Click the following for an Origin of Life Student Learning Guide Handout

1. After Making Monomers, Things Gets Harder

We saw in the last tutorial how, based on the work of Stanley Miller and many others, it seems that monomers could have formed abiotically on Earth or in space. But the next steps are harder, and few (if any) have been definitively recreated in laboratory simulations. To review these steps, fill in the blanks in the table below. 

[qwiz style=”width: 550px” qrecord_id=”sciencemusicvideosMeister1961-Steps in the Origin of Life, Table 2″]

[h]Steps in the Origin of LIfe, Table 3 (with follow up questions)

[i]Another Origin of Life Haiku

Primordial Soup

A warm stew of monomers

Could this be the start?


FIRST [hangman] creation of monomers (the molecular building blocks of life)
NEXT Abiotically link monomers to form [hangman] Origin of [hangman]. Create a  system for processing matter and energy and for removing wastes. Origin of [hangman]. Provide the system with a way to pass on instructions for maintenance, growth, and reproduction Encapsulate the system with a [hangman] to keep it from dissolving away, creating the first primitive [hangman] .







[q multiple_choice=”true”] Based on what you know about biology, the first self-replicating informational molecule would probably be a(n) __________ acid.

[c] amino

[f] No. Amino acids are the monomers of proteins. They’re not informational.

[c*] nucleic

[f] Excellent. In life today, informational molecules are nucleic acids: either DNA or RNA.

[c] fatty

[f] No. Fatty acids are components of lipids. They’re not used for information, and it’s hard to see how they could be.

[q multiple_choice=”true”] From the choices below, the type of molecule that would make up an encapsulating membrane would probably be primarily composed of _________ acids.

[c] amino

[f] No. Amino acids are the monomers of proteins. They are crucially important parts of membranes, but they’re not the main structural component of membranes.

[c] nucleic

[f] No. In life today, informational molecules are nucleic acids. You’re looking for a molecule that would make up one of the components of membranes.

[c*] fatty

[f] Excellent. Fatty acids are a key component of the molecules that make up membranes (phospholipids in bacteria and eukarya, a related lipid molecule in archaea).



Moving beyond the abiotic creation of monomers, the science becomes more speculative. Here are just two of the problems we’ll have to resolve.  

  1. How were the first polymers created on an enzyme-free, watery Earth? Life is based on molecules with complex shapes that can catalyze the anabolic (building up) and catabolic (breaking down) reactions that happen in cells. These catalytic molecules are polymers, and include enzymes (which are polymers of amino acids) and RNAs (which are polymers of ribonucleotides). Polymers are also how life stores hereditary information, a role carried out mostly by the nucleic acid polymer DNA, though some viruses use RNA.
    Here’s the problem: to make proteins and RNA, life needs proteins and RNA. To make proteins, for example, cells use ribosomes, a two unit structure that consists of thousands of RNA nucleotides (and dozens of amino acids) organized into a finely tuned molecular machine. To synthesize RNA, cells use the enzyme RNA polymerase, a protein consisting of hundreds of amino acids. So, how, during the emergence of life, could RNA and proteins form in the absence of already existing RNA and proteins?

    A dehydration synthesis reaction

    An additional problem related to polymer creation has to do with the relationship between the process of polymer formation and water. It’s a bit of paradox, because life is dependent on water, but the complex molecules of life don’t easily form in water — at least, not without a lot of enzymatic help. Monomers form into polymers through dehydration synthesis reactions. In these reactions, water molecules are formed as a hydrogen atom from one monomer and a hydroxyl group from another are pulled out by an enzyme, which simultaneously catalyzes the bond between the two monomers. Polymers break apart into monomers through the opposite process, hydrolysis, during which an enzyme splits a water molecule apart, adding a hydrogen to one of the resulting monomers, and a hydroxyl group to the other one. The key point is that the presence of water works against dehydration synthesis, and for hydrolysis. Since the surface of the early Earth was a very wet place, it’s hard to see how, in the absence of enzymes, polymers could form and accumulate.

