The Never-Ending Story of Life: A Brief Journey through Concepts of Biology

By Carlos E. Semino

For humankind, the most irreducible idea is the concept of life itself. In order to understand that life is essentially an infinite process, transmitted from generation to generation, this book takes the reader on a fascinating journey that unravels one of our greatest mysteries. 

It begins with the premise that life is a fact—that it is everywhere; that it takes infinite forms; and, most importantly, that it is intrinsically self-perpetuating. Rather than exploring how the first living forms emerged in our universe, the book begins with our first primordial ancestor cell and tells the story of life—how it began, when that first cell diversified into many other cell types and organisms, and how it has continued until the present day. On this journey, the author covers the fundaments of biology such as cell division, diversity, regeneration, repair and death. The rather fictional epilogue even goes one step further and discusses ways how to literally escape the problemof limited recourse and distribution on our planet by looking at life outside the solar system.   

This book is designed to explain complex ideas in biology simply, but not simplistically, with a special emphasis on plain and accessible language as well as a wealth of hand-drawn illustrations. Thus, it is suitable not only for students seeking for an introduction into biological concepts and terminology, but for everyone with an interest in the fundamentals of life at the crossroad of evolutionary and cell biology.  

• Language: English
• Publisher: Springer
• Release date: Jun 18, 2021
• ISBN: 9783030759698

Book preview

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021

C. E. SeminoThe Never-Ending Story of Lifehttps://doi.org/10.1007/978-3-030-75969-8_1

1. The Origin of Eukaryotic Cells and Multicellular Organisms

Carlos E. Semino¹  

(1)

Tissue Engineering Research Laboratory, Department of Bioengineering, IQS-School of Engineering, Ramon Llull University, Barcelona, Spain

From the moment the invaders arrived, breathed our air, ate and drank, they were doomed. They were undone, destroyed, after all of man’s weapons and devices had failed, by the tiniest creatures that God in his wisdom put upon this earth. By the toll of a billion deaths, man had earned his immunity, his right to survive among this planet’s infinite organisms. And that right is ours against all challenges. For neither do men live nor die in vain.

―H. G. Wells, The War of the Worlds

Summary

First signs of life on Earth were most probably in the form of unicellular organisms that rapidly diverged into different types while adapting to all conceivable environments. From those, the first eukaryotic cells appeared giving rise to the origin of multicellular organisms that after an unimaginable series of changes and adaptations ended in what we know today as fungi, plants, and animals. This chapter explains how this long and complex process most probably happened in the last billions of years since the origin of life.

First Steps of Life on Earth

We do not really know how the first cells were created, but we do know that 3.7 billion years ago (BYA), the first unicellular organisms were already populating our planet. This is why whether these organisms developed here on Earth, came from outer space, or formed as a hybrid between terrestrial and extraterrestrial organisms, we call this original cell or common cell the ancestor.

Now, the study of the prehistory of cells is a difficult job, because we do not have physical registries for cells in the way paleontologists have registries for fossils. Interestingly, the evolution of cells is therefore studied by comparing the differences among the genetic material of organisms that are alive today. Why? Because genomes—the genetic material that is passed down from generation to generation, which is composed in most organisms of deoxyribonucleic acid (DNA)—contain not only information about how each particular organism will be able to build its cells, tissues, organs, body shapes, etc. but also a record of the different modifications (mutations) that an organism has experienced over time. The information we obtain from comparing genomes is so powerful that it can take us almost all the way back to the origin of cellular evolution. To put it simply, more closely related organisms have more similar genomes than organisms that are less closely related. By comparing this genetic material, it is possible not only to classify all the cell types that presently exist but also to predict all their potential ancestors. Thus, from looking at cells’ family trees, we now have a good idea of how they have evolved over the last 3.7 BY and of their almost infinite capacity to generate diversity.

