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8.2: Astrobiology - Biology

8.2: Astrobiology - Biology



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8.2: Astrobiology

30.2 Astrobiology

Scientists today take a multidisciplinary approach to studying the origin, evolution, distribution, and ultimate fate of life in the universe this field of study is known as astrobiology . You may also sometimes hear this field referred to as exobiology or bioastronomy. Astrobiology brings together astronomers, planetary scientists, chemists, geologists, and biologists (among others) to work on the same problems from their various perspectives.

Among the issues that astrobiologists explore are the conditions in which life arose on Earth and the reasons for the extraordinary adaptability of life on our planet. They are also involved in identifying habitable worlds beyond Earth and in trying to understand in practical terms how to look for life on those worlds. Let’s look at some of these issues in more detail.

The Building Blocks of Life

While no unambiguous evidence for life has yet been found anywhere beyond Earth, life’s chemical building blocks have been detected in a wide range of extraterrestrial environments. Meteorites (which you learned about in Cosmic Samples and the Origin of the Solar System) have been found to contain two kinds of substances whose chemical structures mark them as having an extraterrestrial origin—amino acids and sugars. Amino acids are organic compounds that are the molecular building blocks of proteins. Proteins are key biological molecules that provide the structure and function of the body’s tissues and organs and essentially carry out the “work” of the cell. When we examine the gas and dust around comets, we also find a number of organic molecules—compounds that on Earth are associated with the chemistry of life.

Expanding beyond our solar system, one of the most interesting results of modern radio astronomy has been the discovery of organic molecules in giant clouds of gas and dust between stars. More than 100 different molecules have been identified in these reservoirs of cosmic raw material, including formaldehyde, alcohol, and others we know as important stepping stones in the development of life on Earth. Using radio telescopes and radio spectrometers, astronomers can measure the abundances of various chemicals in these clouds. We find organic molecules most readily in regions where the interstellar dust is most abundant, and it turns out these are precisely the regions where star formation (and probably planet formation) happen most easily (Figure 30.4).

Clearly the early Earth itself produced some of the molecular building blocks of life. Since the early 1950s, scientists have tried to duplicate in their laboratories the chemical pathways that led to life on our planet. In a series of experiments known as the Miller-Urey experiments, pioneered by Stanley Miller and Harold Urey at the University of Chicago, biochemists have simulated conditions on early Earth and have been able to produce some of the fundamental building blocks of life, including those that form proteins and other large biological molecules known as nucleic acids (which we will discuss shortly).

Although these experiments produced encouraging results, there are some problems with them. The most interesting chemistry from a biological perspective takes place with hydrogen-rich or reducing gases, such as ammonia and methane. However, the early atmosphere of Earth was probably dominated by carbon dioxide (as Venus’ and Mars’ atmospheres still are today) and may not have contained an abundance of reducing gases comparable to that used in Miller-Urey type experiments. Hydrothermal vents—seafloor systems in which ocean water is superheated and circulated through crustal or mantle rocks before reemerging into the ocean—have also been suggested as potential contributors of organic compounds on the early Earth, and such sources would not require Earth to have an early reducing atmosphere.

Both earthly and extraterrestrial sources may have contributed to Earth’s early supply of organic molecules, although we have more direct evidence for the latter. It is even conceivable that life itself originated elsewhere and was seeded onto our planet—although this, of course, does not solve the problem of how that life originated to begin with.

Link to Learning

Hydrothermal vents are beginning to seem more likely as early contributors to the organic compounds found on Earth. Read about hydrothermal vents and watch videos and slideshows on these and other deep-sea wonders at the Woods Hole Oceanographic Institution website.

Try an interactive simulation of hydrothermal-vent circulation at the Dive and Discover website.

The Origin and Early Evolution of Life

The carbon compounds that form the chemical basis of life may be common in the universe, but it is still a giant step from these building blocks to a living cell. Even the simplest molecules of the genes (the basic functional units that carry the genetic, or hereditary, material in a cell) contain millions of molecular units, each arranged in a precise sequence. Furthermore, even the most primitive life required two special capabilities: a means of extracting energy from its environment, and a means of encoding and replicating information in order to make faithful copies of itself. Biologists today can see ways that either of these capabilities might have formed in a natural environment, but we are still a long way from knowing how the two came together in the first life-forms.

We have no solid evidence for the pathway that led to the origin of life on our planet except for whatever early history may be retained in the biochemistry of modern life. Indeed, we have very little direct evidence of what Earth itself was like during its earliest history—our planet is so effective at resurfacing itself through plate tectonics (see the chapter on Earth as a Planet) that very few rocks remain from this early period. In the earlier chapter on Cratered Worlds, you learned that Earth was subjected to a heavy bombardment—a period of large impact events—some 3.8 to 4.1 billion years ago. Large impacts would have been energetic enough to heat-sterilize the surface layers of Earth, so that even if life had begun by this time, it might well have been wiped out.

When the large impacts ceased, the scene was set for a more peaceful environment on our planet. If the oceans of Earth contained accumulated organic material from any of the sources already mentioned, the ingredients were available to make living organisms. We do not understand in any detail the sequence of events that led from molecules to biology, but there is fossil evidence of microbial life in 3.5-billion-year-old rocks, and possible (debated) evidence for life as far back as 3.8 billion years.

Life as we know it employs two main molecular systems: the functional molecules known as proteins, which carry out the chemical work of the cell, and information-containing molecules of DNA (deoxyribonucleic acid) that store information about how to create the cell and its chemical and structural components. The origin of life is sometimes considered a “chicken and egg problem” because, in modern biology, neither of these systems works without the other. It is our proteins that assemble DNA strands in the precise order required to store information, but the proteins are created based on information stored in DNA. Which came first? Some origin of life researchers believe that prebiotic chemistry was based on molecules that could both store information and do the chemical work of the cell. It has been suggested that RNA (ribonucleic acid) , a molecule that aids in the flow of genetic information from DNA to proteins, might have served such a purpose. The idea of an early “RNA world” has become increasingly accepted, but a great deal remains to be understood about the origin of life.

Perhaps the most important innovation in the history of biology, apart from the origin of life itself, was the discovery of the process of photosynthesis , the complex sequence of chemical reactions through which some living things can use sunlight to manufacture products that store energy (such as carbohydrates), releasing oxygen as one by-product. Previously, life had to make do with sources of chemical energy available on Earth or delivered from space. But the abundant energy available in sunlight could support a larger and more productive biosphere, as well as some biochemical reactions not previously possible for life. One of these was the production of oxygen (as a waste product) from carbon dioxide, and the increase in atmospheric levels of oxygen about 2.4 billion years ago means that oxygen-producing photosynthesis must have emerged and become globally important by this time. In fact, it is likely that oxygen-producing photosynthesis emerged considerably earlier.

Some forms of chemical evidence contained in ancient rocks, such as the solid, layered rock formations known as stromatolites , are thought to be the fossils of oxygen-producing photosynthetic bacteria in rocks that are almost 3.5 billion years old (Figure 30.5). It is generally thought that a simpler form of photosynthesis that does not produce oxygen (and is still used by some bacteria today) probably preceded oxygen-producing photosynthesis, and there is strong fossil evidence that one or the other type of photosynthesis was functioning on Earth at least as far back as 3.4 billion years ago.

