Information

Multicellular organisms as DNA banks

Multicellular organisms as DNA banks



We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

Animal -> bacterial gene transfer seems easier than bacteria -> animal (rotifers are an interesting exception); there are bacteria live in close contact to us but our germ-line cells are protected. Given enough time, even free-living bacteria would start to pick up some of our genes (once the introns were lost).

Is this true? If so, do we see animal/plant genes gradually spreading into single cell organisms as time goes on (although "seeing" this would be difficult)? Is this effect "significant" for evolution in microbes?


This paper seems relevant. I just found it and don't have access, so I haven't read it. It does seem to suggest that there is evidence for eukaryotic genes being taken up by a prokaryote.

I would imagine this is rare, though. Eukaryotic cells don't tend to just spew their genetic material everywhere. Most death pathways involve breaking down any genetic material in the cell, I believe.


This sea slug is one example of prokaryotic genes ending up in an animal. The slug ingests chloroplasts from algae and incorporates them into its own cytoplasm. It has also acquired, presumably through horizontal gene transfer, some or all of those genes necessary to maintain the chloroplast. While this is not a gene transfer from a free-living prokaryote, chloroplasts are essentially cyanobacteria.

For the paper (PDF), see here.

Also see a more general review here (free full text).


DNA repair and genome maintenance in Bacillus subtilis

From microbes to multicellular eukaryotic organisms, all cells contain pathways responsible for genome maintenance. DNA replication allows for the faithful duplication of the genome, whereas DNA repair pathways preserve DNA integrity in response to damage originating from endogenous and exogenous sources. The basic pathways important for DNA replication and repair are often conserved throughout biology. In bacteria, high-fidelity repair is balanced with low-fidelity repair and mutagenesis. Such a balance is important for maintaining viability while providing an opportunity for the advantageous selection of mutations when faced with a changing environment. Over the last decade, studies of DNA repair pathways in bacteria have demonstrated considerable differences between Gram-positive and Gram-negative organisms. Here we review and discuss the DNA repair, genome maintenance, and DNA damage checkpoint pathways of the Gram-positive bacterium Bacillus subtilis. We present their molecular mechanisms and compare the functions and regulation of several pathways with known information on other organisms. We also discuss DNA repair during different growth phases and the developmental program of sporulation. In summary, we present a review of the function, regulation, and molecular mechanisms of DNA repair and mutagenesis in Gram-positive bacteria, with a strong emphasis on B. subtilis.

Figures

Model for activation of the…

Model for activation of the SOS response in B. subtilis. (A) In this…

Model for repair of a single double-strand break by homologous recombination in B.…

Schematic representation of the domain…

Schematic representation of the domain structure of B. subtilis DNA helicases RecQ and…

Model for double Holliday junction…

Model for double Holliday junction formation during homologous recombination and repair of DSBs…

Crystal structure of Holliday junction…

Crystal structure of Holliday junction resolvase RecU of B. subtilis. (Adapted from reference…

Model for mismatch repair in…

Model for mismatch repair in B. subtilis. (A and B) The β clamp…

Schematic diagram of the genome…

Schematic diagram of the genome maintenance checkpoints in B. subtilis. (A) The interplay…


Contents

Cells are of two types: eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular.

Prokaryotic cells

Prokaryotes include bacteria and archaea, two of the three domains of life. Prokaryotic cells were the first form of life on Earth, characterized by having vital biological processes including cell signaling. They are simpler and smaller than eukaryotic cells, and lack a nucleus, and other membrane-bound organelles. The DNA of a prokaryotic cell consists of a single circular chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid. Most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 μm in diameter. [13]

A prokaryotic cell has three regions:

  • Enclosing the cell is the cell envelope – generally consisting of a plasma membrane covered by a cell wall which, for some bacteria, may be further covered by a third layer called a capsule. Though most prokaryotes have both a cell membrane and a cell wall, there are exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea) which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, serving as a protective filter. The cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting (cytolysis) from osmotic pressure due to a hypotonic environment. Some eukaryotic cells (plant cells and fungal cells) also have a cell wall.
  • Inside the cell is the cytoplasmic region that contains the genome (DNA), ribosomes and various sorts of inclusions. [4] The genetic material is freely found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular. Linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. [14] Though not forming a nucleus, the DNA is condensed in a nucleoid. Plasmids encode additional genes, such as antibiotic resistance genes.
  • On the outside, flagella and pili project from the cell's surface. These are structures (not present in all prokaryotes) made of proteins that facilitate movement and communication between cells.