  2. A chloroplast, showing the reactions of photosynthesis. Click to enlarge.

    In the absence of photosynthesis, what energy source could have been channeled to create the first living things? Life is highly ordered, and creating order requires energy. With one important exception (hydrothermal vent systems, which we’ll explore below), almost all life today is powered by sunlight. Unlike other forms of electromagnetic radiation, sunlight has enough energy to drive the reactions of photosynthesis, but not so much energy that it would destroy molecules like protein or DNA (which is what ultraviolet or X-ray radiation does). As life was evolving, what consistent, powerful, non-destructive energy source could have played sunlight’s role?

As we look at where and how life could have emerged, we’ll have to be able to resolve these (and other) questions in a satisfactory way.

2. Darwin’s “Warm Little Pond,” and a few other Speculations about Life’s Cradle

2a.Problems with the Pond

In 1871, Charles Darwin wrote to his friend, the botanist Joseph Hooker (Darwin Correspondence).

But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity [and so on being] present, that a protein compound was chemically formed, ready to undergo still more complex changes…

This was Darwin’s version of the primordial soup. It set the stage for the Oparin-Haldane hypothesis, and Miller-Urey’s attempt to test that hypothesis. But if an essential stage in the evolution of  life is the formation of polymers from monomers, there are a couple of reasons why warm ponds, tidepools, or shallow seas were an unlikely place for that to have happened.

  1. The was very little land on which ponds or tide pools could have formed. The early Earth was covered by one global ocean, punctuated by a few volcanic islands.
  2. From 4.5 to about 3.8 bya, the Earth was in the period of heavy bombardment. Earth’s surface was being pummeled by comets and meteors, sterilizing the impact zones.
  3. The much closer Moon would have created enormous tides that would have washed any emerging concentration of monomers in a warm little pool out to sea. As a result, pools of concentrated monomers were unlikely, and without concentrated monomers, it’s hard to imagine monomers linking together to form polymers.
  4. If that weren’t enough, re-read the material above about dehydration synthesis and polymer formation. Put monomers together in water, and the last thing they’ll spontaneously do is to combine.
  5. There’s no energy source. As biochemist Nick Lane points out in Life Ascending, The Ten Great Inventions of Evolution, the primordial soup is “thermodynamically flat.” Randomly run energy through such a soup and the most likely thing to happen is that the molecules inside will break down, not grow in complexity.

2b. Directed Panspermia

These difficulties have led to some alternative speculations about where life might have begun. Francis Crick, the co-discoverer of DNA, and Leslie Orgel, an eminent origin of life experimenter and an originator of the RNA world hypothesis (discussed in the next tutorial), speculated that life might have arrived on Earth through directed panspermia. The idea is that an alien civilization wanted to seed the universe (or at least our galaxy) with life. To do so, they filled rockets with bacteria and sent them into space. One of these rockets landed on Earth billions of years ago, seeding the Earth with life. If that leaves you wondering how life evolved on the alien’s planet, it’s a good question. You can read Crick and Orgel’s speculations here.

2c.The Case for a Martian Cradle

Artist’s depiction of the NASA Mars Exploration Rover on the surface of Mars. Source NASA, via Wikipedia

Another idea is that life originated on Mars. Mars had shallow seas early in its history. But Mars has always been a drier world than Earth. In this scenario, abiotically formed monomers in drying pools on Mars could have formed into polymers through dehydration synthesis, a process that would have been coaxed along by inorganic mineral catalysts. A series of linked pools on Mars would have acted as reaction chambers, with polymers becoming increasingly concentrated, interacting with one another, and eventually becoming complex enough to become self replicating molecules. These would have become encapsulated in cells, which would develop a metabolism, and evolve into the first bacteria.

How would these bacteria get to Earth? Over 100 meteorites on Earth have been identified as being of Martian origin. This happens when a meteor strikes Mars and blasts Martian rocks into space. These Martian rocks then become meteors, which spiral in toward Earth. If one of these Martian rocks harbored bacteria, and if these bacteria survived the trip through space and their crash-landing on Earth, then Martian life could have taken hold here. That means that both you and I (according to this scenario) would have Martian ancestors. (See Mars, Panspermia, and the Origin of Life: Where Did it All Begin, or pages 58 to 60 in A New History of Life, Peter Ward and Joe Hirschvink, 2015; or read this article in Smithsonian Magazine).