The free oxygen produced by photosynthesis began accumulating in our atmosphere about 2.4 billion years ago. The interaction of sunlight with oxygen can produce ozone (which has three atoms of oxygen per molecule, as compared to the two atoms per molecule in the oxygen we breathe), which accumulated in a layer high in Earth’s atmosphere. As it does on Earth today, this ozone provided protection from the Sun’s damaging ultraviolet radiation. This allowed life to colonize the landmasses of our planet instead of remaining only in the ocean.

The rise in oxygen levels was deadly to some microbes because, as a highly reactive chemical, it can irreversibly damage some of the biomolecules that early life had developed in the absence of oxygen. For other microbes, it was a boon: combining oxygen with organic matter or other reduced chemicals generates a lot of energy—you can see this when a log burns, for example—and many forms of life adopted this way of living. This new energy source made possible a great proliferation of organisms, which continued to evolve in an oxygen-rich environment.

The details of that evolution are properly the subject of biology courses, but the process of evolution by natural selection (survival of the fittest) provides a clear explanation for the development of Earth’s remarkable variety of life-forms. It does not, however, directly solve the mystery of life’s earliest beginnings. We hypothesize that life will arise whenever conditions are appropriate, but this hypothesis is just another form of the Copernican principle. We now have the potential to address this hypothesis with observations. If a second example of life is found in our solar system or a nearby star, it would imply that life emerges commonly enough that the universe is likely filled with biology. To make such observations, however, we must first decide where to focus our search.

Link to Learning

Just how did life arise in the first place? And could it have happened with a different type of chemistry? Watch the 15-minute video Making Matter Come Alive in which a chemistry expert explores some answers to these questions, from a 2011 TED Talk.

Habitable Environments

Among the staggering number of objects in our solar system, Galaxy, and universe, some may have conditions suitable for life, while others do not. Understanding what conditions and features make a habitable environment —an environment capable of hosting life—is important both for understanding how widespread habitable environments may be in the universe and for focusing a search for life beyond Earth. Here, we discuss habitability from the perspective of the life we know. We will explore the basic requirements of life and, in the following section, consider the full range of environmental conditions on Earth where life is found. While we can’t entirely rule out the possibility that other life-forms might have biochemistry based on alternatives to carbon and liquid water, such life “as we don’t know it” is still completely speculative. In our discussion here, we are focusing on habitability for life that is chemically similar to that on Earth.

Life requires a solvent (a liquid in which chemicals can dissolve) that enables the construction of biomolecules and the interactions between them. For life as we know it, that solvent is water, which has a variety of properties that are critical to how our biochemistry works. Water is abundant in the universe, but life requires that water be in liquid form (rather than ice or gas) in order to properly fill its role in biochemistry. That is the case only within a certain range of temperatures and pressures—too high or too low in either variable, and water takes the form of a solid or a gas. Identifying environments where water is present within the appropriate range of temperature and pressure is thus an important first step in identifying habitable environments. Indeed, a “follow the water” strategy has been, and continues to be, a key driver in the exploration of planets both within and beyond our solar system.

Our biochemistry is based on molecules made of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. Carbon is at the core of organic chemistry. Its ability to form four bonds, both with itself and with the other elements of life, allows for the formation of a vast number of potential molecules on which to base biochemistry. The remaining elements contribute structure and chemical reactivity to our biomolecules, and form the basis of many of the interactions among them. These “biogenic elements,” sometimes referred to with the acronym CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), are the raw materials from which life is assembled, and an accessible supply of them is a second requirement of habitability.

As we learned in previous chapters on nuclear fusion and the life story of the stars, carbon, nitrogen, oxygen, phosphorus, and sulfur are all formed by fusion within stars and then distributed out into their galaxy as those stars die. But how they are distributed among the planets that form within a new star system, in what form, and how chemical, physical, and geological processes on those planets cycle the elements into structures that are accessible to biology, can have significant impacts on the distribution of life. In Earth’s oceans, for example, the abundance of phytoplankton (simple organisms that are the base of the ocean food chain) in surface waters can vary by a thousand-fold because the supply of nitrogen differs from place to place (Figure 30.6). Understanding what processes control the accessibility of elements at all scales is thus a critical part of identifying habitable environments.

With these first two requirements, we have the elemental raw materials of life and a solvent in which to assemble them into the complicated molecules that drive our biochemistry. But carrying out that assembly and maintaining the complicated biochemical machinery of life takes energy. You fulfill your own requirement for energy every time you eat food or take a breath, and you would not live for long if you failed to do either on a regular basis. Life on Earth makes use of two main types of energy: for you, these are the oxygen in the air you breathe and the organic molecules in your food. But life overall can use a much wider array of chemicals and, while all animals require oxygen, many bacteria do not. One of the earliest known life processes, which still operates in some modern microorganisms, combines hydrogen and carbon dioxide to make methane, releasing energy in the process. There are microorganisms that “breathe” metals that would be toxic to us, and even some that breathe in sulfur and breathe out sulfuric acid. Plants and photosynthetic microorganisms have also evolved mechanisms to use the energy in light directly.

Water in the liquid phase, the biogenic elements, and energy are the fundamental requirements for habitability. But are there additional environmental constraints? We consider this in the next section.

Life in Extreme Conditions

At a chemical level, life consists of many types of molecules that interact with one another to carry out the processes of life. In addition to water, elemental raw materials, and energy, life also needs an environment in which those complicated molecules are stable (don’t break down before they can do their jobs) and their interactions are possible. Your own biochemistry works properly only within a very narrow range of about 10 °C in body temperature and two-tenths of a unit in blood pH (pH is a numerical measure of acidity, or the amount of free hydrogen ions). Beyond those limits, you are in serious danger.

Life overall must also have limits to the conditions in which it can properly work but, as we will see, they are much broader than human limits. The resources that fuel life are distributed across a very wide range of conditions. For example, there is abundant chemical energy to be had in hot springs that are essentially boiling acid (see Figure 30.7). This provides ample incentive for evolution to fill as much of that range with life as is biochemically possible. An organism (usually a microbe) that tolerates or even thrives under conditions that most of the life around us would consider hostile, such as very high or low temperature or acidity, is known as an extremophile (where the suffix -phile means “lover of”). Let’s have a look at some of the conditions that can challenge life and the organisms that have managed to carve out a niche at the far reaches of possibility.

Both high and low temperatures can cause a problem for life. As a large organism, you are able to maintain an almost constant body temperature whether it is colder or warmer in the environment around you. But this is not possible at the tiny size of microorganisms whatever the temperature in the outside world is also the temperature of the microbe, and its biochemistry must be able to function at that temperature. High temperatures are the enemy of complexity—increasing thermal energy tends to break apart big molecules into smaller and smaller bits, and life needs to stabilize the molecules with stronger bonds and special proteins. But this approach has its limits.

Nevertheless, as noted earlier, high-temperature environments like hot springs and hydrothermal vents often offer abundant sources of chemical energy and therefore drive the evolution of organisms that can tolerate high temperatures (see Figure 30.8) such an organism is called a thermophile . Currently, the high temperature record holder is a methane-producing microorganism that can grow at 122 °C, where the pressure also is so high that water still does not boil. That’s amazing when you think about it. We cook our food—meaning, we alter the chemistry and structure of its biomolecules—by boiling it at a temperature of 100 °C. In fact, food begins to cook at much lower temperatures than this. And yet, there are organisms whose biochemistry remains intact and operates just fine at temperatures 20 degrees higher.

