Life in the Bathypelagic Zone

Here is a paper I wrote in March of 2018 about the outlandish life of the bathypelagic zone, part of the deep ocean layer known as the midnight zone where pressures are extremely high and no light penetrates. I hope you enjoy learning about it and let me know what you think below and comment in the forum with any questions.


Oceanographers divide the open sea into layers, drawing boundaries according to the distance that light penetrates through the ocean. The surface layer of the ocean is known as the epipelagic zone, the sunlit zone, or the euphotic zone. Photosynthesis is prevalent in this zone to utilize the abundant sunlight. It extends from the surface of the ocean down to 200 meters below. Here, little to no light can filter through; the quality of the lighting is eternal dusk. Levels of light are insufficient to support photosynthesis in this zone, but here a new light source shines, known as bioluminescence. This zone is known as the twilight zone, mesopelagic zone, or disphotic zone. It extends from 200 meters below sea level to 1000 meters below sea level. The next layer receives no sunlight whatsoever; it is called the aphotic zone or the midnight zone. This layer is commonly divided into three sub-layers: the bathypelagic zone, abyssopelagic zone, and hadalpelagic zone. Sometimes the bathypelagic zone by itself is called he aphotic zone or the midnight zone. Since no sunlight passes past 1000 meters below sea level, the next layers must be determined on an alternative basis: The  bathypelagic zone beginning at the continental slope and extending past it, extending from about -1000 meters -4000 meters; Below is the Abyssopelagic zone which is the zone beginning where the continental slope levels off, extending from approximately -4000 meters to -6000 meters; The lowest zone is the hadalpelagic zone which is the volume inside oceanic trenches, extending from around -6000 meters to a maximum depth of -10994 meters (2). (1).

            Since light penetrates to varying depths in different areas according to the transparency of the water, the boundaries determined according to light penetration cannot be absolute or precise. For example, in some tropical waters, light can penetrate as far as 600 meters (3), but in other places . The same degree of uncertainty applies to the aphotic zones as the continental slope is not entirely uniform and oceanic trenches vary in depth (2).

            The particular focus of this paper shall be the bathypelagic zone. It is unique in several ways: there is no sunlight, there is very high pressure (100-400 atm.), it is relatively cold, it has a high mineral and nutrient density, and the conditions are constant, due to lack of wind, sunlight, and because water in the deep sea comes from dense, polar water which sinks to the bottom and slowly flows across the ocean floor and thus the deep sea water is a constant temperature. These extreme conditions have selected for some rather extreme adaptations, the lack of sunlight having the greatest adaptive repercussions; since there is no sunlight, there is no photosynthesis which means that almost no primary production occurs. All of the food in the bathypelagic zone comes in the form of organic particles drifting down from the layers above. There is only enough to support a very low population density; even though the bathypelagic zone accounts for ninety percent of the oceans’ volume,  it has a very low population and biodiversity relative to the layers above. And these things continue to decline as a function of depth. (4).

            What few organisms are supported by this organic snow are not over-abundantly supplied with sustenance; they were forced to develop means of conserving energy and, in a world of dark darkness, of luring the prey to them. Creatures, such as jellyfish and angler-fish of the deep can often be found floating motionless. (2). Due to cold temperatures, they have very low metabolic rates which helps further to conserve energy. Since they don’t move very often, they don’t waste energy in forming a streamlined body; they tend to be bulky and lumpy. Many are merely living lures; traps baited with light. (4).

            The light is produced by a phenomenon called bioluminescence, caused by reaction between a molecule called luciferin and oxygen. Some animals that produce luciferin also produce a catalyst to speed up the reaction called luciferase. An organism can control the intensity and color of the reaction called bioluminescence, as well as when they light up. Some organisms borrow bioluminescence from glowing bacteria; they provide a favorable environment and the bacteria glow for them. (5).

            This is a tool used all throughout the animal kingdom from insects to plankton to deep sea fishes and invertebrate. Even humans bioluminesce, although the intensity is one thousand times fainter than would be visible and does not involve luciferin or serve any purpose (6).. Nor is it limited to the deep sea; the phenomenon can be observed all throughout the water column, only it is very common in the aphotic zone; about ninety percent of deep sea species have the capability to produce bioluminosity. Bioluminescence can serve multiple purposes from mate attraction to luring prey to startling predators. (5).