Eukaryotic cells

Plants, animals, fungi, slime moulds, protozoa, and algae are all eukaryotic. These cells are about fifteen times wider than a typical prokaryote and can be as much as a thousand times greater in volume. The main distinguishing feature of eukaryotes as compared to prokaryotes is compartmentalization: the presence of membrane-bound organelles (compartments) in which specific activities take place. Most important among these is a cell nucleus, [4] an organelle that houses the cell's DNA. This nucleus gives the eukaryote its name, which means "true kernel (nucleus)". Other differences include:

  • The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present.
  • The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. [4] Some eukaryotic organelles such as mitochondria also contain some DNA.
  • Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, mechanosensation, and thermosensation. Each cilium may thus be "viewed as a sensory cellular antennae that coordinates a large number of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation." [15]
  • Motile eukaryotes can move using motile cilia or flagella. Motile cells are absent in conifers and flowering plants. [16] Eukaryotic flagella are more complex than those of prokaryotes. [17]

All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, regulates what moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the membrane, the cytoplasm takes up most of the cell's volume. All cells (except red blood cells which lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin) possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells. This article lists these primary cellular components, then briefly describes their function.

Membrane

The cell membrane, or plasma membrane, is a biological membrane that surrounds the cytoplasm of a cell. In animals, the plasma membrane is the outer boundary of the cell, while in plants and prokaryotes it is usually covered by a cell wall. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of phospholipids, which are amphiphilic (partly hydrophobic and partly hydrophilic). Hence, the layer is called a phospholipid bilayer, or sometimes a fluid mosaic membrane. Embedded within this membrane is a macromolecular structure called the porosome the universal secretory portal in cells and a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell. [4] The membrane is semi-permeable, and selectively permeable, in that it can either let a substance (molecule or ion) pass through freely, pass through to a limited extent or not pass through at all. Cell surface membranes also contain receptor proteins that allow cells to detect external signaling molecules such as hormones.

Cytoskeleton

The cytoskeleton acts to organize and maintain the cell's shape anchors organelles in place helps during endocytosis, the uptake of external materials by a cell, and cytokinesis, the separation of daughter cells after cell division and moves parts of the cell in processes of growth and mobility. The eukaryotic cytoskeleton is composed of microtubules, intermediate filaments and microfilaments. In the cytoskeleton of a neuron the intermediate filaments are known as neurofilaments. There are a great number of proteins associated with them, each controlling a cell's structure by directing, bundling, and aligning filaments. [4] The prokaryotic cytoskeleton is less well-studied but is involved in the maintenance of cell shape, polarity and cytokinesis. [19] The subunit protein of microfilaments is a small, monomeric protein called actin. The subunit of microtubules is a dimeric molecule called tubulin. Intermediate filaments are heteropolymers whose subunits vary among the cell types in different tissues. But some of the subunit protein of intermediate filaments include vimentin, desmin, lamin (lamins A, B and C), keratin (multiple acidic and basic keratins), neurofilament proteins (NF–L, NF–M).

Genetic material

Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Cells use DNA for their long-term information storage. The biological information contained in an organism is encoded in its DNA sequence. [4] RNA is used for information transport (e.g., mRNA) and enzymatic functions (e.g., ribosomal RNA). Transfer RNA (tRNA) molecules are used to add amino acids during protein translation.

Prokaryotic genetic material is organized in a simple circular bacterial chromosome in the nucleoid region of the cytoplasm. Eukaryotic genetic material is divided into different, [4] linear molecules called chromosomes inside a discrete nucleus, usually with additional genetic material in some organelles like mitochondria and chloroplasts (see endosymbiotic theory).

A human cell has genetic material contained in the cell nucleus (the nuclear genome) and in the mitochondria (the mitochondrial genome). In humans the nuclear genome is divided into 46 linear DNA molecules called chromosomes, including 22 homologous chromosome pairs and a pair of sex chromosomes. The mitochondrial genome is a circular DNA molecule distinct from the nuclear DNA. Although the mitochondrial DNA is very small compared to nuclear chromosomes, [4] it codes for 13 proteins involved in mitochondrial energy production and specific tRNAs.

Foreign genetic material (most commonly DNA) can also be artificially introduced into the cell by a process called transfection. This can be transient, if the DNA is not inserted into the cell's genome, or stable, if it is. Certain viruses also insert their genetic material into the genome.

Organelles

Organelles are parts of the cell which are adapted and/or specialized for carrying out one or more vital functions, analogous to the organs of the human body (such as the heart, lung, and kidney, with each organ performing a different function). [4] Both eukaryotic and prokaryotic cells have organelles, but prokaryotic organelles are generally simpler and are not membrane-bound.