As we’ll see below, there are some viable and reasonable Earthly locations and scenarios for the origin of life. But first, take the following quiz.

3. Difficulties in Polymer Formation: Checking Understanding:

[qwiz qrecord_id=”sciencemusicvideosMeister1961-Difficulties with Polymer Formation”]

[h]Difficulties in Polymer Formation; Warm Little Ponds and other Speculations

[i]Another Origin of life Haiku

A Warm Little Pond,

Pummeled by Meteor Strikes.

Not a nice cradle.

[q] A problem associated with any account of abiotic polymer formation is that in living systems today, monomers form into polymers through[hangman] synthesis reactions, which are catalyzed by [hangman]

[c] dehydration

[c] enzymes

[q] In today’s living systems, amino acids are polymerized through the action of a two unit molecular machine called a  [hangman]. Any origin of life scenario needs to be able to explain how with these being absent, [hangman], the polymers of amino acids, could still form.

[c] ribosome

[c] proteins

[q] Since life’s emergence, almost all life has been powered by [hangman], which has provided the energy for chloroplasts (and certain bacteria) to carry out  [hangman].

[c] sunlight

[c] photosynthesis

[q] Visible light is powerful enough to power the photosynthesis. Unlike lightning, visible light doesn’t destroy molecules like [hangman] or protein. 

[c] DNA

[q multiple_choice=”true”] According to Darwin, life possibly started

[c] in the highly reduced atmosphere of Early planet earth.

[f] No. That was more like Stanley Miller’s idea.

[c*] in a warm little pond.

[f] Excellent. That was Darwin’s idea about the origin of life.

[c] In the boiling Hot Springs in places like Greenland, or Yellowstone National Park.

[f] No. It’s not likely that Darwin, with the tools he had available at his time, could even conceive of life existing in hot springs.

[q multiple_choice=”true”] Which of the following is the least probable reason why life is unlikely to have first emerged in ponds or tidepools at or near the surface of the Earth.

[c] Large comets and meteors were striking the Early earth, making life impossible.

[f] No. That WAS happening to the surface of early earth. Find the least probable reason.

[c] There was very little land, meaning very few tide pools or ponds where life could have started.

[f] No. That is true of the early earth. Find something that wasn’t true.

[c*] The young sun had too much energy to allow life to form

[f] Correct. The early sun was actually weaker than today’s sun, and nothing about that sun would have prevented the formation of life in tidepools (but many other things would have).

[q] The difficulty of envisioning a scenario for life’s emergence on Earth led Francis Crick (co-discoverer of the structure of [hangman] and Leslie Orgel to hypothesize that life was inoculated on earth through alien rockets, an idea known as directed [hangman].

[c] DNA

[c] panspermia

[q] Because of the difficulties of polymer formation on the watery early Earth, some scientists have theorized the life might have begun on [hangman] and then subsequently transported to earth on [hangman].

[c] Mars

[c] meteors



4. Alkaline Hydrothermal Vents are a Possible Site for Life’s Origins

4a. Black Smoker Vents Support Diverse Ecosystems

A “Black Smoker” hydrothermal vent. The “smoke” is particle laden fluid rising from the vent. The red-tipped tubes are tube worms. Click the photo to enlarge. Source: Wikipedia.

In 1977, deep sea hydrothermal vent ecosystems were discovered. These ecosystems are not powered by sunlight. Found at depths of 2500 meters below the surface of the ocean (and much deeper), they are powered by molten magma rising up toward the ocean floor. In these areas, seawater percolates into the ocean floor, becomes superheated, and then rises full of dissolved minerals like iron sulfides. Deposition of these and other minerals leads to formation of chimneys that emit a continuous stream of black, smokey water (see the photo at left). As a result, these vents are called “Black Smokers.”