These first primitive, unicellular organisms adapted to colonize every single niche in the surface of the Earth. It is believed that the first primitive cellular common ancestor evolved into two main cell lineages: early bacteria and archaea¹-proto-eukaryotic² cells. Both cell types were composed of a cellular membrane and a circular DNA molecule that contained their genetic material. Bacteria have continued evolving independently ever since into hundreds of different species with innumerable adaptations. Crucially, very early on, a group of bacteria called cyanobacteria started photosynthesizing—using light energy to reduce carbon dioxide (CO2) into carbon-containing molecules, like carbohydrates—and producing molecular oxygen (O2) as residue. At that time, oxygen was toxic for most existing anaerobic bacteria. Over the course of 1 BY, O2 accumulated in the atmosphere until it became so prevalent that anaerobiosis was only possible in special niches, causing a drastic reduction in the number of anaerobic species on Earth. Interestingly, by 2.5 BYA, O2 was used by aerobic heterotrophic bacteria, which expanded very quickly. These new bacteria were capable of oxidizing reduced carbon-containing molecules to produce highly energetic molecules like adenosine-5-triphosphate (ATP), generating CO2 and water (H2O). In this way, phototrophic and heterotrophic bacteria conquered practically the entire planet; today, they constitute what is called the prokaryotes.

In the other lineage that evolved from those first unicellular organisms, archaea-proto-eukaryotic cells diverged and gave rise to archaea and eukaryotic cells (Fig. 1.1, The origin of eukaryotic cells). Archaea have continued evolving, developing into their own group, but the eukaryotic group’s evolutionary path was not so straightforward. Several theories have been postulated to explain the evolution of eukaryotic cells, and the most plausible ones have been selected and described here. The first currently used theory suggests that the early eukaryote cell was generated after a series of events that occurred about 1.5 BYA, including cell membrane invaginations that created specialized internal endomembrane systems such as the nucleus, which contained the cell’s DNA, and the endoplasmic reticulum, which is a specialized organelle localized around the nucleus in charge of synthesizing proteins that could then be secreted to the exterior of the cell. Therefore, this was the origin of the first nucleated cell (Fig. 1.1a, The origin of eukaryotic cells).

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Fig. 1.1

The origin of eukaryotic cells. (a) A common ancestor cell appeared on Earth about 3.7 billion years ago (BYA). It initially diverged into bacteria (which later became its own kingdom) and archaea-proto-eukaryotic cells. Archaea-proto-eukaryotes diverged into archaea (which also formed its own kingdom) and early eukaryotic cells. These latter cells underwent cell membrane invagination to form the nucleus (which contains their DNA) and the endoplasmic reticulum (which provides the capacity to synthesize proteins that can be secreted). Then, an endosymbiotic event took place: ancestral aerobic heterotrophic bacteria entered into a eukaryotic cell ancestor, which later turned into mitochondria. This marked the formation of the first eukaryotic cell, which diverged into today’s fungi and animal cells. In a second endosymbiotic event, ancestral aerobic photosynthetic bacteria (cyanobacterium) entered into the early eukaryotic cell, which later turned into a chloroplast. This new cell type became the origin of vegetal cells. Fungi, animal, and vegetal cells all belong to the Eukarya Kingdom. (b) An early common ancestor with RNA-based genome appeared on Earth about 3.7 BYA. From this ancestor, three basic types of cell domains emerged, a common bacteria-archaea ancestor with a DNA-based genome that later diverged into bacteria and archaea, respectively, and, a third one, a proto-eukaryotic cell (RNA-based genome). This proto-eukaryotic cell presented an active cytoskeleton and an invaginated cell membrane that formed an early endoplasmic reticulum, which provides the Fig. 1.1 (continued) capacity to synthesize proteins that can be, eventually, secreted. This proto-eukaryotic cell is called chronocyte after engulfing an archaea. The achaea turned later into the nucleus, containing the achaea’s DNA and, later, the retrotranscribed RNA-based genome that progressively was transported into the nucleus. After a second endosymbiotic event, chronocyte engulfed ancestral heterotrophic aerobic bacteria, which later turned into mitochondria, generating the first eukaryotic cell. Same as above, the first eukaryotic cell diverged into today’s fungi and animal cells. In a third endosymbiotic event, ancestral aerobic photosynthetic bacteria (cyanobacterium) were engulfed by the primitive eukaryotic cell. The cyanobacteria later turned into chloroplasts. This was the origin of vegetal cells