            Living in an area devoid of visibility, the organisms inhabiting the bathypelagic zone have developed alternative sensory techniques, enhanced old ones, and dropped others. Some organisms, like angler-fish, have long tentacles that act like feline whiskers to increase the distance at which they can detect predators and prey. (7). Another adaptation of the angler-fish is its extreme sexual dimorphism and sexual parasitism. The male is minute in comparison to the female and lacks a fishing rod and bioluminescence. He locates a female mainly utilizing his enlarged nasal orifices, but also perhaps by the female’s bioluminescence once he reaches the appropriate proximity. When he finds her, he bites into her underside and fuses with her body, sharing her blood in exchange for sperm. This is often how bioluminescence is used, to distinguish between the sexes. (8).

            But some organisms lack functional eyes because they serve no purpose in a world of darkness, save for detecting bioluminescence. And if an organism has no eyes, it can’t be lured in the bell of a jellyfish or the maw of an angler-fish. (9).

            This leads to an interesting question: why are organisms attracted to the light in the first place? At night, when humans introduce an artificial light, little zooplankton become illuminated. This makes them a target for small fish that hunt by sight to whom they were invisible prior to illumination. When the little fish begin feeding, they too become illuminated and attract larger predators, and so on. Fishermen take advantage of this phenomenon. (10). A similar chain of events may occur in the bathypelagic zone as well.

            Another important characteristic of the bathypelagic zone is the extreme pressure. This does not have an enormous effect on the creatures because they were born there and spend most of their lives their, so the pressures inside and outside their bodies are equalized leaving no net effect. But, at least one adaptation has arisen due to high pressure and it involves an organ common to many fish species called a swim bladder. It is a gas-filled chamber inside some fish that allows for passive flotation. Regulation of the amount of gas stored can help the fish rise or sink. The swim bladder is absent from the physiology of bathypelagic organisms, or it is filled with fluid, not gas. This is because gases are compressible while fluids are not. This also explains the complete lack of air spaces in deep sea organisms. (11).

            Oxygen is something that might be expected to exist only in very small amounts in the bathypelagic zone; Because no photosynthesis occurs, no oxygen is replenished and it is constantly consumed. But, the cold polar waters are actually saturated with oxygen. (4). However, above the bathypelagic zone exists, from about -300 to -400 meters, a so called oxygen minimum zone. Here, adaptations to this lower oxygen environment may include the utilization of more efficient oxygen processing enzymes (12) and increased surface area. (13).

            Many deep sea organisms at some point travel nearer to the surface, for various reasons. An innumerable quantity of small organisms move up at night and descend to safety during the day, when they would be visible beyond the bathypelagic zone. At night, they like to take advantage of the increased availability of food in shallower, warmer layers. (10). This exposes them to varying pressure and temperature, which alters certain bilayer membranes of functional importance. Adaptations are required to handle this. (14). Some organisms, like the angler-fish, rise near the surface to breed, and require the same environmental versatility to survive, although many of them don’t survive anyway (7).

            Those described above are just a few of the numerous adaptations necessary for the survival of life in the bathypelagic zone.


References

  1. Nelson, Rob. (2018). “Deep Sea Biome.” Untamed Science. http://www.untamedscience.com/biology/biomes/deep-sea-biome/. Date-accessed: 4/4/2018.
  2. Stenstrom, Jonas. (2018). “Pelagic Biome.” Untamed Science. http://www.untamedscience.com/biology/biomes/pelagic-biome/. Date-accessed: 4/4/2018.
  3. The editors of Encyclopaedia Britannica. (2015). “Bathyal Zone.” Encylopaedia Britannica. https://www.britannica.com/science/bathyal-zone. Date-accessed: 4/4/2018.
  4. “Ocean Zones.” (n.d.). Ocean Explorer. http://oceanexplorer.noaa.gov/edu/curriculum/section5.pdf. Date-accessed: 4/4/2018.
  5. The Ocean Portal Team. (2017). “Bioluminescence.” Smithsonian National Mutseum of Natural History. http://ocean.si.edu/bioluminescence. Date-accessed: 4/4/2018.
  6. Kobayashi, Masaki et. al. (2009). “Imaging of Ultraweak Spontaneous Photon Emission from Human Body Displaying Diurnal Rhythm.” PlOS ONE. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006256. Date-accessed: 4/4/2018.
  7. Langin, Katie. (2018). “Exclusive: ‘I’ve never seen anything like it.’ Video of mating deep-sea anglerfish stuns biologists.” Science. http://www.sciencemag.org/news/2018/03/exclusive-i-ve-never-seen-anything-it-video-mating-deep-sea-anglerfish-stuns-biologists.
  8. Pietsch, Theodore W. (2005). “Dimorphism, parasitism, and sex revisited: modes of reproduction among deep-sea ceratioid anglerfishes (Teleostei: Lophiiformes).” Ichthyological Research. file:///C:/Users/Abram/Downloads/20-Dimorphism.pdf. Date-access: 4/42018.
  9. NOAA Ocean Explorer Webmaster. (2013). “The Bulk of the Ocean is Deep Sea Habitat with no Light.” Ocean Explorer. http://oceanexplorer.noaa.gov/facts/light-distributed.html. Date-accessed: 4/4/2018.
  10. Carilli, Jessica. (2016). “Why Lights Attract Ocean Life at Night.” Scitable by nature education. https://www.nature.com/scitable/blog/saltwater-science/why_lights_attract_ocean_life. Date-accessed: 4/4/2018.
  11. “If a giant squid has a soft body, how can it survive in such deep water pressure, when even the best submarines can’t got as deep that deep?” (2004). USCB ScienceLine. http://scienceline.ucsb.edu/getkey.php?key=685. Date-accessed: 4/4/2018.
  12. Han, Huazhi et. al. (2011). “Adaptation of aerobic respiration to low O2 environments.” PNAS. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161551/. Date-accessed: 4/4/2018.
  13. Levin, Lisa A. (2002). “Deep Ocean Life Where Oxygen is Scarce.” American Scientist. http://levin.ucsd.edu/research/Am%20Sci%202002.pdf.
  14. Cossins, A. R. Macdonald, A. G. (1989). “The adaptation of biological membranes to temperature and pressure: fish from the deep and cold.