There are several types of organelles in a cell. Some (such as the nucleus and golgi apparatus) are typically solitary, while others (such as mitochondria, chloroplasts, peroxisomes and lysosomes) can be numerous (hundreds to thousands). The cytosol is the gelatinous fluid that fills the cell and surrounds the organelles.

Eukaryotic

  • Cell nucleus: A cell's information center, the cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell's chromosomes, and is the place where almost all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and separated from the cytoplasm by a double membrane called the nuclear envelope. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called messenger RNA (mRNA). This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. The nucleolus is a specialized region within the nucleus where ribosome subunits are assembled. In prokaryotes, DNA processing takes place in the cytoplasm. [4]
  • Mitochondria and chloroplasts: generate energy for the cell. Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. [4]Respiration occurs in the cell mitochondria, which generate the cell's energy by oxidative phosphorylation, using oxygen to release energy stored in cellular nutrients (typically pertaining to glucose) to generate ATP. Mitochondria multiply by binary fission, like prokaryotes. Chloroplasts can only be found in plants and algae, and they capture the sun's energy to make carbohydrates through photosynthesis.
  • Endoplasmic reticulum: The endoplasmic reticulum (ER) is a transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface that secrete proteins into the ER, and the smooth ER, which lacks ribosomes. [4] The smooth ER plays a role in calcium sequestration and release.
  • Golgi apparatus: The primary function of the Golgi apparatus is to process and package the macromolecules such as proteins and lipids that are synthesized by the cell.
  • Lysosomes and peroxisomes: Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. Peroxisomes have enzymes that rid the cell of toxic peroxides. The cell could not house these destructive enzymes if they were not contained in a membrane-bound system. [4]
  • Centrosome: the cytoskeleton organiser: The centrosome produces the microtubules of a cell – a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells.
  • Vacuoles: Vacuoles sequester waste products and in plant cells store water. They are often described as liquid filled space and are surrounded by a membrane. Some cells, most notably Amoeba, have contractile vacuoles, which can pump water out of the cell if there is too much water. The vacuoles of plant cells and fungal cells are usually larger than those of animal cells.

Eukaryotic and prokaryotic

  • Ribosomes: The ribosome is a large complex of RNA and protein molecules. [4] They each consist of two subunits, and act as an assembly line where RNA from the nucleus is used to synthesise proteins from amino acids. Ribosomes can be found either floating freely or bound to a membrane (the rough endoplasmatic reticulum in eukaryotes, or the cell membrane in prokaryotes). [20]

Many cells also have structures which exist wholly or partially outside the cell membrane. These structures are notable because they are not protected from the external environment by the semipermeable cell membrane. In order to assemble these structures, their components must be carried across the cell membrane by export processes.

Cell wall

Many types of prokaryotic and eukaryotic cells have a cell wall. The cell wall acts to protect the cell mechanically and chemically from its environment, and is an additional layer of protection to the cell membrane. Different types of cell have cell walls made up of different materials plant cell walls are primarily made up of cellulose, fungi cell walls are made up of chitin and bacteria cell walls are made up of peptidoglycan.

Prokaryotic

Capsule

A gelatinous capsule is present in some bacteria outside the cell membrane and cell wall. The capsule may be polysaccharide as in pneumococci, meningococci or polypeptide as Bacillus anthracis or hyaluronic acid as in streptococci. Capsules are not marked by normal staining protocols and can be detected by India ink or methyl blue which allows for higher contrast between the cells for observation. [21] : 87

Flagella

Flagella are organelles for cellular mobility. The bacterial flagellum stretches from cytoplasm through the cell membrane(s) and extrudes through the cell wall. They are long and thick thread-like appendages, protein in nature. A different type of flagellum is found in archaea and a different type is found in eukaryotes.

Fimbriae

A fimbria (plural fimbriae also known as a pilus, plural pili) is a short, thin, hair-like filament found on the surface of bacteria. Fimbriae are formed of a protein called pilin (antigenic) and are responsible for the attachment of bacteria to specific receptors on human cells (cell adhesion). There are special types of pili involved in bacterial conjugation.

Replication

Cell division involves a single cell (called a mother cell) dividing into two daughter cells. This leads to growth in multicellular organisms (the growth of tissue) and to procreation (vegetative reproduction) in unicellular organisms. Prokaryotic cells divide by binary fission, while eukaryotic cells usually undergo a process of nuclear division, called mitosis, followed by division of the cell, called cytokinesis. A diploid cell may also undergo meiosis to produce haploid cells, usually four. Haploid cells serve as gametes in multicellular organisms, fusing to form new diploid cells.

