About life: what does it take to be an organism?
Table of contents
Homeostasis and metabolism
Defense: self-preservation or disintegration
Rise of the colonies
Giving back what you’ve taken: death
If you've stumbled upon this, you might want to look at the previous parts before this. I've not continued with this for a long period for a variety of reasons, but I’m feeling the itch to start this up again and seeing it through like how it was originally intended to. Certain topics I was originally going to touch might've changed, or completely scrapped, while others are added. I can't say for sure, because I can't look back to what I was originally planning to do with this series as my laptop was stolen where I kept the drafts for this project.
Anyway, let's delve a little bit deeper into what life is, what needs to be done to maintain it, grow, pass on a heritage and ultimately perish and give back to what sculpted it from the mud it once came.
I'll lay down some foundation and hopefully neat things about single celled organisms and multicellular organisms. Sometimes I might go on a rant, speculation or even nonsense, but the goal will generally still be: food for thought, a few "wow's and cool's" and definitely easy-to-digest and engaging reading. Let's go!
In the previous entry we've looked at the basic building blocks. Now let's put these things together in a soup pot and… voila, we should have life, shouldn't we? Everything is present for little things to be swimming around in your broth, looking for things to consume. There are many reasons life doesn't just form spontaneously + Show Spoiler +
. One very good reason is that these basic building blocks are in a high order of compartmentalization which they just won’t naturally do; another one being molecular combinations need very specific circumstances or enzymes - which are biocatalyst - to occur, which will make these molecular combinations; a last example might be that there needs to be a way to extract (chemical) energy from the environment. Let’s go a little more into detail about the last one so we can figure out how life manages to do this.
cough, God, cough
Homeostasis and metabolism
I'll start off with the last one, extracting energy. This is, for me, one of the fundamental principles and insights that I've stumbled across when thinking about life. Here, we have a higher order structure, next to non-life, which can maintain a highly flexible form in time, by interacting with the non-living and living surroundings. Organic molecules form spontaneously: amino acids, nucleotides, small sugars. The hydrothermal vents, the initial atmospheric conditions and lightning strikes are all players in this scheme of abundancy. How exactly we come from organic compounds to what is able to be observed on Earth today will sadly stay nothing but speculation for now, though. But, for the early life form we can agree we have organic compounds, and lots of them.
For a unicellular organism to survive (let's start with the indefinite lifespan, in an abundance of useable molecules), it needs to consider a few things: finding access to compounds it can use to extract energy from, getting away from compounds that are harmful to it, dumping its waste where the energy has been extracted from. Failing each of these things will make sure it'll perish and making sure that doesn't happen is basically what we call homeostasis, of which metabolism is a subset of (but I kind of see them as equal).
Now, let's get ahead of ourselves for a little bit here. Why would an organism, a proto-lifeform, have the need to do something extra, next to this homeostasis, for instance grow or reproduce? I won’t delve into that in this paragraph yet, but it might be that the organic molecules that are incorporated are inherently self-replicating. In other words: once it started to self-assemble, there was no stopping it. Perhaps what we've built around it is a way to contain it, moving to higher order structures (human, elephants, wales, ...) that reproduce much slower than the average E. coli bacteria (every ~20 minutes in optimal conditions).
Perhaps in the end game of the universe the only things that will be left are DNA and black holes.. Perhaps DNA is the anti-entropic measure our universe has undertaken, trying to sequester mass as a desperate attempt not to succumb to its fate. Whatever the reason for this reproduction phenomenon, it's bizarre to say the least.
So, there's homeostasis, of which metabolism lays at its core. Turning simple molecules into complex ones, picking up highly energetic compounds from the environment to extract energy from them (or store it), dumping the used-up molecules back into the environment. The nice thing about dumping your waste is that something will inevitably thrive off it. Usually though, if something novel is produced as a waste product, like molecular oxygen, it can cause an extinction event to happen and it’s possible this is what we're doing with the current rate of plastic production as well.
But ultimately things arise (or are already there) that can benefit from your waste. It's what we could call the Circle Of Life I suppose. When things produce waste (or die) the micro-organisms will deconstruct the complex materials into its most basic forms, only to be re-utilized and be pumped back into the higher order structures. While saying this, we do have to credit our - for now - perpetuum mobile, Sol, which has provided all the extra energy most of the life forms are utilizing today (next to the stockpile we have on Terra). If it wasn't for the light (and heat, but I think light is slightly more important), we wouldn't have Life in its current form. There are highly complex organized molecular structures that use the light to guide an electron to fuel a proton gradient that ultimately is able to sequester chemical energy. This chemical energy can then be used to sequester carbon, and this is what plants, or phototrophic life in general does. There's also life that doesn't use this light and was probably there before phototrophic organisms were formed and they are called chemotrophs when they use organic compounds and chemolithotrophs when they use inorganic compounds -some even use ferric iron as an electron donor source, like Geothrix-; they use compounds to take the electron to fuel a proton gradient to ultimately sequester chemical energy. This seems to be the central theme within all life: being able to sequester chemical energy (in the form of ATP). The electron guiding system is more commonly called the electron chain and the ATP production through the proton gradient is called oxidative phosphorylation. Much more can be said about the fundamental biochemical principles that enable life a central metabolism, but I'll leave with this central theme to maybe expand on it in the future.