Are Crystals Alive?

Here is a paper I wrote in October of 2018 examining the question: “Are crystals living things?” This seemingly simple question bifurcates into an inconclusive study of the many definitions of life and an intriguing comparison of crystals to living things based off of these definitions. What do you think; are crystals alive? Comment down below or in the forum, and feel free to be as intuitive and/or scientific as you want!


Abram Leyzorek

15 October 2017

Analysis of the Shared Characteristics Between Crystals and Living Things and Study on Definitions of life

Definitions for “life”

Life is defined differently in dictionaries (1) (7), by different scientific fields addressing the subject (2) (3), and by individual scientists studying those fields (9) (10). Entities such as viruses and self replicating proteins fuel a debate concerning whether or not they should be classified as alive or dead. In addition they also provide gray areas, blurring many definitions of life and spawning new ones (2). One conventional and well accepted definition for life requires:

  1. Cellular composition.
  2. Capacity for metabolism.
  3. Capacity for growth and development.
  4. Capacity to reproduce.
  5. Capacity to pass on individual characteristics to offspring through DNA: Heredity.
  6. Tends toward homeostasis.
  7. Capacity to respond to stimuli.
  8. The capacity for adaptation through evolution.

A definition similar to this can be found in many textbooks on biology (4). It will be referred to in this paper as the textbook definition. The aforementioned dictionary definitions (1) (7) will not feature in this paper, as their content and more is provided by the textbook definition and, therefore, reviewing them seems irrelevant to the following purpose: This paper explores whether or not crystals can be considered living under the above definition and others, first by scrutinizing crystals under the textbook definition criteria and then under other definitions. This paper then speculates about the definitions of life and why they are important or not.

Do crystals have cells?

A crystal is defined as a grouping of atoms or molecules arranged in an ordered, repeating pattern. The specific patterns are known as crystal lattices and are defined by the geometric structure of their unit cell. A unit cell is the basic structure that is repeated to form a crystal lattice (5). All crystals must maintain a charge balance; an equal amount of positive and negative charge. Crystals whose external boundaries are described by well developed faces are known as euhedral. However, not all crystal possess this feature. Additionally, crystals may not maintain their structures under changing conditions such as increased or decreased temperature, pressure, etc, but rather will assume different forms, called polymorphs, under certain conditions, while maintaining original elemental composition (6). These characteristics of crystals may demonstrate that they can be defined as living.

1. The structural, functional and biological unit of all organisms.

2. An autonomous self-replicating unit that may exist as functional independent unit of life (as in the case of unicelluar organisms), or as sub-unit in a multicelluar organism (such as in plants and animals) that is specialized into carrying out particular functions towards the cause of the organisms as a whole.

3. A membrane bound structure containing biomolecules such as nucleic acids and polysaccharides.

Definition number one is the most general and will be considered first. Different domains of living creatures have cells organized different ways, i.e. prokaryotic, eukaryotic, and archaeic (11), and have different although similar functions and composition. The same is true even at the taxonomic level of kingdom, e.g. plant cells vs. animal cells (12). If science were to accept another general classification of living creatures, e.g. crystals, it might find that that kingdom also differed in its cellular structure.