These Black Smoker vents support biological communities with population densities that rival those in coral reefs or tropical rainforests. At the base of these food chains are bacteria that can perform chemosynthesis. Chemosynthesis parallels photosynthesis, with the important difference of using hydrogen sulfide (H2S) in place of water (H2O). Here’s the chemosynthetic reaction that occurs at the vents.

12H2S + 6CO2 → C6H12O6 (carbohydrate) + 6H2O + 12S

The carbohydrate formed sustains giant tube worms (which harbor these chemosynthetic bacteria in an organ inside their bodies, and have lost their mouths, gut and anus). Shrimp graze on mats of these bacteria. The vents also support clams, mussels, and crabs, each of which has some type of relationship with the chemosynthetic bacteria. If you want to explore the biology of these Black Smoker Vents in more detail, click the following link for an amazing video with science journalist Ed Yong about the biology of vent tube worms.

Upon their discovery, origin of life researchers began speculating that these hydrothermal vents, with their constant flow of energy and their sheltered location — far away from the tides and meteor strikes that were occuring at the early Earth’s surface — could have been life’s cradle. But a second type of undersea vent, discovered in the year 2000, has properties that would have been even more favorable for serving as a site for the origin of life. These are called alkaline hydrothermal vents, and here’s how they work.

4b. Alkaline Hydrothermal Vents

Alkaline Hydrothermal vents are also powered by geothermal energy, but less directly than the Black Smoker vents described above. The first of these vents to be discovered, called the Lost City, is located about 20 kilometers away from the mid-Atlantic ridge. It was discovered by a team from the University of Washington, led by Deborah Kelley.

Geology of Alkaline Hydrothermal Vents. Click image to enlarge (all images will appear in a new tab)

In the diagram at left, you can see the overall geography of these vents. Number 1 shows rising magma. The magma’s rise causes seafloor spreading and creates structures like the mid-Atlantic Ridge and its rift valley (shown at “3”). Number “2” is a black smoker vent. At “4” is an alkaline hydrothermal vent.

Calcium carbonate chimneys at the Lost City, an Alkaline Hydrothermal Vent System. Click to enlarge.

Like black smoker vents, the Lost City vents are created by mineral deposition. Chimneys composed of calcium carbonate grow up to 60 meters tall. Water leaving the vents is hot (40° C to 90° C), but nothing like the 400° C fluid emerging from black smoker vents. As their name indicates, the fluids emerging from these vents are alkaline (pH 9 to 11, as opposed to the slightly acidic effluent from Black Smoker Vents). They’re also rich in highly reduced compounds, including molecular hydrogen (H2) and methane (CH4). The Lost City spires are also much longer lived than Black Smokers: radiometric dating sets the age of the Lost City system as at least 30,000 years old, making these vents hundreds of times older than Black Smoker Chimneys.

Internal structure of Calcium Carbonate chimneys in the Lost City alkaline hydrothermal vents. Click to enlarge.

Another important difference between alkaline hydrothermal vents and Black Smoker vents is their internal structure. Alkaline hydrothermal vents are riddled with tiny interconnected pores, some of which are as small as a micrometer. Note that this scale is within the range of the size of bacterial cells, which range from 0.5 to 5 micrometers in diameter.

Serpentinisation leading to hydrogen release at alkaline hydrothermal vents (click to enlarge)

Driving the chemistry at the vents is a reaction called serpentinisation. The fracturing rock, composed of a mineral called olivine (magnesium iron silicate), chemically reacts with seawater (“1”). The reaction is exergonic, and results in formation of a new mineral called serpentine, along with the release of hydrogen gas (hydrogen is at “3”), alkaline fluids, and heat.