Cold can also be a problem, in part because it slows down metabolism to very low levels, but also because it can cause physical changes in biomolecules. Cell membranes—the molecular envelopes that surround cells and allow their exchange of chemicals with the world outside—are basically made of fatlike molecules. And just as fat congeals when it cools, membranes crystallize, changing how they function in the exchange of materials in and out of the cell. Some cold-adapted cells (called psychrophiles) have changed the chemical composition of their membranes in order to cope with this problem but again, there are limits. Thus far, the coldest temperature at which any microbe has been shown to reproduce is about –25 ºC.

Conditions that are very acidic or alkaline can also be problematic for life because many of our important molecules, like proteins and DNA, are broken down under such conditions. For example, household drain cleaner, which does its job by breaking down the chemical structure of things like hair clogs, is a very alkaline solution. The most acid-tolerant organisms (acidophiles) are capable of living at pH values near zero—about ten million times more acidic than your blood (Figure 30.9). At the other extreme, some alkaliphiles can grow at pH levels of about 13, which is comparable to the pH of household bleach and almost a million times more alkaline than your blood.

High levels of salts in the environment can also cause a problem for life because the salt blocks some cellular functions. Humans recognized this centuries ago and began to salt-cure food to keep it from spoiling—meaning, to keep it from being colonized by microorganisms. Yet some microbes have evolved to grow in water that is saturated in sodium chloride (table salt)—about ten times as salty as seawater (Figure 30.10).

Very high pressures can literally squeeze life’s biomolecules, causing them to adopt more compact forms that do not work very well. But we still find life—not just microbial, but even animal life—at the bottoms of our ocean trenches, where pressures are more than 1000 times atmospheric pressure. Many other adaptions to environmental “extremes” are also known. There is even an organism, Deinococcus radiodurans, that can tolerate ionizing radiation (such as that released by radioactive elements) a thousand times more intense than you would be able to withstand. It is also very good at surviving extreme desiccation (drying out) and a variety of metals that would be toxic to humans.

From many such examples, we can conclude that life is capable of tolerating a wide range of environmental extremes—so much so that we have to work hard to identify places where life can’t exist. A few such places are known—for example, the waters of hydrothermal vents at over 300 °C appear too hot to support any life—and finding these places helps define the possibility for life elsewhere. The study of extremophiles over the last few decades has expanded our sense of the range of conditions life can survive and, in doing so, has made many scientists more optimistic about the possibility that life might exist beyond Earth.


8.2: Astrobiology - Biology

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How did life emerge on Earth? How have life and Earth co-evolved through geological time? Is life elsewhere in the universe? Take a look through the 4-billion-year history of life on Earth through the lens of the modern Tree of Life! This course will evaluate the entire history of life on Earth within the context of our cutting-edge understanding of the Tree of Life. This includes the pioneering work of Professor Carl Woese on the University of Illinois Urbana-Champaign campus which revolutionized our understanding with a new "Tree of Life." Other themes include: -Reconnaissance of ancient primordial life before the first cell evolved -The entire

4-billion-year development of single- and multi-celled life through the lens of the Tree of Life -The influence of Earth system processes (meteor impacts, volcanoes, ice sheets) on shaping and structuring the Tree of Life This synthesis emphasizes the universality of the emergence of life as a prelude for the search for extraterrestrial life.

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Enjoyed every minute of the course and learned so much at the same time!

Excellent lectures. Personal transformation observed while watching.

Week 8 - Astrobiology and the Search for Life in the Cosmos

No matter where you are or what you believe, sometime in your life you will look up into the sky and ask: What is out there? Where are we going? Is there life elsewhere in the universe? This course is dedicated to searching for answers to these questions. The fundamental concepts of life and habitable environments, established upon the modern synthesis of the Tree of Life, will direct us in recognizing biospheres that might be quite different from our own. In the last week of this course, we will look in detail at what the future has in store for space exploration and the search for life in the cosmos.


2. Section I

2.1. Considering life's origin through the metaphors of computer science

The first question we address concerns a mechanism by which selection and evolution can begin. In his book Life: Its Nature, Origin and Development, Oparin (1962) asked whether life could in fact be understood as a mechanism. He even considered cybernetics, which is pertinent to the thought experiment we describe next. Oparin decided that the properties of life went far beyond mechanical explanations:

“Of course, we may, and should try to understand the physical and chemical basis of the various vital phenomena by means of the construction and study of models which will reproduce the same phenomena as occur in organisms but in a simplified form. In doing so, however, we must always remember that we are dealing with models and not confuse them with living things.”

Keeping Oparin's caveat in mind, we note that computational approaches have gone far beyond the primitive cybernetics he envisaged. Computer-based software tools and metaphors have infiltrated all branches of the scientific enterprise. From the perspective of computer science, the intracellular processes of life have been aptly compared with the functioning of a computer operating system (Bray, 2011 Pang and Maslov, 2013). It is an interesting and perhaps enlightening exercise to compare in silico programs to the operating system of life. Rather than patterns of electrons flowing in silicon circuits, the programs of the cell are embedded in monomer sequences of biopolymers. Base sequences in DNA are linear data stores, analogous to a read-only memory, which are transcribed into base sequences in messenger RNA, then loaded into ribosomes, which generate application programs fashioned out of proteins. Like an operating system's message queues and protocols, a finely tuned chemical network of signaling and feedback enables a cell to execute specific protein programs in a highly regulated manner.

This comparison brings us to the question we are addressing here: Can a chemical computer emerge spontaneously on a sterile yet habitable planet such as the early Earth? The answer is obviously yes, because life did begin, but the process by which this occurred remains a fundamental problem in biology. We argue that by analogy to the development of computers, the hardware of the first forms of life is represented by organic molecules that become self-organized into supramolecular structures (Lehn, 2002) capable of capturing free energy available in the environment and used it to drive polymerization and growth. The programs of life spontaneously developed when initially random systems of polymeric molecules underwent cycles of selection and amplification to express functions within the system of self-assembling hardware.

However, how it is possible for programs to emerge in the absence of a programmer? Figure 1 illustrates how this can work by referring to early computers that used holes punched in a paper tape as a way to code instructions using binary bits. The goal is to spontaneously generate a program that will turn on a series of light-emitting diodes (LEDs) in a front panel attached to the computer. At the outset, the tape puncher is linked to a random number generator. The punched tapes are then read one at a time into a simple computer that uses electrical energy to read each tape and then execute the purely random instructions through a primitive processor. Most programs “crash” in that they switch on no LEDs and so are discarded. However, if by chance a rare random program (such as “A” in the example) happens to light up at least one LED, it is then automatically selected and fed back into the puncher. The puncher stores the program “A” and punches it out multiple times, adding new random instructions “B,” “C,” and “D” onto extended sections of tape. The next cycle runs the new programs A-B, A-C, A-D and A-C is similarly selected to go forward into a new generation of punched programs. Over time a further extended program (A-C-F) will emerge, which operates an even larger number of LEDs on the front panel. This method of programming is inefficient, but given enough time it will create a program that switches on all of the LEDs.

FIG. 1. Metaphor for how a computer program can be developed without a programmer.