Around that time, it is believed that the DNA molecule (which was circular in ancestor cells) became linear and associated with a special type of proteins, the histones (basic proteins with barrel-like structure used to roll up the DNA molecule to minimize it volume), which helped pack the DNA into a highly organized structure called chromatin, giving rise to the first eukaryotic chromosomes. In this way, very long pieces of linear DNA can be condensed, reduced in volume to fit into the cell, and placed together with other chromosomes. Essentially, this new eukaryotic cell type stored its genetic material (all the chromosomes) in a specialized organelle (nucleus) keeping it separate from the rest of the cell, the cytoplasm, where the main metabolic and synthetic activities take place. Remarkably, eukaryotic genetic material is in general very long. For instance, if all the chromosomes present in one single human cell are unpacked and linearized, they measure all together around 2 m long. In addition, if of all the linearized genetic material of all the cells present in a human of around 70 kg is measured (approximately 37 trillion cells or 37,000,000,000,000 cells), it will be 74,000,000,000 km long, which is equivalent to about 500 times the distance between the Earth and the Sun.

Moreover, if we do the same with other eukaryote cell types, for instance, a simple amoeba (a single-cell microorganism living in aquatic environments, which belong to the group of amoebae³), its genetic material will measure around 300 m, which is extremely large considering its simple lifestyle. Other examples like lilies, wheat, and salamanders are also very long (all around dozens of meters). This means that DNA packing by histones plays a very important role on eukaryotic cells because all this genetic material needs to fit into a very tiny nucleus of a cell of about 10 μm long, which is equivalent to 100 times smaller than a millimeter.

Then, this early nucleated cell underwent a process called endosymbiosis,⁴ which means that ancestral aerobic heterotrophic bacteria were somehow incorporated into the eukaryote ancestor without having been digested. The bacterium therefore adapted to live inside of its new host and later evolved (maintaining its own original circular DNA) into what is known today as the mitochondrion, an organelle that is dedicated to produce energy in the form of ATP [1–3]. This new cell was the early eukaryote, which then evolved to form the ancestors of fungi and animal cells. Next, in a second endosymbiotic event, our early eukaryotic cell incorporated then an ancestral photosynthetic bacteria (cyanobacteria), which later evolved into what is called chloroplast (an organelle that has the capacity to use light to reduce CO2 into carbon-containing molecules, like carbohydrates), creating the first vegetal cell. In this way, these three cell types (fungi, animal, and vegetal) evolved to form the kingdom of unicellular and multicellular eukaryote organisms. Since mitochondria and chloroplasts maintain its original circular DNA, they were therefore used by evolutionary biologists to compare their sequences and conclude that they are indeed related to ancestral heterotrophic prokaryote and cyanobacteria, respectively.

Two alternative theories about the origin of the nucleus in early eukaryotic cells suggest that it was also produced after an endosymbiotic event. The first in proposing such idea was the Russian botanist named Konstantin Mereschkowski in 1905, who suggested that the nucleus evolved from bacteria engulfed by and entity named amoebaplasm which was not a bacterium [1]. Briefly, Mereschkowski sustained after looking at hundreds of species of lichens⁵ that eukaryotic organelles, including the nucleus and the chloroplast, were the result of an intracellular symbiosis of bacteria with amoeba-like cell (or amoebaplasm). This idea was the fundamental principle of the previously described endosymbiont theory (or symbiogenesis theory) popularized by Lynn Margulis, who mainly pursued the idea that mitochondria and chloroplasts are the descendants of heterotrophic prokaryote and cyanobacteria, respectively.

The first theory in favor of endosymbiont origin of the nucleus claims that the early eukaryotic cells were the product of a fusion of an archaeon with a bacterium. In this model, the archaeon become the nucleus. This theory is symbolized as E = A + B or in words Eukarya = Archaea + Bacteria and is called the AB hypothesis. Then, the second alternative theory about the origin of the eukaryotic nucleus was postulated by Hyman Hartman, an evolutionary biologist at MIT (Massachusetts Institute of Technology), who extended Mereschkowski’s theory in favor of the nucleus being the product of