DNA replication, or the process of duplicating a cell's genome, [4] always happens when a cell divides through mitosis or binary fission. This occurs during the S phase of the cell cycle.

In meiosis, the DNA is replicated only once, while the cell divides twice. DNA replication only occurs before meiosis I. DNA replication does not occur when the cells divide the second time, in meiosis II. [22] Replication, like all cellular activities, requires specialized proteins for carrying out the job. [4]

DNA repair

In general, cells of all organisms contain enzyme systems that scan their DNA for damages and carry out repair processes when damages are detected. [23] Diverse repair processes have evolved in organisms ranging from bacteria to humans. The widespread prevalence of these repair processes indicates the importance of maintaining cellular DNA in an undamaged state in order to avoid cell death or errors of replication due to damages that could lead to mutation. E. coli bacteria are a well-studied example of a cellular organism with diverse well-defined DNA repair processes. These include: (1) nucleotide excision repair, (2) DNA mismatch repair, (3) non-homologous end joining of double-strand breaks, (4) recombinational repair and (5) light-dependent repair (photoreactivation).

Growth and metabolism

Between successive cell divisions, cells grow through the functioning of cellular metabolism. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules and perform other biological functions. Complex sugars consumed by the organism can be broken down into simpler sugar molecules called monosaccharides such as glucose. Once inside the cell, glucose is broken down to make adenosine triphosphate (ATP), [4] a molecule that possesses readily available energy, through two different pathways.

Protein synthesis

Cells are capable of synthesizing new proteins, which are essential for the modulation and maintenance of cellular activities. This process involves the formation of new protein molecules from amino acid building blocks based on information encoded in DNA/RNA. Protein synthesis generally consists of two major steps: transcription and translation.

Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol, where they are translated into polypeptide sequences. The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to the polypeptide sequence by binding to transfer RNA (tRNA) adapter molecules in binding pockets within the ribosome. The new polypeptide then folds into a functional three-dimensional protein molecule.

Motility

Unicellular organisms can move in order to find food or escape predators. Common mechanisms of motion include flagella and cilia.

In multicellular organisms, cells can move during processes such as wound healing, the immune response and cancer metastasis. For example, in wound healing in animals, white blood cells move to the wound site to kill the microorganisms that cause infection. Cell motility involves many receptors, crosslinking, bundling, binding, adhesion, motor and other proteins. [24] The process is divided into three steps – protrusion of the leading edge of the cell, adhesion of the leading edge and de-adhesion at the cell body and rear, and cytoskeletal contraction to pull the cell forward. Each step is driven by physical forces generated by unique segments of the cytoskeleton. [25] [26]

Navigation, control and communication

In August 2020, scientists described one way cells – in particular cells of a slime mold and mouse pancreatic cancer–derived cells – are able to navigate efficiently through a body and identify the best routes through complex mazes: generating gradients after breaking down diffused chemoattractants which enable them to sense upcoming maze junctions before reaching them, including around corners. [27] [28] [29]


Contents

Occurrence Edit

Multicellularity has evolved independently at least 25 times in eukaryotes, [7] [8] and also in some prokaryotes, like cyanobacteria, myxobacteria, actinomycetes, Magnetoglobus multicellularis or Methanosarcina. [3] However, complex multicellular organisms evolved only in six eukaryotic groups: animals, fungi, brown algae, red algae, green algae, and land plants. [9] It evolved repeatedly for Chloroplastida (green algae and land plants), once or twice for animals, once for brown algae, three times in the fungi (chytrids, ascomycetes and basidiomycetes) [10] and perhaps several times for slime molds and red algae. [11] The first evidence of multicellularity is from cyanobacteria-like organisms that lived 3–3.5 billion years ago. [7] To reproduce, true multicellular organisms must solve the problem of regenerating a whole organism from germ cells (i.e., sperm and egg cells), an issue that is studied in evolutionary developmental biology. Animals have evolved a considerable diversity of cell types in a multicellular body (100–150 different cell types), compared with 10–20 in plants and fungi. [12]