To summarize the four obvious steps, (1) a source of energy (an electrical current) drives a process that punches random holes in a tape, feeds the tape into our simple computer, and operates the computer's CPU. At some point, one set of holes happens to cause an LED to light up and that set is (2) selected, (3) replicated, and (4) extended, and functional instructions are thereby drawn out of a population of randomly punched tapes. Another chance sequence of holes in an elongated tape causes a second LED to light up, and so on, until all of the LEDs are operating. A fifth often overlooked step is essential, which is a feedback loop between the LED status and the punching apparatus, a testing subroutine that instructs the system to save, incorporate, and amplify any chance program that happens to turn on an LED. This simple test could be called combinatorial selection and can enable programming without the need for a programmer, suggesting how similar steps driving combinatorial chemistry could lead to an origin of life. In a chemical system, the energy sources are hot water and sunlight, the paper tapes are polymers such as nucleic acids or proteins, and the holes are chance patterns in monomer sequences. The programs are collections of interacting polymers that undergo selection and amplification if they happen to have functions that increase survivability of those same polymers over time. The collections are contained within membrane-bounded compartments and referred to as protocells.

Using this metaphor of self-writing computer code allows a reframing of the origin of life as a testable hypothesis that incorporates the biophysics of self-assembly, the chemistry of polymerization, and the geophysical properties associated with volcanic land masses on the early Earth. Although this reframing provides a new perspective for life's origin, it also raises many questions. First, we must define an operating protocell. The sole measure of operability of a microbial cell is that encapsulated systems of catalytic polymers use nutrients and energy to undergo growth by polymerization, supporting an eventual division into viable daughter cells. Akin to the punched paper tapes, the system we propose generates immense numbers of microscopic protocells, each different in composition from all the rest, and these protocell populations must then undergo a primitive version of Darwinian selection we have termed combinatorial selection, at the molecular and supramolecular level.

How can the earliest protocells composed of primitive, self-assembled membranes encapsulate cargoes of random polymers?

How can functional chemical “programs” spontaneously emerge by selection and begin to operate?

What environmental stresses provide selective factors and how can polymer programs be extended so that protocells can survive these factors and propagate sets of polymers into subsequent generations?

Are there prebiotically plausible natural environments in which protocells can emerge and then undergo evolution through a primitive form of selection before the emergence of life?

How can such populations of primitive protocells eventually evolve into the self-sustaining and self-reproducing forms that comprise living systems?

We first address the question of a plausible environment that is conducive to the emergence of protocells. Darwin (1871) provided a clue in an insightful sentence written in a letter to his friend J.D. Hooker:

“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 & etc. present, that a protein compound was chemically formed, ready to undergo still more complex changes [..]”

Most readers are probably familiar with this quote, but we reiterate it here because Darwin's intuition of a warm little pond makes perfect sense. In contrast to the dilution that inevitably would occur in a global salty ocean, potential organic reactants can accumulate and be concentrated sufficiently for reactions to occur in small bodies of fresh water on volcanic land masses emerging from the ocean (Pearce et al., 2017 Ranjan et al., 2019). Darwin also proposed that a “protein compound” must first form, “ready to undergo still more complex changes.” Although he did not know that proteins were linear chains composed of linked amino acids, Darwin intuitively understood that proteins were important, and that they could somehow be synthesized by an unspecified source of energy. Darwin also hinted that the proteins must be able to undergo evolutionary cycles generating more complex changes, which today is described as an away-from-equilibrium chemical system.

This brings us to a conundrum known as the “water problem” (Benner et al., 2012). Proteins and the other key polymers of life, RNA and DNA, must function in an aqueous medium, but in the absence of continuous synthesis, they undergo hydrolytic decomposition at varying rates depending on temperature and pH. In life today, polymers are continuously synthesized and repaired by enzyme-catalyzed condensation reactions driven by adenosine triphosphate (ATP) as an energy source. However, there were no enzymes or ATP available on the prebiotic Earth, so how could the first polymers form? It has long been understood that condensation reactions can occur if monomers undergo dehydration at elevated temperatures (Fox and Harada, 1958 Lohrmann and Orgel, 1971 Lahav et al., 1978). However, a single cycle might lead to a few oligomers, but these would begin to undergo hydrolysis upon rehydration. We propose that not just a single cycle but instead continuous wet-dry cycles would allow polymers to exist in a steady state and grow more complex as solutes in a prebiotic warm little pond (Hargrave et al., 2018). As long as the rate of synthesis exceeds the rate of hydrolysis, multiple cycles operating in conjunction with a kinetic trap will inevitably produce an accumulation of polymers (Higgs, 2016). In other words, a kinetic trap emerges in a reaction or a series of linked reactions if the rate of synthesis exceeds the rate of a back reaction (Ross and Deamer, 2016). All life on Earth incorporates a kinetic trap because the rate of synthesis of biopolymers by condensation reactions exceeds the rate of their hydrolysis.

One possible site for the emergence of a kinetic trap would be mineral surfaces where fluctuating water levels cause cycles of wetting and drying that localize concentrated, dry solutes. Fast wet-dry cycles happening in seconds to minutes occur when geysers splash water on surrounding hot rocks, medium duration cycles measured in minutes to hours occur with the rise and fall of pool levels caused by regularly fluctuating hot springs, and slower cycles measured in hours to days would be associated with complete evaporation of smaller pools followed by refilling during precipitation.

Volcanoes emerging through a global ocean would be the original land masses on the Hadean Earth (Van Kranendonk, 2010 Bada and Korenaga, 2018), analogous to Hawaii and Iceland today. If we were to travel 4 billion years back in time to visit volcanic landscapes on the Hadean Earth (Fig. 2), we would see abundant hydrothermal fields with multiple hot spring systems replenished by precipitation evaporating from the surrounding ocean. The distilled fresh water would percolate into hot rocks and then circulate back to the surface as springs and geysers. Hydrothermal fields provide sources of heat and chemical energy to drive polymerization reactions in films of concentrated organic solutes that form on mineral surfaces during repeated cycles of wetting and drying (inset A). Inset B shows an example of such a pool on Mount Mutnovsky, an active volcano in Kamchatka, Russia (Kompanichenko et al., 2015). The recent discovery of a 3.5-billion-year-old hot spring setting on a volcanic plateau that formed in the absence of direct plate tectonic involvement is a good analog for an early Earth volcanic landscape emerging from a global ocean just 500 million years after the approximate time frame we are proposing for life's origins (Pearce et al., 2018 Van Kranendonk et al., 2020).

FIG. 2. An artist's conception of a geyser-driven Hadean volcanic hot spring system in which cycles of evaporation and rehydration can occur. Inset A shows a ring of dried solutes on the mineral surfaces at the edge of a fluctuating pool. Inset B shows a boiling pool associated with a hot spring site on Mount Mutnovsky in Kamchatka, Russia. (Art credit Ryan Norkus Photo credit Tony Hoffman.)

In summary, the primary polymers of life today—proteins and nucleic acids—are synthesized enzymatically by condensation reactions. The chemical energy of ATP is used to remove the equivalent of water molecules from the amine and carboxyl groups on amino acids to form peptide bonds, or the phosphate and ribose hydroxyl groups on nucleotides to form ester bonds. A certain degree of caution should be exercised when envisaging prebiotic versions of condensation reactions driving polymerization processes. For instance, Krishnamurthy (2018) wrote: “Coincidentally, it turns out that this ester-to-amide mechanism is part of extant biology, with more evolved molecules, as exemplified by (a) the peptidyl-transfer reaction within the confines of the ribosome and (b) the thioester-amide exchange equivalent in the nonribosomal peptide synthesis pathway. Whether this is a ‘preservation’ of a primordial reaction mechanism or a case of convergence due to chemical contingency is an open-ended debate.”

