of molecules, but necessity provides the natural selection. All inheritable biological changes are based on molecular evolution. In some ways, natural selection resembles modern computer aided design methods: Engineers develop and evaluate multiple designs. They refine the best designs and re-compete them several times. They don’t evaluate every possible design. Genetic computing algorithms are becoming more popular among engineering designers. While many people cannot accept or imagine how evolution works, its principles are used routinely to design better products these days.
How does molecular selection influence relative abundance? Any factor that favors a 1% per day increase in the abundance of a molecule over its rivals corresponds not to a 365% increase per year, but a 40-fold increase, thanks to the magic of compounding. In a decade the 40-fold increase does not become 400-fold, but an astounding 6 million billion increase per decade. A faster rate, say 1% per hour leads to an astronomical 4 x 1037 per year. In less than two years that would consume every atom in the universe.
Protocells feed on molecules in the prebiotic soup. Replication processes of the protocells evolve over time as do their metabolic processes. Any inheritable change in composition, structure, or process that provides an advantage can be passed on to descendants. Eventually the last common ancestor of all life on Earth appears. The descendants of the LCA branch into the three domains of archaebacteria, eubacteria, and the predecessors of the eukaryotes. Metabolic processes diversify and gain complexity and efficiency. Autotrophs evolve and make their own food from chemical sources, sometimes using the Sun as an energy source. Horizontal and vertical gene transfers allow early cells to share their best traits with each other so that it may be hard to trace exact lineages.
The first eukaryote grew 10,000 times larger than other bacteria because its membrane lost its cell wall. After losing its cell wall, eukaryotes could surround, capture, and digest food internally within the folds of the membrane, gaining mobility from the food supply. Eventually eukaryotes engulfed other bacteria, which evolved into the nucleus, mitochondria, and chloroplasts.
One of the larger naturally occurring molecules, HC11N, is a building block of complex lipids that form membranes and other fatty substances in cells. Phospholipids self assemble into bilayers with hydrophilic heads in water and hydrophobic tails touching. Endocytosis transports materials into a cell. Modern cells have extremely complex membranes to control matter and energy. Proteins transport molecules through cell membranes.
Eukaryotes are world champions of multicellularity and cell differentiation. Identical cells multiply by dividing. Identical cells differentiate to develop into a multicellular organism. This subject will be discussed in greater detail in the next lecture.
To summarize the facts of life: All cells come from other cells. All cells have membranes, proteins, carbohydrates, and DNA. All cells use similar metabolic processes. All cells use the same genetic code for replication. All cells descended from a common ancestor. The first cells came from non-cellular materials and were much simpler than any modern cells.
To summarize some key ideas in the origin of life: Science provides plausible natural explanations. Cells use energy to make and break molecules. The diversity and abundance of complex molecules depend on chance variations and natural selection of simple building blocks. Simple proto-cells enabled early molecules and metabolic processes to survive and evolve. Complex cells acquired efficient and reliable metabolic processes by chance variations and natural selection of simple building blocks.
My final comment: Complex designs do not require intelligent designers! If you have doubts, then consider the billions of billions of unique snowflakes that self assemble without a designer!
The Beginnings of Life on Earth by Christian de Duve http://www.americanscientist.org/articles/95articles/cdeduve.html
Origin of Life on Earth by Leslie E. Orgel
http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html
Cosmic Evolution by Eric Chaisson
http://www.tufts.edu/as/wright_center/cosmic_evolution/index.html
A Story of Cosmic Evolution
http://bcn.boulder.co.us/~neal/uu/evolutionstory.html
1. Philip Whitfield, From So Simple A Beginning: The Book of Evolution, Macmillan 1993
2. H. Robert Horton et al, Principles of Biochemistry, Prentice Hall 1993
3. J. William Schopf, Cradle of Life, Princeton University Press 1999
4. J. William Schopf, Life’s Origin, University of California Press 2002
5. Andrew Knoll, Life on a Young Planet, Princeton 2003
6. Christian de Duve, Life Evolving: Molecules, Mind, and Meaning, Princeton 2002
7. Christian de Duve, Vital Dust: Life as a Cosmic Imperative, Basic Books 1994. QH325.D42
8. Franklin Harold, The Way of the Cell: Molecules, Organisms, and …, Oxford 2001
9. J. Darnell, H. Lodish, D. Baltimore, Molecular Cell Biology, Scientific American 1990
10. Lawrence Krauss, Atom: An Odyssey from the Big Bang to Life on Earth, Little Brown 2001
11. Eric Chaisson, Cosmic Evolution: The Rise of Complexity in Nature, Harvard U. P. 2001