The definition of a crystal, as provided above, includes that crystals are made up of cells. They are called unit cells and are the basic building blocks of crystals. They make up the crystal lattice, the structural component. They control the functional aspects of crystals by having interstices, vacancies, and other “defects” that shape the physical properties of crystals and control the movement of atoms in and on crystals. They do this by a process where atoms move from areas of higher atomic concentration to lower atomic concentration called solid state diffusion (13). This process also controls the uptake of elements and compounds into solid solution (15). Since crystals are composed of one of the seven types of unit cells (16), their functioning on a “cellular” level is determined by their unit cells. Unit cells are the basic unit of crystalline solids, so, granted crystals are alive, unit cells are biological units. Thus the first definition of a cell can be satisfied.

In the second definition, the word “autonomous” is used. It is, of course, defined in the biological sense of the word. In that sense, it simply means having an independent existence and governing laws (17). Certainly a unit cell satisfies this definition.

The second term in definition number two is “self-sustaining.” Now, as an article by Astrobiology Magazine entitled, “Defining Life”, (18) points out, no organism can survive by itself; all life needs access to free energy and materials. So, it seems that “self sustaining” must mean that the organism can gather the energy needed to survive from some necessary materials, if they are available. Could a human, for example, self-sustain itself in space? Of course not; the proper environment in which a human could survive is not provided in space. One would not stretch logic to say that every organism needs a specialized environment to survive with proper temperature, weather conditions, food supply, etc. For a crystal to form, it needs its constituent elements close at hand. One example of a favorable environment for a crystal is a solution supersaturated with its constituent element(s). In this environment, crystals will form via nucleation (19) and will impose their structural template onto free atoms of their constituent element and organize them into more crystals (20).

The stipulations of the second definition have all been covered save one: the requirement for cells to be “specialized.” The biological definition for this term is to be set apart for a particular function (21). There are several types of defects in crystals that can enhance certain ones of their functions (13). These “defective” unit cells are set apart from the others and perform a different function; arguably, they are specialized.

At the tertiary definition of a biological cell comes a screen that some crystals cannot pass through. That is the requirement for cells to contain biomolecules and to be wrapped in a membrane. A “biomolecule” is simply an organic (containing carbon) molecule produced by a living creature (22). Obviously this criterion is impossible for a crystal not containing carbon, i.e. inorganic, to meet. But many crystals are organic (23). And therefore all of those, except those solely of carbon, contain biomolecules, if it is granted that crystals are alive. Yet if one grants that crystals are alive, obviously the current scientific conclusion that all life as we know it is carbon-based (25), dissolves. Furthermore, the article referenced (25) goes on to accept the possibility that, although the carbon atom seems the most suited for life, life forms could be based around other elements such silicon or germanium. Why, then, should the definition of life be shackled to carbon?

The next hurdle, however, seems too lofty to leap: the unit cells of these crystals are not surrounded by any membranes. This shortcoming is perhaps excusable because nothing is surrounded by a physical, as opposed to an electrical, membrane at the molecular and atomic levels. Organic cells are enormous in comparison to unit cells. For example, a red blood cell is eight micrometers across (39) and a unit cell of Nickel is about 350 picometers across (40): the red blood cell is about a little under 5000 times larger than a unit cell of nickel, length wise, and even more astronomically tiny by volume. Since membranes, in general, are made up of molecules, how could something the size of a molecule, such as a unit cell, have a membrane? Additionally, if one could grant, for the purposes of argument, that crystals are alive, they would be an entirely different sort of living creature from those biologists are accustomed to. There is no reason to assume that such an entirely different form of life would necessarily depend upon membranes.

In sum, it has been determined that crystals are composed of cells, granted a general definition of the term.

Do crystals have metabolism?

            Crystals are now going to tested by the second criterion: the capacity for metabolism. As above, the discussion will begin with a definition; the Cambridge Dictionary (24) defines metabolism as “the chemical and physical processes by which a living thing uses food for energy and growth.” The previous section on the cellular composition of crystals explained that crystals do grow. Their “food” is comprised of the elements that constitute them. These elements align themselves into the crystal lattice, so the crystal is using their energy to grow. This growth will be covered in further detail in the following section. Crystals, then have a capacity for metabolism.

Can crystals grow and develop?

            Closely related to metabolism is the capacity for growth and development, the third criterion. Anabolism is the specific term for growth (26).  Crystals can grow out of supersaturated solution (20), vapor, and solid mineral deposits (27). The process by which crystals grow has been explained above. As crystals grow, they attain a greater size and their individual compliment of defects and impurities. This is the unequivocal growth and development of a crystal.