One last thing about this electron chain thing. This system isn't foolproof. Sometimes the electrons escape the chain and they hit up oxygen, creating superoxide. This is an inherent flaw in the most fundamental part of life, which possibly causes DNA damage and oxidation of organic compounds, which might compromise their functionality. It might be that this causes senescence (the phenomenon of ageing) or even cancer in some cases. In other words, growth and reproduction might not be so silly when working with an inherent design flaw. If only we've found a way to live without metabolizing! As you can see, it’s quite complex, with the self-replication and the inherently flawed system. And this is just this tip of the proverbial self-governing iceberg. What about the harshness of the environment itself (i.e. climate change) that continuously tries to melt it?
Defense: self-preservation or disintegration
Leaving your house can be a bad idea, think about the cold, wind, wild animals, disease, rain, floods, fire, lightning and the list can go on and on. Now imagine you don’t have a house. Imagine you are your own house and you must defend it from being eaten all the time and you have to fight for resources to pile up in your house and then you need to find another house to share stuff with so you can reproduce (somewhere the analogy got a little muddied, but I don’t exactly know where). Evolution has provided almost all organisms with defense mechanisms against other organisms trying to use you as a nutrient source, because let’s face it, a concentrated amount of resources is a lot easier to thrive off than resources scattered around everywhere. Prokaryotes have an awesome defense mechanism against bacteriophages (viruses that specifically target bacteria and Archaea), where they degrade foreign DNA that enters their cell. They do this by recognizing the invading DNA, cutting it and integrating it into a sort of collection of snippets of foreign DNA, so they can in a sense “remember” what to degrade the next time. This is actually a system us humans are now abusing and researching a whole lot. You might know it by the name CRISPR/Cas9, but I like to call it the cut-and-paste-technology. You’ve probably heard about the Chinese guy that used the technology to genetically engineer a human already, which might be too early since much more research needs to be done to look at the long-term effects of using this transgenic system, but it hopefully might still turn out fine for the kid. We can call this defense system a type of adaptive immunity, just like we have ours, but ours is way, waaaaaaayyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy more complex. It’s so complex that entire research departments are dedicated to sole aspects of it. They cover the mechanisms of infection (there are many different types of way infection can occur), how the immune system battles infections and how it goes wrong (auto-immunity, not being able to clear certain infections etc.) and how it battles (and fails to battle) issues from within (cancer, gout) or starts to battle itself (leukemia). The immune system is probably the most fascinating thing in the human body, because it’s so adaptive. I’ll try to cover a bit of basic immunology in a later entry, but there’s a lot to cover and I’m not an expert in the field so I’ll probably miss a few key things here and there (apologies in advance).
This is a bacteriophage (Escherichia virus T4) infecting E. coli.
Very early on, single celled organisms have acquired mechanisms to react to light (phototaxis), get away from toxic substances (chemotaxis, but this also covers going to favorable substances) and detoxify toxic substances if they still enter their cell. The last one is one of the reasons we have so many antibiotic resistant bacteria nowadays. They produce enzymes that break them down or literal protein channels that pump it back out. I don’t know enough about the nervous system and these mechanisms that govern moving to/from energy sources, but I have a hunch these might be the earliest precursors to neurons, or at the very least the sensory organs.
Some compounds just kill you, though, and there’s very little you can do to help it. Much can be stored or even detoxified. Some plants take up heavy (toxic) metals from the soil, in effect cleaning it from pollution, which humans are using in a thing called phytoremediation. Apparently, over 500 species can be considered hyperaccumulators. This mechanism might stem from the fact that certain metal transporters are in se color blind for other metals coupled with the fact that they can tolerate them. This molecular nonchalance might be used favorably since heavy metals are toxic to herbivores and thus might act as an anti-herbivory tool. Other examples include rice, which accumulates arsenic and cassava (a staple food for part of the developing world), which contains cyanide. This cyanide is actually sequestered in a sugar compound, but is released upon destruction of the plant cell through herbivory or other means. These examples hopefully show the adaptations certain organisms (among many more) have undergone to be able to survive in a dog eat dog world. There are many more situation which arise and there’s an entire part I haven’t touched, namely abiotic stress (like heat, drought, flooding, hyperoxic/hypoxic/anoxic environments, cold, etc.) and just like dealing with other organisms, adaptation to these circumstances is key. If you can’t adapt to your situation, you perish. It continuously happens as the environments certain niche organisms thrive in change and we shouldn’t be too conservationist, but if we have a way of slowing or even stopping certain disastrous trends, we should definitely try to.