4c. Why Alkaline Hydrothermal Vents May Have Been Life’s Hatchery

In the ancient Earth, there would be two additional features of the vents that aren’t seen today. First, today’s seas are alkaline: the average pH of seawater is about 8.2. In Archaean times, before the advent of photosynthesis (which absorbs carbon dioxide), the oceans would have been acidic. To review, acidic means more hydrogen ions (H+) than hydroxide ions (OH); alkaline or basic means the reverse). Second, the ancient seas had large amounts of dissolved iron. Put all of this together, and according to biologists like Mike Russell (from NASA’s Jet Propulsion Laboratories), William Martin (University of Dusseldorf), and Nick Lane (University College, London), the stage would have been set for the alkaline vent environment to have served as the perfect incubator for the emergence of of life.

Let’s list the components of these vents, as they would have existed on the Early Earth.

1. At thousands of meters below the surface of the ocean, they provided a sheltered environment, safe from the heavy bombardment the Earth was experiencing in Archaean times.

2. They provided a consistent flow of gentle energy (which parallels the flow of sunlight that powers life today).

3. They provided a source of highly reduced electrons. Hydrogen gas is rare on Earth, yet it’s constantly released from alkaline vents. This amounts to early life gaining the product of photosynthesis (highly reduced compounds), without all of the highly structured membrane-bound machinery involved in photosynthesis. At the vents, the hydrogen (along with its chemical energy and reducing power) is provided for free. 

Iron Sulfur and NIckel Sulfur Clusters forming at the vent/seawater interface. Click to enlarge. From

4. The dissolved iron in seawater, along with other metals like nickel, would have combined with sulfur, creating iron sulfur clusters. These clusters have catalytic properties, and often form the catalytic core of key enzymes that are still at work in living cells today.

An acetyl thioester. From “Origin of LIfe,” Mike Russell, Youtube.

5. These catalytic metals could have promoted the combination of the the hydrogen gas emanating from the vents with carbon dioxide dissolved in the seawater, creating reduced carbon compounds like methane (CH4) or acetate (C2H3O2). Further catalytic reactions could promote the formation of more complex molecules.
The molecule shown to the right is an acetyl thioester, formed from a combination of methane, sulfur, carbon monoxide, and another methane. One acetyl thioester that you’ve probably learned about when studying respiration is acetyl-CoA, which is the highly reduced molecule that diffuses from the cytoplasm to the the mitochondria, powering the Krebs cycle. At least one eminent origin of life researcher, Nobel Laureate Christian de Duve, has built an entire theory about the origin of life around the idea of a thioester world, where thioesters played the role that ATP plays in modern life.

Mineral compartments in Archaean alkaline hydrothermal vents

6. The porous structure of the alkaline vents would create microscopic chambers that could concentrate these monomers, promoting polymer formation. The formation of polymers would be further promoted by catalytic minerals lining the pores within the vents.

Proton Motive force in inorganic vesicles and in cells, from “How Did LUCA Make a Living,” BioEssays 32:271–280, (c) 2010 Wiley Periodicals, Inc. Click image to enlarge.

7. The difference in pH between the alkaline fluids emerging from the vents and early Earth’s acidic seawater would have created a proton (H+) gradient. There would have been a higher concentration of protons outside the vents (in the acidic seawater), and a lower concentration of protons in the alkaline vent fluid. Protons would be pulled across breaks in the walls of the vent microchambers, creating proton-motive force. This is another flow of energy, like water flowing down a turbine, ready to be harnessed by emerging life. In all cells today, this flow powers the synthesis of ATP as protons diffuse through the ATP synthase channel.

The image above and to the right, from “How did LUCA Make a Living? Chemiosmosis in the Origin at Life,” by Lane, Allen, and Martin, shows the parallel between proton gradients in hypothetical vesicles in Hadean/Archaean alkaline hydrothermal vents, and those in modern cells.

5. Origin of Life Video: Mike Russell and Bill Martin

Watch the video below, which pulls all of this together. The video stops at 3:07. My plan is to dig deeper into issues relating to the origins of heredity (the “RNA World”) and the origins of cell membranes, and then return to the vents at the end of the next tutorial.

6. Alkaline Hydrothermal Vents: Checking Understanding

[qwiz qrecord_id=”sciencemusicvideosMeister1961-Alkaline Hydrothermal Vents, Quiz 1″]

[h]Alkaline Hydrothermal Vents


[q] Both “black smoker” vents and alkaline hydrothermal vents are powered by molten [hangman] rising toward the ocean floor.   