Can crystals reproduce?

            The next criterion and perhaps the most important is the capacity to reproduce. Reproduction simply means “the production of offspring by organized bodies” (28). In addition to being able to form naturally by nucleation (19), crystals can form much more quickly by a process called seeding. Seeding involves placing microscopic crystals into a favorable environment for crystallization to accelerate the growth of crystals (29). This is the way in which a crystal reproduces: a piece of a crystal is chipped off the parent and the chip, or seed, carries the information to form new crystals in its unit cells. When it finds a favorable environment abundant with “food”, new crystals, or offspring, are made. This process is asexual, because the offspring are clones of the parent (28).

            The offspring described in the previous paragraph cannot rightly be offspring if they don’t share characteristics of their parent through heredity, the capacity for which is the fifth criterion. The offspring of asexual reproducers are clones of the parent and have essentially identical features. This is, of course, untrue if the offspring grow up in a much different environment than the parent did, and develop differently. The way in which crystals pass their traits to offspring is through a universal code that defines the structure of each crystal. The crystal structure acts as the blue print, like DNA for a new organic organism, a new crystal.

Unfortunately, this process cannot meet the definition of heredity which is complex and restrictive. Heredity is defined as the natural process by which parents pass genes to offspring (30). Genes are chemical patterns on chromosomes that shape the development of offspring (31). Crystals cannot be said to have this characteristic. However, the purpose of genes is to shape the offspring to be like the parent. Although the process described above cannot be called heredity in the strict sense, it clearly accomplishes the same thing. If crystals are a new life form, they have simply found a different way of passing on their characteristics to offspring.

Do crystals maintain homeostasis?

            Every living organism needs a specific needs a specific set of conditions to survive; temperature, pH, salinity, etc must all be within a certain range for a given creature to live. Internal conditions are even more important than external ones. Homeostasis is the process that an organism uses to maintain the same internal conditions despite external changes (32). These processes only work within limits, of course: if a human were plunged into the Sun, homeostasis would not help it.

Crystals have something which could be thought of as homeostasis: an equilibrium crystal shape (ECS). ECS is the shape of a crystal at which it has minimum surface free energy, given a constant volume (33). This is the shape at which a crystal is “happiest.” To demonstrate,  imagine a crystal at its ECS. If one filed off a corner, after a while the crystal would reorganize itself back into the ECS (34). A NASA article acknowledges that crystals can maintain equilibrium (2). These data affirm that crystals perform homeostasis.

Can crystals respond to stimuli?

            Probably the easiest criterion to satisfy, the capacity of life to respond to stimulation, is considered next. Several pieces of information already provided exemplify response to stimulation. The homeostasis of crystals described above constitutes a response to stimulation. Also, liquid crystals can respond to light, heat, and mechanical stress (35). Certain photonic crystals are responsive, as well (36). The aforementioned NASA article (2) also states that crystals can “move” in response to stimuli. Surely this point is affirmed.

Can crystals evolve?

            The final criterion: The capacity to evolve through adaptation. This is, arguably, the characteristic furthest from relevance to the discussion, because it is unclear and hitherto unproven whether bodies normally considered alive today do indeed evolve (3). However, according to the article referenced, there is an enormous collection of data that perhaps the majority of scientists think validates the evolutionary process, as described by a website entitled “Understanding Evolution” (14). Seemingly, though, another individual could consider the facts and develop a different interpretation, or theory. Furthermore, Steven Benner in an article entitled, “Defining Life” (8) describes how fictional characters, such as androids, that humans today would be forced to consider alive, would not be subject to Darwinian evolution.

Benner posited that humans would acknowledge the living status of such hypothetical creatures, based on our “values” concerning what is alive. For example, if an unconventional being such as a cloud were to float one day into a person’s path, and verbally refused to move, displaying sentience, could that person consider the cloud dead? The capacity for evolution does not seem to be one of the characteristics of life familiar to us that people value, such as response to stimulation, reproduction, etc. The reason for this may simply be that evolution is  not observable. It is inconsequential to transient individuals. In fact, most creatures, including some humans, normally only think about reproduction, growth and development, and response to stimuli. The other, less visible ones, such as heredity and cellular composition, are at least observable within a lifetime.

If this weren’t enough, some definitions for life completely exclude the capacity for evolution as a criterion (37). So even if crystals do fail this test, that will not negatively impact their prospects of meeting the criteria of accepted definitions. But, for the purposes of argument, let us assume universal evolution to be true; Do crystals undergo this process?