Rise of the colonies
Earlier, we’ve established that organisms grow. They mainly grow because cells divide, which is a consequence of continuous replicating DNA and production of proteins. Other organisms, like single-celled organisms grow and divide, but have a fixed cell size and each can go their way. Single cells don’t always go their own way after being born, though. Sometimes they form colonies, which is a way of grouping together. Certain organisms can, when a specific density has been acquired, start forming biofilms (more technically called quorum sensing), to further their agenda of synergistic single-celled organisms. The disease called cystic fibrosis, while horrible and having many issues next to the toughening of mucosa, isn’t actually a terminal illness in itself. The heightened viscosity of the lungs makes it possible for opportunistic bacteria, like Pseudomonas aeruginosa to thrive there and ultimately produce a biofilm, which makes it progressively difficult to breathe, until fatal. Biofilms are a way of defending the huge colony and even making pores at strategic places to optimize nutrient passage. Humans might have complex body builds with many different cell types, but single-celled organisms are definitely no simpletons either. Sometimes different single celled species act in concert with each other as one species metabolizes some molecule and the waste product is then used as an energy source (i.e. electron donor) for the other.
Entertain the following idea: we evolved from single celled organisms. These single celled organisms have learned to work together; first in simple ways, then next more elaborately by specifying roles (like nutrient capturing, processing, reproduction; Volvox is a great example), then it becomes even more elaborate depending on how the organism evolved and by the habitat it resided in. Sponges seem like very primitive multicellular organisms but are quite organized already. In any case, the specialization keeps occurring over time. Suddenly the organism becomes so elaborate it needs an actual transport network for nutrients, it needs to regulate food intake and breakdown, it needs to regulate the impulses from the environment and from within and it needs to keep everything safe. It needs to grow, differentiate and ultimately reproduce. We are still that single-celled organism, only have we become highly intricate. Our skin, bones, muscles, neurons and organs are the amalgamation of billions of years of being more and more adapted to the environment and slowly unveiling the possibilities the set of basic molecules can provide. Soon we will integrate other organisms’ properties into our own core to assimilate and further this archaic concept. It might seem artificial in the beginning, but careful introspection will reveal this is what nature had in store for us all along. I’ve written an essay about post-humanism and the integrative aspect of it all as opposed to the present duality seems very appealing nowadays.
This is a video of Volvox swimming towards light, while Euglena is swimming away from light.
Who doesn’t like sex? I mean, it feels good. But don’t you think it’s kind of strange that for the vast majority of species it’s a necessity and we’re the ones enjoying it, like it had to be enjoyable in order to actually do it? Of course, this has probably been selected for in the long run; individuals where it felt good wanted to have more sex, because it felt good and now we have a global culture that’s completely oriented towards that. Sexual reproduction is a strange thing, though, because it’s not exactly clear why it’s come into evolutionary play. One could come with the easily to diversify the genetic pool argument, but bacteria still outpace us while cloning themselves. Bacteria also have a way of sexually reproducing, by the way. One of the bacteria will form a pilus that extends towards and docks with the other cell, so they can exchange genetic information. Seems to be a bit more straightforward than what we do, doesn’t it?
Plants seem to have a weird thing going on, but to my realization a few years ago, the most evolutionary successful clade, the Embryophyta (which covers basically everything you see of vegetation on the planet; includes grasses, pine trees and flowering plants), but more specifically the flowering plants, or Angiospermae, have a mechanism of spreading and bearing their next of kin in a very similar way as mammals do. The pollen that falls on the stigma of the pistil needs to be genetically compatible with the plant (this isn’t always the case, but it’s a nice expansion on the subject), which is checked by the female reproductive organ, or the gynoecium. It delivers small inhibitory RNA fragments to the growing pollen tube, which will arrest its growth into the pistil (while searching for the egg cell) if the genetic makeup of the pollen is too similar. This is a mechanism we call self-incompatibility.
So, if a suitable pollen grain finds the stigma, it’ll grow a pollen tube, where the sperm cells are homed to the egg chamber, which contains a convoluted number of cells, for unclear reasons. This egg chamber is akin to a humans’ uterus, with the seed(s) being the children that are grown inside. The pollen grains are small and are aptly called microsporangia, while the egg cell is large and called macrosporangia. The structures involved in making the sperm and egg cells for sexual reproduction are the gametophytes, and, just like our reproductive organs (testes and ovaries), produce cells/structures with n copies of genetic material (or are haploid), while the actual plant is diploid (2n) and is called the sporophyte. This wasn’t always the case however and in early evolution and more basal photosynthetic life forms, like mosses, this is actually the reverse. Oh, before I forget, the process of germination (getting the sperm into to the egg cell) is done mostly in situ, meaning that it’s on/in a part of the plant itself. Ferns and mosses will make spores. What comes out of those spores are different than the typical spore producing structure (although with mosses they’re mostly attached), which then produce the gametes to make a new spore making plant. And the mosses you actually see are mostly the gametophyte and not the spore producing part. Yes, the sexual intricacies of Viridiplantae are very elaborate and fascinating. It’s also very difficult to devote time for molecular research, if there’s no economic interest. Who knows what amazing mechanisms we can discover by studying some obscure photosynthesizing organism?