As noted earlier, heating dry amino acids at elevated temperatures was among the first and most obvious energy sources to be tested as a way to drive polymerization. Over ensuing years, dry heat was abandoned because the yields were minimal and products were too short to be able to fold into catalytically active structures such as ribozymes. Furthermore, the bonds formed were often not related to the kinds of bonds used in biology and there was a concern that intractable “tars and asphalts” were the most likely products (Benner et al., 2012). Therefore, researchers went on to explore condensing agents, activated mononucleotides, and mineral surfaces as a way to generate longer polymers.

We do not intend to exclude other versions of activated polymerization or possible involvement of condensing agents, but it seems appropriate to focus first on polymerization that does not require activated monomers or condensing agents. Wet-dry cycles in fresh water would be abundant in the prebiotic environment as long as volcanic land masses had emerged from the global ocean, and a surprising amount of chemical energy is introduced by concentrating potential reactants in dilute solutions as they evaporate to form dry films on mineral surfaces (Ross and Deamer, 2016). Furthermore, wet-dry cycles pump mixtures of reactants toward ever increasing complexity as products accumulate in kinetic traps. Such cycles have the additional advantage that if amphiphilic compounds are present in the mixture of reactants, encapsulation of polymers in membranous compartments occurs as a system goes through cycles of hydration and dehydration.

We conclude that hot springs and fluctuating freshwater pools are plausible candidates for prebiotic sites supporting the assembly of protocells, defined as encapsulated systems of random polymers forming in numerous pools over many millions of years. As described in the next section, protocell populations can be exposed to a variety of environmental stresses. Most protocells are likely to be unstable and their components will be dispersed, but a few will have properties that enhance their robustness. These will be selected in a process representing the first step in a pre-Darwinian version of evolution.


8.2: Astrobiology - Biology

Chris Chyba, Cynthia Phillips, Kevin Hand- The project has two components. The first, an overview of the astrobiological potential of various geological features on Europa, is proceeding well — we are continuing the study of various proposed formation mechanisms for different feature types such as ridges, bands, and chaotic terrain.

Project Progress

Chris Chyba, Cynthia Phillips, Kevin Hand- The project has two components. The first, an overview of the astrobiological potential of various geological features on Europa, is proceeding well — we are continuing the study of various proposed formation mechanisms for different feature types such as ridges, bands, and chaotic terrain. The second, a search for current geological activity by comparing Galileo images taken on different orbits, is also in progress. We have completed a first-stage search of the Galileo Europa images to find overlapping images, and are continuing to work on improving our automated search method to make sure that we find all possible comparison images. We have processed a number of comparison pairs, and are currently working on automated techniques for speeding up the comparison process.

Max Bernstein- As part of performing lab measurements to enable the detection of signs of life and the discrimination between these and false biomarkers we have measured IR spectra of Nitrogen Heterocycles, the class of compounds found in meteorites that include nucleobases. We have been concentrating on the kind of conditions found on icy outer Solar System bodies such as Europa.

Rocco Mancinelli and Amos Banin- In a set of soil samples from the Yungay region of the Atacama desert we have conducted detailed analyses of organic and inorganic C and N concentrations. Organic carbon (OC) and organic nitrogen (ON) were low, especially in the soils from the most extreme arid region. OC/ON ratio was in the range typical for biotically synthesized organic matter. Comparison to estimates of C content in the Mars soil analyzed by the Viking Landers show that the Atacama soils, even in the hard-core extreme desert sites, have very low biological activity as terrestrial soils are concerned, but still have higher concentrations of total organic carbon compared to the Mars soils analyzed by the Viking Pyrolytic experiment.

When soil samples collected from the Yungay region of Atacama desert were analyzed for DNA encoding the genes for the nitrite reductase S gene the gene encoding for the key denitrification enzyme, it was not found. These data combinded with last years data where no trace of nitrogen cycling was detected in the field, even under wet conditions suggests that that either there are no organisms capable of N-cyclein in the soil, or the soil contains somethin inhibiting their activity.

Peter Backus, Jill Tarter, Rocco Mancinelli – We held a two and a half day workshop on July 18-20, 2005 on the topic of the Habitability of Planets Orbiting M Stars. Thirty scientists from nineteen institutions in the US and UK participated. Thirteen of the participants were from six other NAI Teams. Results of the workshop are reported in a paper submitted to the journal Astrobiology. The paper was written over many months through the use of email lists and a secure private web site. Another web site http://mstars.seti.org provided information for the general public.

Nathalie Cabrol- Despite harsh weather conditions in the altiplano this year, both planned ascents were completed successfully, one on the Licancabur volcano to continue our work from previous years, and the other one on our new site (Poquentica), another volcano hosting a lake located 800 km north of Licancabur. During our one-month, 800 km, trek through the Bolivian altiplano, the team also sampled about a half-a-dozen new sites (evaporating lakes, salars, and geothermal centers) Achievements include: (1) a new stratigraphical transect in the geological record of Laguna Verde to study the evolution of paleohabitats and life during fast changing climate conditions (2) Biological sampling and water chemistry of the summit and lower lakes (3) Retrieval of data from the meteorological station at the summit of Licancabur which logged for one year (4) Geophysics: Measurements of UVA , UVB , PAR and UVC were performed (5) Sampling of frozen soil (or permafrost) on the shore of the Licancabur and Poquentica lakes and sampling of ice from those lakes which were both frozen to depth this year preventing diving. Bin Chen has analyzed salt samples from the 2005 trip. She has identified organic composition in the Laguna Blanca samples. She is using the database to characterize the concentration and structure stability of biogenic carbonaceous contents, especially biomarkers such as hopane and the derivatives, which likely existed in the prokaryotic and eukaryotic membranes study the chemical structures of the organic species and their interactions with the host environment (as in rock, salt and soil mixtures) to understand the preservation and evolution of the life in local conditions that include extremes of UV radiation, desiccation, cold temperature and salinity. She investigates abiogenic organics and components such as carbonate, oxyanionic mineral groups, sulfides and hydroxides produced from the biological activities. The next step will be to study the chemical stability and relative abundance of the biomarkers in the samples obtained from the geological transects in conjunction with the geochemistry, temperatures, pH (current lakes), salinity, UV radiation level, elevation in the transect and paleoenvironment. The correlation will help us understand how both extant and extinct life adapt to changes.

David Summers & Bishun Khare- A paper is currently under review in the journal Astrobiology. Effort has partially turned to study of the stable isotope fractionation and the effects of water layers on mineral surfaces. (This data could then be combined with future isotopic composition work from the Atacama where nitrates may be of abiotic origin.) This included designing and constructing a new irradiation apparatus (now finished). Work also contributed to the study of the isotope fractionation in next step in the reaction sequence, reduction of nitrite to ammonia FeS + NO 2 at pH

5, shows an average fractionation of +6 per mil FeCl 2 + NO 2 at pH 8.2 shows an average fractionation of -4 per mil). This work will also contributes to experiments to include the action of Fe(II) in the aqueous phase on the fixation processes.