To answer this question the Cairns-Smith theory will be considered. It stipulates that the first organic life arose from clay crystals that stored and replicated a genome simple enough to have spontaneously arisen (38). The article referenced explores how hypothetical clay crystals might have evolved due to resource scarcity. An ability of crystals to run programs that predict the most abundant resource available in their environment, which would allow crystals to grow faster, might have developed. The research in the paper concludes that it is conceivable for real crystals to have evolved into responsive, sensitive, creatures. This is no real evidence, but a possible proof of concept.

Although this paper has failed to demonstrate that crystals evolve, and therefore failed to completely satisfy the definition it set out to, other definitions that, perhaps rightly, exclude the evolution criterion, have been satisfied.

Cybernetic definition of life

            The textbook definition scrutinized above is not the only proposed definition of life. A cybernetic definition defines life as a network of regulatory mechanisms subordinated to a potential for expansion (9). Crystals certainly possess a network of regulatory mechanisms, and harness these to expand. Unless that extrapolation harbors a misinterpretation of the cybernetic definition, crystals do satisfy it and contain “the essence of life” which, as the authors of the referenced article suggest, the cybernetic definition embodies.

Value based definitions of life

            A previously referenced article mentioned that one way of determining whether or not something is alive based on our values (14). People in general seem to value life for its responsiveness, its growth and development, and its reproduction. The one of those features that isn’t obvious in crystals is responsiveness, although they do possess this characteristic, as argued above. More importantly, though, they don’t respond in ways that humans can naturally interpret. This lack of intuitive understanding is probably a reason why people generally do not consider crystals alive.

At first glance, a coral reef may look inanimate, but with a scientific background one knows that they are alive. Science has provided this viewpoint. It is hard for the unaided human to observe the living properties, such as growth, of a coral reef. Crystals naturally grow very slowly as well. This slow growth of crystals is perhaps another reason that crystals aren’t considered living.

In contrast, a tree seems to grow just quickly enough for people to observe considerable growth in a lifetime. In addition, trees are far more abundant and ubiquitous. Crystals, however, are less obvious and generally paid less attention. Seemingly, for a long time humans in general failed to observe these important characteristics of crystals as a consequence of there inattentiveness and short life spans. Yet, when science began to study crystals, it was too late: people had already developed a system of somewhat arbitrary values that determined in their minds what was alive and what was not. 

In consequence, humans have thought nothing of harvesting and exploiting crystals for their beauty and their great utility in electronics, building, etc. However, this would not be surprising even if humans did consider crystals to be alive. Consider what they have done to creatures in the modern farming and livestock industries. Obviously nothing can be done for the unfortunate case of crystals while those atrocities on more obviously living things (including humans) continue. Of course all living creatures depend on each other for survival, but humans have learned to satisfy their greed for wealth and convenience at an unprecedented level, to the detriment of all life, crystals (perhaps) included.