I won’t delve into mating patterns, because I have no formal education in biology or zoology or whatever studies mating patterns in animals. Male birds puff their feathers or try to make the most elaborate song; things with horns or claws fight for the rights to mate; you have champion species that have harems or still need to convince the female; there’s polyandry, polygamy, matriarchy, patriarchy, hives, sexual dimorphism (and the opposition of it) and much, too much more to actually discuss here.
Giving back what you’ve taken: death
You were born, you’ve grown, you’ve sexed – it was a blast – and finally, you can’t go on any longer, it’s time to return to what you once were. For now, it seems that the fundamentals of biology keep death as an inevitability. But next to cellular respiration causing internal damage through hyperoxide formation, food being depleted and toxic “waste products” being produced en masse, there are some more mechanisms that are at the basis of aging and ultimately death.
First off, cells die all the time. They die from being targeted by the immune system, they die from inaccuracies in mitosis, they die as a natural part of their life cycle (skin cells), they die from infection (lysis from bacteria or viruses), …
There are some key concepts here we must address when we talk about cells dying though: sometimes they choose to die, i.e. they are programmed to self-destruct for the benefit of the entire system and sometimes they die because of no agency of their own. The first is called apoptosis (i.e. programmed cell death), while the latter is called necrosis. The mechanisms underlying both are vast, have some overlap and can be reached through a variety of ways. One of the key events in the apoptotic pathway is when the mitochondria essentially start to dissolve, releasing all sorts of molecules that signal “time to walk the apoptotic path now”.
Secondly, each cell cycle (cells having divided through mitosis and cytokinesis), telomeres become shorter. Telomeres are sequences of repeating DNA at the ends of chromosomes that basically have no function other than protection against the shortening of chromosomal DNA. It’s essentially a buffer against another shortcoming of biology, albeit I don’t know the intricacies of how it happens.
Thirdly, mutations happen all the time. They will happen more frequently the longer you live, because of accumulation of mutagens and carcinogens and overall less cellular wellbeing.
Fourthly, DNA methylation, a big mechanism in what is called epigenetics, seems happen and has a dampening effect gene expression, which means that less will be able to be produced over time to maintain cellular functions. This means that the turnover of cells will ultimately be greater, with more cells dying than can be replenished, thus making you wither (age) and eventually die when a critical threshold has been reached.
Obviously, I don’t know that much about aging and it is a very complex subject, but I think these are key mechanism that have a big stake in it.
Now how to combat the process of aging, or how to boost your cellular health in general? Well, I’m not a nutrition expert or a doctor, but I can share some things I’ve thought about:
- Get in plenty of antioxidants, they’re sponges for reactive oxygen species.
- Eat healthy and varied.
- Move a lot but not too intensely, move into an as much of a clean air area as possible.
- Don’t be afraid to try out these esoteric calming/soothing oils/smell/whatever therapy, much of traditional Eastern (herbal) medicine is frowned upon by the West, but plants (and micro-organisms) harbor the most potent medicinal/longevity substances of them all.
- Eat sulforaphane rich foods (kayle, broccoli, cauliflower), seriously, it’s going to be the next big thing. It seems to be tapping into many protective things our bodies innately have.
- Get an NAD+ treatment. NAD+ and FAD are electron carriers (or more scientifically, redox cofactors), that are intricately involved in the electron transfer chain. A heavy dose of the stuff will be able to boost you significantly, and maybe even slow down aging. I also think it will cause less electrons to leak, but I can’t back that claim up lol. I haven’t done this myself, but am eager to try this!
Next to this, we’ll have to wait for significant breakthroughs in genetics, both on the aspects from a developmental standpoint (maintaining stem cell viability and what are the genes keeping us young so to speak), an epigenetic standpoint (how to avoid progressive gene silencing without disrupting the normal machinery) and the finetuning (and long term effects from) the CRISPR system.
I hope you’ve enjoyed and learned a bit from this quite long entry. I’m definitely up for feedback/discussions/whatever else you want to do here. The next entry, I think, will be about DNA, replication and evolution (and the techniques that go along with it). See you next time.
PS I’ve renamed this series “About life” instead of “Blog of life”, since it felt more appropriate and rolls off the tongue a little better imo.