Emma Bakes- Our mapping of the chemical sequences for anions, neutrals and cationic nitrogenated aromatic molecules in Titan’s organic haze layer is well underway, utilizing the participation of quantum chemist Alessandra Ricca. We are mapping the chemical energetics and the plausibility of each suggested reaction pathway for bicyclic nitrogenated aromatics suggestive of purine and pyrimidine bases of RNA and DNA molecules to probe the plausibility of their photochemical formation in an atmsosphere. UV penetration directly affects the survival or destruction of organic molecules and the irradiation of potential life forms and we have completed and published our investigation of how the UV radiation interacts with large molecules, tholins and the gas phase and to what degree it penetrates to the surface of Titan. Our laboratory study of hydrogen molecule synthesis on aromatics and aerosols to seek a physically plausible pathway to the accelerated oxidation of Titan and the early Earth is complete and published.

Friedemann Freund & Lynn Rothschild – The major objective of this task is to study the causes for the slow but inextricable oxidation of the Earth over the first 3 Gyr of its history. Contrary to the widely held belief that planet Earth became oxidized due to the activity of early photosynthetic microorganisms (akin to present-day blue-green algae and cyanobacteria), we have convincingly shown that there is an alternative and entirely abiogenic pathway toward global oxidation: the presence of oxygen anions in the minerals of common igneous rocks that have converted from a valence of 2— to a valence of 1— (peroxy). Upon weathering this peroxy fraction hydrolyzes to hydrogen peroxide, which in turn oxidizes reduced transition metal cations, foremost ferrous iron to ferric iron. This leads to the precipitation of ferric oxides in the ocean and, hence, to the deposition of Banded Iron Formations ( BIF ). After this process has gone on for sufficiently long time, 1-2 billion years, the rocks on the continents will evolve toward andesitic-granitic compositions and free oxygen will begin to be injected into the atmosphere.

Janice Bishop & Lynn Rothschild- This year we completed analyzing the data from our initial lab experiments and summarized our results in a paper that is in press in the International Journal of Astrobiology. This work showed that nanophase iron oxide-bearing minerals can facilitate growth of photosynthetic organisms by providing protection from UV radiation. Based on the spectral properties of iron oxides and the results of experiments with two photosynthetic organisms, we propose a scenario where photosynthesis, and ultimately the oxygenation of the atmosphere, depended on the protection of early microbes by nanophase ferric oxides/oxyhydroxides. Such niches may have also existed on Mars.

We have begun evaluating the OMEGA hyperspectral visible/near-infrared ( VNIR ) spectra of Mars in an effort to characterize deposits of nanophase ferric oxide-bearing minerals that could provide UV protected niches for photosynthetic microbes if they were present on Mars. This part of the project will be expanded this year as the CRISM hyperspectral VNIR images become available. Concurrent with other projects, we are evaluating the spectral properties of Fe-bearing Mars analog sites on earth and analyzing spectra of Mars for Fe oxide-bearing components. We have collected some material containing nanophase ferric oxides/oxyhydroxides from Yellowstone that we have begun analyzing. From the chemical and spectral data this sample appears interesting and we are hoping to perform some in situ field measurements during the next year.

PROJECT INVESTIGATORS:

Rocco Mancinelli
Project Investigator

Sciences

This page is a gateway to the resources I have curated for the various integrated MYP science classes I teach.

Science is the process by which we learn how our world works. We call this process “the scientific method”. It involves asking questions, generating hypotheses (making predictions), designing investigations to test those hypotheses, collecting and analyzing data, and evaluating the results and the procedure to reach conclusions about our hypotheses. The presentation embedded below shows how the scientific method is applied within the context of my MYP science classes.

You’ll find almost all the resources you need for MYP general sciences on their respective pages: astronomy, biology, chemistry, earth science and ecology, and physics. I’ve tried to make navigation through the notes, videos, homework, and summative tasks as easy as possible by extensively hyperlinking within the “official class notes” presentations shared through Google Drive and Google Classroom. If you’re visiting this site from a school other than where I teach, you may not be able to navigate through all those hyperlinks.

Below you’ll find scoring rubrics for all 4 assessment criteria in MYP sciences. The rubrics are intended for MYP years 4 & 5 but may easily be scaled for MYP years 1 to 3.

Criterion A: Knowing and understanding

MYP Criterion A assesses students’ ability to explain scientific concepts, solve problems, and evaluate information.

Criterion B: Inquiring and designing

MYP Criterion B assesses students’ ability to design scientific investigations. It’s about explaining the question, developing testable hypotheses, changing and measuring variables, and designing safe, logical methods using appropriate materials and equipment.

Criterion C: Processing and evaluating

MYP Criterion C assesses students’ ability to evaluate an investigation and reach a conclusion based on its results. It’s about collecting, organizing, and presenting data reliably, interpreting the results, and evaluating the investigation to determine how it could be improved or extended.

Criterion D: Reflecting on the impacts of science

MYP Criterion D assesses students’ ability to examine and evaluate how scientific innovations shape our planet and our society.


2) Planetary Driver of Environmental Change

The Earth has evolved dramatically over time, from a hot, molten ball (magma ocean) immediately following the giant Moon-forming Impact at c. 4.5 Ga, to the cool planet of today with a dozen or so large tectonic plates that are created at mid-ocean ridges and partly recycled back into the mantle across steep subduction zones. My research on early Earth has suggested that this “modern” (i.e. steep) style of subduction commenced at c. 3.1 Ga, due to a crossover point in time when the amount of conductive heat emanating from the mantle first declined to values beneath the capacity of the crust to lose that heat. This allowed the tectonic plates to grow and to cool and thicken away from mid-oceanic ridges, resulting in the onset of steep subduction (through plate sinking).

Ongoing research into the proposed Mesoarchean change in the tectonic style of the planet includes:

  • Analysis of geochemical proxies of subduction through time, specifically high field strength elements in magmatic rocks, and oxygen and Hf isotopes in zircons. Preliminary results show that onset of steep subduction is accompanied by the start of the supercontinent cycle, which evolved and changed over time, peaking at c. 1 Ga and declining in intensity thereafter (Fig. 1).
  • Analysis of a proposed Paleoarchean suture zone in South Africa, where high-P metamorphic mineral assemblages have been used to infer a suture zone. Detailed mapping in 2012 will be combined with geochronology and geochemistry to test this claim. Preliminary results suggest a more complex situation than previously reported.
  • Analysis of oxygen isotopes in zircons from dated samples from Pilbara, Western Australia. Samples were specifically identified to test the subduction-accretion model developed for this area. Preliminary results show evidence for both high and low oxygen isotope values in zircons dated at exactly the age identified independently for subduction and accretion of the West Pilbara Superterrane, and not from zircons of any other age.

Collaborators: Chris Kirkland (Geol. Survey Western Australia) John Cliff (U. Western Australia)

Figure 1: Schematic diagram of Earth evolution through time, showing steps in crustal growth following on from pulses of mantle heat arising from the aftermath of subduction avalanches during supercontinent amalgamation that were accompanied by changes to Earth tessellation (T1-T4).