References

  1.  “Life.” Merriam-Webster, Merriam-Webster, www.merriam-webster.com/dictionary/life. Accessed 20 Jan. 2020.
  2. Dunbar, Brian. “Life’s Working Definition: Does It Work?” NASA, NASA, www.nasa.gov/vision/universe/starsgalaxies/life’s_working_definition.html. Accessed 20 Jan. 2020.
  3. Benner, Steven A. “Defining Life.” Astrobiology, Mary Ann Liebert, Inc., Dec. 2010, www.ncbi.nlm.nih.gov/pmc/articles/PMC3005285/. Accessed 20 Jan. 2020.
  4. “Reading Essentials for Biology: an Interactive Student Textbook.” Reading Essentials for Biology: an Interactive Student Textbook, by Glencoe, Glencoe Mcgraw-Hill, 2011.
  5. “What Is a Crystal? – International Gem Society – IGS.” International Gem Society, http://www.gemsociety.org/article/crystal/. Accessed 20 Jan. 2020.
  6. “What Is a Crystal?” What Is a Crystal?, University of California, Berkely, nature.berkeley.edu/classes/eps2/wisc/Lect4.html.
  7.  “Life.” Dictionary.com, Dictionary.com, www.dictionary.com/browse/life. Accessed 20 Jan. 2020.
  8. Steiger, Frank. Is Evolution Only a Theory? Tufts University, 1996, chem.tufts.edu/science/FrankSteiger/theory.htm.
  9. Korzeniewski, Bernard. “Cybernetic Formulation of the Definition of Life.” Journal of Theoretical Biology, Academic Press, 25 May 2002, www.sciencedirect.com/science/article/pii/S0022519301922623.
  10. Chaltin, G. J. “To a Mathematical Definition of ‘Life’.” ACM SIGACT News, dl.acm.org/citation.cfm?id=1247052.
  11. Ruiz-Mirazo, Kepa, et al. “A Universal Definition of Life: Autonomy and Open-Ended Evolution.” SpringerLink, Kluwer Academic Publishers, June 2014, link.springer.com/article/10.1023/B:ORIG.0000016440.53346.dc.
  12. “17 Differences Between Plant and Animal Cells: Plant Cell vs Animal Cell.” Bio Explorer, 22 June 2019, http://www.bioexplorer.net/difference-between-plant-and-animal-cells.html/. Accessed 20 Jan. 2020.
  13. “Solid State Diffusion.” University of Oslo, 2005, https://www.uio.no/studier/emner/matnat/kjemi/KJM5120/v05/undervisningsmateriale/KJM5120-Ch5-Diffusion.pdf.
  14. Welcome to Evolution 101!, evolution.berkeley.edu/evolibrary/article/evo_01. Accessed 20 Jan. 2020.
  15. Stipp, Susan L., et al. “Cd2+ Uptake by Calcite, Solid-State Diffusion, and the Formation of Solid-Solution: Interface Processes Observed with near-Surface Sensitive Techniques (XPS, LEED, and AES).” Geochimica Et Cosmochimica Acta, Pergamon, 3 Apr. 2003, http://www.sciencedirect.com/science/article/pii/0016703792903219.
  16.  “Unit Cells.” Bodner Research Web, chemed.chem.purdue.edu/genchem//topicreview/bp/ch13/unitcell.php.
  17. “Autonomous.” Biology Online, 12 May 2014, http://www.biology-online.org/dictionary/Autonomous.
  18. “Defining Life.” Astrobiology Magazine, 19 June 2002, http://www.astrobio.net/origin-and-evolution-of-life/defining-life/. Accessed 20 Jan. 2020.
  19. Deniz Erdemir, Alfred Y. Lee, and Allan S. Myerson, “Nucleation of Crystals from Solution: Classical and Two-Step Models.” Accounts of Chemical Research 2009 42 (5), 621-629. DOI: 10.1021/ar800217x
  20. Seely, Oliver. “Crystallization of Sodium Acetate from a Supersaturated Solution.” Crystallization from a Supersaturated Solution, www2.csudh.edu/oliver/demos/supersat/supersat.htm.
  21. “Specialization.” Biology Online, 12 May 2014, http://www.biology-online.org/dictionary/Specialization. Accessed 20 Jan. 2020.
  22.  “Biomolecule.” Biology Online, 12 May 2014, http://www.biology-online.org/dictionary/Biomolecule. Accessed 20 Jan. 2020.
  23. Schnieders, Michael J, et al. “The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.” Journal of Chemical Theory and Computation, U.S. National Library of Medicine, 8 May 2012, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348590/.
  24. “METABOLISM: Meaning in the Cambridge English Dictionary.” Cambridge Dictionary, dictionary.cambridge.org/dictionary/english/metabolism. Accessed 21 Jan. 2020.
  25. Cosmic Evolution – Future, http://www.cfa.harvard.edu/~ejchaisson/cosmic_evolution/docs/fr_1/fr_1_future5.html. Accessed 21 Jan. 2020.
  26. Customers. “Anabolism.” Biology, 12 May 2014, http://www.biology-online.org/dictionary/Anabolism. Accessed 21 Jan. 2020.
  27. Minerals, Rocks & Rock Forming Processes, https://geol105.sitehost.iu.edu/1425chap5.htm. Accessed 25 Jan 2020.
  28. Customers. “Reproduction.” Biology, 12 May 2014, http://www.biology-online.org/dictionary/Reproduction. Accessed 21 Jan. 2020.
  29. Bergfors, Terese. “Seeds to Crystals.” Journal of Structural Biology, Academic Press, 19 Apr. 2003, http://www.sciencedirect.com/science/article/pii/S104784770300039X.
  30. “HEREDITY: Definition in the Cambridge English Dictionary.” HEREDITY | Definition in the Cambridge English Dictionary, dictionary.cambridge.org/us/dictionary/english/heredity.
  31. “GENE: Definition in the Cambridge English Dictionary.” GENE | Definition in the Cambridge English Dictionary, dictionary.cambridge.org/us/dictionary/english/gene.
  32. “HOMEOSTASIS: Definition in the Cambridge English Dictionary.” HOMEOSTASIS | Definition in the Cambridge English Dictionary, dictionary.cambridge.org/us/dictionary/english/homeostasis. Accessed 21 Jan. 2020.
  33. Kovalenko, O., et al. “The Equilibrium Crystal Shape of Iron.” Scripta Materialia, Pergamon, 18 June 2016, http://www.sciencedirect.com/science/article/pii/S1359646216302494.
  34. Equilibrium Crystal Shapes, http://www.lassp.cornell.edu/sethna/CrystalShapes/Equilibrium_Crystal_Shapes.html. Accessed 21 Jan. 2020.
  35. Akamatsu, N, et al. “Thermo-, Photo-, and Mechano-Responsive Liquid Crystal Networks Enable Tunable Photonic Crystals.” Soft Matter, U.S. National Library of Medicine, 25 Oct. 2017, http://www.ncbi.nlm.nih.gov/pubmed/28902226.
  36. Iqbal, et al. “Photo-Responsive Shape-Memory and Shape-Changing Liquid-Crystal Polymer Networks.” MDPI, Multidisciplinary Digital Publishing Institute, 2 Jan. 2013, http://www.mdpi.com/1996-1944/6/1/116. Accessed 21 Jan. 2020.
  37. Wilkin, Douglas, and Niamh Gray-Wilson. “Characteristics of Life.” CK, CK-12 Foundation, 20 Nov. 2019, http://www.ck12.org/c/biology/characteristics-of-life/lesson/Characteristics-of-Life-Advanced-BIO-ADV/. Accessed 21 Jan. 2020.
  38. Cell Size and Scale, learn.genetics.utah.edu/content/cells/scale/. Accessed 21 Jan. 2020.
  39. Schulman, Rebecca, and Erik Winfree. “How Crystals That Change and Respond to the Environment Evolve.” Metabolism.dvi, California Institute of Technology, www.dna.caltech.edu/Papers/metabolism_preprint.pdf.
  40. Face-Centered Cubic Problems, http://www.chemteam.info/Liquids&Solids/WS-fcc-AP.html. Accessed 21 Jan. 2020.