[c] magma

[f] Good!

[q multiple_choice=”true”] Of the two hydrothermal vents discussed above, the type with hotter temperatures are

[c] alkaline hydrothermal vents

[f] No. The alkaline vents are significantly cooler than Black Smoker type vents

[c*] Black smoker vents

[f] Excellent. The effluent at black smoker vents can be up to 400 C

[q] Black smoker type vents support a food chain that is not based on photosynthesis, but on [hangman] . 

[c] chemosynthesis

[f] Good!

[q] At alkaline hydrothermal vents, a reaction with rock called serpentinisation causes the release of [hangman] gas into the seawater surrounding the vents. 

[c] hydrogen

[f] Correct!

[q] In the diagram below, an alkaline hydrothermal vent is indicated by number

[textentry single_char=”true”]

[c*] 4

[f] Correct! Number 4 shows an alkaline vent.

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. Note that these alkaline hydrothermal vents are also known at “off ridge” vents.

[q] In the diagram below, a black smoker type vent is indicated by number

[textentry single_char=”true”]

[c*] 2

[f] Good!

[c] Enter word

[f] No, that’s not correct.

[c] *

[f] No. The black smoker vents are directly above rising magma.

[q] In the diagram below, a molecule of hydrogen (H2), still embedded in crust in the ocean floor, is indicated, by what number? (Hint: look at water, H2O, at “1.”).

[textentry single_char=”true”]

[c*] 3

[f] Excellent. “3” represents hydrogen gas, still within the ocean floor.

[c] Enter word

[f] No.

[c] *

[f] No. Here’s a hint. Look again at the water molecule at “1.” What’s the color of the hydrogen atoms.

[q] The lattice of iron, sulfur, and nickel shown below could have acted to   [hangman] bonds between molecules at the vent, creating more complex monomers , and connecting the monomers together to form [hangman].

[c] catalyze

[c] polymers

[q multiple_choice=”true”] Which idea below is connected with the he hypothetical mineral compartments that would have formed in alkaline hydrothermal vents?

[c] each vent could have reproduced itself, spreading vents over the ocean floor.

[f] No. Vents are situated only where there is upwelling heat and magma. They can’t reproduce themselves.

[c*]The structure of the vents would lend itself to concentrating monomers, facilitating the formation of polymers.

[f]Exactly. Unlike the “warm little pond” scenario, alkaline hydrothermal vents provide a structure for concentrating monomers and facilitating polymer formation.

[q labels = “top”]

Alkaline hydrothermal Vents Black smoker vents
temperature ___________ __________
pH __________ ___________
vent structure _______________ ______________
releases H2? _______ _______
Age of vents ______________ ______________
Location ______________ ___________________
 Magma powered? ________________ ______________
Sun powered? __________ _________

[l] acidic

[fx] No, that’s not correct. Please try again.

[f*] Good!

[l] basic

[fx] No. Please try again.

[f*] Excellent!


[fx] No, that’s not correct. Please try again.

[f*] Correct!

[l]complex, porous

[fx] No. Please try again.

[f*] Correct!

[l]Above ocean ridges

[fx] No, that’s not correct. Please try again.

[f*] Good!

[l]100s of years

[fx] No. Please try again.

[f*] Excellent!

[l]40°C to 90°C

[fx] No, that’s not correct. Please try again.

[f*] Excellent!


[fx] No. Please try again.

[f*] Great!

[l]Off ridge

[fx] No. Please try again.

[f*] Correct!


[fx] No, that’s not correct. Please try again.

[f*] Great!

[l]10,000s of years

[fx] No. Please try again.

[f*] Good!


[fx] No, that’s not correct. Please try again.

[f*] Great!


7. Links

In the next tutorial, we’ll look at origins of heredity (the “RNA World”) the making of the first cells, and some issues related to metabolism. Then we’ll return to the vents.

  1. The RNA world, and Making Cells (the next tutorial in this module)
  2. Origin of Life, Main Menu