8.2: Astrobiology - Biology

Abe, Y., Abe-Ouchi, A., Sleep, N. H., & Zahnle, K. J. (2011). Habitable Zone Limits for Dry Planets. Astrobiology, 11(5), 443–460. doi:10.1089/ast.2010.0545

Catling, D. C., & Zahnle, K. J. (2009). The Planetary Air Leak. Scientific American, 300(5), 36–43. doi:10.1038/scientificamerican0509-36

Catling, D. C., Claire, M. W., Zahnle, K. J., Quinn, R. C., Clark, B. C., Hecht, M. H., & Kounaves, S. (2010). Atmospheric origins of perchlorate on Mars and in the Atacama. Journal of Geophysical Research, 115. doi:10.1029/2009je003425

Goldblatt, C., & Zahnle, K. J. (2010). Clouds and the Faint Young Sun Paradox. Climate of the Past Discussions, 6(3), 1163–1207. doi:10.5194/cpd-6-1163-2010

Goldblatt, C., & Zahnle, K. J. (2011). Clouds and the Faint Young Sun Paradox. Clim. Past, 7(1), 203–220. doi:10.5194/cp-7-203-2011

Goldblatt, C., & Zahnle, K. J. (2011). Faint young Sun paradox remains. Nature, 474(7349), E1–E1. doi:10.1038/nature09961

Goldblatt, C., Claire, M. W., Lenton, T. M., Matthews, A. J., Watson, A. J., & Zahnle, K. J. (2009). Nitrogen-enhanced greenhouse warming on early Earth. Nature Geosci, 2(12), 891–896. doi:10.1038/ngeo692

Goldblatt, C., Zahnle, K. J., Sleep, N. H., & Nisbet, E. G. (2009). The Eons of Chaos and Hades. Solid Earth Discuss., 1(1), 47–53. doi:10.5194/sed-1-47-2009

Goldblatt, C., Zahnle, K. J., Sleep, N. H., & Nisbet, E. G. (2010). The Eons of Chaos and Hades. Solid Earth, 1(1), 1–3. doi:10.5194/se-1-1-2010

Konhauser, K. O., Pecoits, E., Lalonde, S. V., Papineau, D., Nisbet, E. G., Barley, M. E., … Kamber, B. S. (2009). Oceanic nickel depletion and a methanogen famine before the Great Oxidation Event. Nature, 458(7239), 750–753. doi:10.1038/nature07858

Marion, G. M., Catling, D. C., Zahnle, K. J., & Claire, M. W. (2010). Modeling aqueous perchlorate chemistries with applications to Mars. Icarus, 207(2), 675–685. doi:10.1016/j.icarus.2009.12.003

Tian, F., Claire, M. W., Haqq-Misra, J. D., Smith, M., Crisp, D. C., Catling, D., … Kasting, J. F. (2010). Photochemical and climate consequences of sulfur outgassing on early Mars. Earth and Planetary Science Letters, 295(3-4), 412–418. doi:10.1016/j.epsl.2010.04.016

Tian, F., Kasting, J. F., & Zahnle, K. (2011). Revisiting HCN formation in Earth’s early atmosphere. Earth and Planetary Science Letters, 308(3-4), 417–423. doi:10.1016/j.epsl.2011.06.011

Zahnle, K. (2008). Atmospheric chemistry: Her dark materials. Nature, 454(7200), 41–42. doi:10.1038/454041a

Zahnle, K., Freedman, R. S., & Catling, D. C. (2011). Is there methane on Mars?. Icarus, 212(2), 493–503. doi:10.1016/j.icarus.2010.11.027

Zahnle, K., Haberle, R. M., Catling, D. C., & Kasting, J. F. (2008). Photochemical instability of the ancient Martian atmosphere. Journal of Geophysical Research, 113(E11), None. doi:10.1029/2008je003160


Life in Extreme Conditions

At a chemical level, life consists of many types of molecules that interact with one another to carry out the processes of life. In addition to water, elemental raw materials, and energy, life also needs an environment in which those complicated molecules are stable (don’t break down before they can do their jobs) and their interactions are possible. Your own biochemistry works properly only within a very narrow range of about 10 °C in body temperature and two-tenths of a unit in blood pH (pH is a numerical measure of acidity, or the amount of free hydrogen ions). Beyond those limits, you are in serious danger.

Life overall must also have limits to the conditions in which it can properly work but, as we will see, they are much broader than human limits. The resources that fuel life are distributed across a very wide range of conditions. For example, there is abundant chemical energy to be had in hot springs that are essentially boiling acid (see [link]). This provides ample incentive for evolution to fill as much of that range with life as is biochemically possible. An organism (usually a microbe) that tolerates or even thrives under conditions that most of the life around us would consider hostile, such as very high or low temperature or acidity, is known as an extremophile (where the suffix -phile means “lover of”). Let’s have a look at some of the conditions that can challenge life and the organisms that have managed to carve out a niche at the far reaches of possibility.

Both high and low temperatures can cause a problem for life. As a large organism, you are able to maintain an almost constant body temperature whether it is colder or warmer in the environment around you. But this is not possible at the tiny size of microorganisms whatever the temperature in the outside world is also the temperature of the microbe, and its biochemistry must be able to function at that temperature. High temperatures are the enemy of complexity—increasing thermal energy tends to break apart big molecules into smaller and smaller bits, and life needs to stabilize the molecules with stronger bonds and special proteins. But this approach has its limits.

Nevertheless, as noted earlier, high-temperature environments like hot springs and hydrothermal vents often offer abundant sources of chemical energy and therefore drive the evolution of organisms that can tolerate high temperatures (see [link]) such an organism is called a thermophile. Currently, the high temperature record holder is a methane-producing microorganism that can grow at 122 °C, where the pressure also is so high that water still does not boil. That’s amazing when you think about it. We cook our food—meaning, we alter the chemistry and structure of its biomolecules—by boiling it at a temperature of 100 °C. In fact, food begins to cook at much lower temperatures than this. And yet, there are organisms whose biochemistry remains intact and operates just fine at temperatures 20 degrees higher.

Figure 5. What appears to be black smoke is actually superheated water filled with minerals of metal sulfide. Hydrothermal vent fluid can represent a rich source of chemical energy, and therefore a driver for the evolution of microorganisms that can tolerate high temperatures. Bacteria feeding on this chemical energy form the base of a food chain that can support thriving communities of animals—in this case, a dense patch of red and white tubeworms growing around the base of the vent. (credit: modification of work by the University of Washington NOAA/OAR/OER)

Cold can also be a problem, in part because it slows down metabolism to very low levels, but also because it can cause physical changes in biomolecules. Cell membranes—the molecular envelopes that surround cells and allow their exchange of chemicals with the world outside—are basically made of fatlike molecules. And just as fat congeals when it cools, membranes crystallize, changing how they function in the exchange of materials in and out of the cell. Some cold-adapted cells (called psychrophiles) have changed the chemical composition of their membranes in order to cope with this problem but again, there are limits. Thus far, the coldest temperature at which any microbe has been shown to reproduce is about –25 ºC.

Conditions that are very acidic or alkaline can also be problematic for life because many of our important molecules, like proteins and DNA, are broken down under such conditions. For example, household drain cleaner, which does its job by breaking down the chemical structure of things like hair clogs, is a very alkaline solution. The most acid-tolerant organisms (acidophiles) are capable of living at pH values near zero—about ten million times more acidic than your blood ([link]). At the other extreme, some alkaliphiles can grow at pH levels of about 13, which is comparable to the pH of household bleach and almost a million times more alkaline than your blood.

Figure 6. With a pH close to 2, Rio Tinto is literally a river of acid. Acid-loving microorganisms (acidophiles) not only thrive in these waters, their metabolic activities help generate the acid in the first place. The rusty red color that gives the river its name comes from high levels of iron dissolved in the waters.