A Short Exposition of Photosynthesis

Here is a short research paper on photosynthesis, that most wonderful and complex phenomenon that makes life possible. It deserves much deeper treatment that a short, high-school level report, but I hope this will provide a decent starting point on your learning journey. Don’t forget to ask your questions in the forum!


Photosynthesis is the process by which energy from the sun is used to chemically combine carbon dioxide (CO2) with water (H2O) to make oxygen and glucose. Green plants, i.e. plants with chlorophyll, and some other organisms utilize this chemical reaction to make food. Plants are primary producers occupying the lowest trophic level. They support all higher trophic levels and thus their level has the highest biomass. Without photosynthesis, most life on Earth would not exist. (1).

            The majority of photosynthesis in plants takes place in the middle layer of the leaves, or the mesophyll. The cells in the mesophyll are equipped with organelles called chloroplasts, specifically designed for carrying out photosynthesis. Inside the chloroplasts are what resemble stacks of coins. Each coin is called a thylakoid and has a green pigment called chlorophyll in its membrane. The entire stack is a called a granum. The grana are occupy a fluid-filled space called the stroma. (1).

            Photosynthesis is actually a complex series of chemical reactions, some being light-dependent and others being light-independent. The light-dependent reactions take place in the thylakoid membranes where the chlorophyll absorbs light which is converted to adenosine triphosphate (ATP), an energy carrying molecule, and NADPH, an electron carrying molecule. It is here that the oxygen we breathe is created from water as a byproduct and diffuses out through the stomata, tiny pores in the surface layer of leaves letting oxygen diffuse out and carbon dioxide diffuse in. (1).

            Then begin the light-independent reactions that are collectively known as the Calvin cycle. They occur in the stroma and use the ATP and NADPH to fix carbon for use in constructing cells and form three-carbon sugars, glyceraldehyde-3-phosphate, or G3P, molecules,  that link up to make glucose. (1).

            In summary, the heat energy from sunlight ends up stored as chemical energy in the bonds of the sugar molecules that can be metabolized by plants and other organisms. (1). The reaction absorbs heat so it can be described as endothermic. (2).

References


  1. “Intro to Photosynthesis.” (2018). Khan Academy. https://www.khanacademy.org/science/biology/photosynthesis-in-plants/modal/a/intro-to-photosynthesis. Date-accessed: 5/14/2018.

2. Helmenstine, Anne Marie. (2018). “Endothermic Reaction Examples.” ThoughtCo. https://www.thoughtco.com/endothermic-reaction-examples-608179