High levels of salts in the environment can also cause a problem for life because the salt blocks some cellular functions. Humans recognized this centuries ago and began to salt-cure food to keep it from spoiling—meaning, to keep it from being colonized by microorganisms. Yet some microbes have evolved to grow in water that is saturated in sodium chloride (table salt)—about ten times as salty as seawater ([link]).

Figure 7. The waters of an evaporative salt works near San Francisco are colored pink by thriving communities of photosynthetic organisms. These waters are about ten times as salty as seawater—enough for sodium chloride to begin to crystallize out—yet some organisms can survive and thrive in these conditions. (credit: modification of work by NASA)

Very high pressures can literally squeeze life’s biomolecules, causing them to adopt more compact forms that do not work very well. But we still find life—not just microbial, but even animal life—at the bottoms of our ocean trenches, where pressures are more than 1000 times atmospheric pressure. Many other adaptions to environmental “extremes” are also known. There is even an organism, Deinococcus radiodurans, that can tolerate ionizing radiation (such as that released by radioactive elements) a thousand times more intense than you would be able to withstand. It is also very good at surviving extreme desiccation (drying out) and a variety of metals that would be toxic to humans.

From many such examples, we can conclude that life is capable of tolerating a wide range of environmental extremes—so much so that we have to work hard to identify places where life can’t exist. A few such places are known—for example, the waters of hydrothermal vents at over 300 °C appear too hot to support any life—and finding these places helps define the possibility for life elsewhere. The study of extremophiles over the last few decades has expanded our sense of the range of conditions life can survive and, in doing so, has made many scientists more optimistic about the possibility that life might exist beyond Earth.


8.2: Astrobiology - Biology

Titan organics comprise a very complex mixture of compounds. Several approaches are being developed that provide targeted detection of specific functional groups, such as nitriles, imines, primary amines, and carbon-carbon multiple bonds.

Project Progress

Titan organics comprise a very complex mixture of compounds. Co-Investigator Jack Beauchamp and Graduate Student Kathleen Upton are developing several approaches that provide targeted detection of specific functional groups, such as nitriles, imines, primary amines, and carbon-carbon multiple bonds. Experiments for the selective and sensitive detection of primary amines through mass spectrometry are currently being conducted due to the biological prevalence of small molecule ( 1

This allows for the selective detection of primary amine functionality in a complex mixture of organic compounds. As a test of this idea, laboratory produced tholins from two different plasma discharge generators (Figure 2) were complexed with 18-Crown-6. These include synthesis as described by Saker et. al. (2003) and the generator most recently developed by Mark Smith and coworkers. 2,3

Each tholin was dissolved in dichloromethane at 2 mg/ml with 2mM 18-Crown-6 ether. Adduct formation with the Saker tholin is shown in Figure 3. The marked peaks in this figure, with M = 18-Crown-6 ether, correspond to two different series (triangles: NH2-(CH2)n-CH2CN, where n=0 is the first in the series, and circles: NH2-(CH2)n-CH(CN)2 ,where n=2 is the first in the series). The results of a similar experiment with the Smith tholin are shown in Figure 4, where several of the crown ether adduct peaks are labeled with an asterisk. Several of these match peaks observed in Figure 3 and others differ by two to six amu. These deviations could indicate the presence of unsaturation (CC or CN multiple bonds) or a different extent of nitrogen incorporation in the Smith tholins.

Complexation with 18-Crown-6 ether leads to the identification of primary amine functionality in both Tholin mixtures. It is particularly noteworthy that the two different preparations yield a very different mixture of primary amines. Beauchamp and Upton are currently trying to understand the origin of these differences in greater detail in addition to starting with fresh preparations of the tholins.

Primary amine functionality can also be selectively detected using an amine reactive reagent with a permanent charge. This can be accomplished with the quaternary ammonium tag , which reacts with primary amines in basic conditions as indicated in Figure 5. The tag is prepared in acetonitrile and is moisture sensitive. 4

They have tested the amine reactive tag illustrated in Figure 5 using a mixture of the neurotransmitters dopamine, serotonin, and norepinephrine, which are all important biological compounds with primary amine functionality. Solutions of 100uM of the neurotransmitter in 0.1M TRIS at a pH of 8.2 with 10ug of the quaternary ammonium tag were allowed to react for 1 hour, after which they were quenched with 0.1% formic acid, and then diluted for analysis. Mass spectrometric analysis using ESI provided excellent yields and greatly enhanced sensitivity for detection of all three neurotransmitters compared to ESI of the underivatized amines.

Unfortunately, due to tholin reactivity with water and acid, the buffer and quench used with the amine reactive tag could not be used to directly derivatize tholin samples. The procedure was modified to use acetonitrile as the solvent. Tholins dissolve well in acetonitrile, as does the amine reactive tag, and tholins are known to be slightly basic due to nitrogen content. 1mg/mL of the Smith tholin and 100uM quaternary ammonium tag were combined in acetonitrle and left at room temperature. Analysis was performed at various points over a two day period, during which no changes indicative of the derivatization were observed in the mass spectrum. Future studies will explore a wider range of reaction conditions to achieve enhanced yields of derivatized products.

Additional experiments in progress include the use of reactive desorption electrospray ionization ( DESI ) 5 for targeted identification of primary amines, using both of the reagents described above. By using this technique, exposure of the tholin to buffers or acids is minimized. The successful 18-Crown-6 adduct formation described earlier is being used as a starting point for reactive DESI , using neurotransmitters as test compounds. Once the ideal reactive DESI conditions are determined, the quaternary ammonium tag methodology will be attempted on neurotransmitters to determine any changes required in the experimental procedure. If successful they will again test the tholin samples to see if primary amines can be selectively detected.

References:
1. Julian R. R. Beauchamp J. L. Int. J. Mass Spectrom. 2001, 210, 613-623.
2. N. Sarker, A. Somogyi, J. I. Lunine, and M. A. Smith, Astrobiology, 2003, 3(4), 719- 726.
3. A. Somogyi, C. Oh, M. A. Smith, J. I. Lunine, J. Am. Soc. Mass Spectrom., Vol. 16, 6, 2005, 850-859.
4. F. Che, L. D. Fricker, J. Mass Spectrom. 2005, 40, 238–249
5. I. Cotte-Rodríguez, Z. Takáts, N. Talaty, H. Chen, R. G. Cooks, Anal. Chem., 2005, 77 (21), 6755–6764

/> Figure 1. 18-Crown-6 ether complexed to protonated butylamine. The complex sequesters the proton at the primary amine site, preventing deprotonation during electrospray ionization. /> Figure 2. Tholin generators used to produce the two samples examined for primary amine content in this study. The Saker generator uses at gas flow system at atmospheric pressure and collects tholins below the discharge, while the Smith generator operates gas flow at low pressure and collects around the discharge

/> Figure 3. ESI/MS spectrum of 18-Crown-6 complexed Saker tholins. The triangles and circles indicated complexed species fitting a particular compound series.

/> Figure 4. ESI/MS spectrum of 18-Crown-6 complexed Smith tholins. The asterisks indicate identified crown ether adducts. /> Figure 5. a) Amine reactive tag for derivatizing primary amines with a permanent charge. b) Derivatization of an arbitrary primary amine RNH2.

PROJECT INVESTIGATORS:

Jesse Beauchamp
Project Investigator


Watch the video: . ASTROBIO - How to look for Biosignatures (August 2022).