Loss of multicellularity Edit

Loss of multicellularity occurred in some groups. [13] Fungi are predominantly multicellular, though early diverging lineages are largely unicellular (e.g., Microsporidia) and there have been numerous reversions to unicellularity across fungi (e.g., Saccharomycotina, Cryptococcus, and other yeasts). [14] [15] It may also have occurred in some red algae (e.g., Porphyridium), but it is possible that they are primitively unicellular. [16] Loss of multicellularity is also considered probable in some green algae (e.g., Chlorella vulgaris and some Ulvophyceae). [17] [18] In other groups, generally parasites, a reduction of multicellularity occurred, in number or types of cells (e.g., the myxozoans, multicellular organisms, earlier thought to be unicellular, are probably extremely reduced cnidarians). [19]

Cancer Edit

Multicellular organisms, especially long-living animals, face the challenge of cancer, which occurs when cells fail to regulate their growth within the normal program of development. Changes in tissue morphology can be observed during this process. Cancer in animals (metazoans) has often been described as a loss of multicellularity. [20] There is a discussion about the possibility of existence of cancer in other multicellular organisms [21] [22] or even in protozoa. [23] For example, plant galls have been characterized as tumors, [24] but some authors argue that plants do not develop cancer. [25]

Separation of somatic and germ cells Edit

In some multicellular groups, which are called Weismannists, a separation between a sterile somatic cell line and a germ cell line evolved. However, Weismannist development is relatively rare (e.g., vertebrates, arthropods, Volvox), as a great part of species have the capacity for somatic embryogenesis (e.g., land plants, most algae, many invertebrates). [26] [27]

One hypothesis for the origin of multicellularity is that a group of function-specific cells aggregated into a slug-like mass called a grex, which moved as a multicellular unit. This is essentially what slime molds do. Another hypothesis is that a primitive cell underwent nucleus division, thereby becoming a coenocyte. A membrane would then form around each nucleus (and the cellular space and organelles occupied in the space), thereby resulting in a group of connected cells in one organism (this mechanism is observable in Drosophila). A third hypothesis is that as a unicellular organism divided, the daughter cells failed to separate, resulting in a conglomeration of identical cells in one organism, which could later develop specialized tissues. This is what plant and animal embryos do as well as colonial choanoflagellates. [28] [29]

Because the first multicellular organisms were simple, soft organisms lacking bone, shell or other hard body parts, they are not well preserved in the fossil record. [30] One exception may be the demosponge, which may have left a chemical signature in ancient rocks. The earliest fossils of multicellular organisms include the contested Grypania spiralis and the fossils of the black shales of the Palaeoproterozoic Francevillian Group Fossil B Formation in Gabon (Gabonionta). [31] The Doushantuo Formation has yielded 600 million year old microfossils with evidence of multicellular traits. [32]

Until recently, phylogenetic reconstruction has been through anatomical (particularly embryological) similarities. This is inexact, as living multicellular organisms such as animals and plants are more than 500 million years removed from their single-cell ancestors. Such a passage of time allows both divergent and convergent evolution time to mimic similarities and accumulate differences between groups of modern and extinct ancestral species. Modern phylogenetics uses sophisticated techniques such as alloenzymes, satellite DNA and other molecular markers to describe traits that are shared between distantly related lineages. [ citation needed ]

The evolution of multicellularity could have occurred in a number of different ways, some of which are described below:

The symbiotic theory Edit

This theory suggests that the first multicellular organisms occurred from symbiosis (cooperation) of different species of single-cell organisms, each with different roles. Over time these organisms would become so dependent on each other they would not be able to survive independently, eventually leading to the incorporation of their genomes into one multicellular organism. [33] Each respective organism would become a separate lineage of differentiated cells within the newly created species.

This kind of severely co-dependent symbiosis can be seen frequently, such as in the relationship between clown fish and Riterri sea anemones. In these cases, it is extremely doubtful whether either species would survive very long if the other became extinct. However, the problem with this theory is that it is still not known how each organism's DNA could be incorporated into one single genome to constitute them as a single species. Although such symbiosis is theorized to have occurred (e.g., mitochondria and chloroplasts in animal and plant cells—endosymbiosis), it has happened only extremely rarely and, even then, the genomes of the endosymbionts have retained an element of distinction, separately replicating their DNA during mitosis of the host species. For instance, the two or three symbiotic organisms forming the composite lichen, although dependent on each other for survival, have to separately reproduce and then re-form to create one individual organism once more.

The cellularization (syncytial) theory Edit

This theory states that a single unicellular organism, with multiple nuclei, could have developed internal membrane partitions around each of its nuclei. [34] Many protists such as the ciliates or slime molds can have several nuclei, lending support to this hypothesis. However, the simple presence of multiple nuclei is not enough to support the theory. Multiple nuclei of ciliates are dissimilar and have clear differentiated functions. The macronucleus serves the organism's needs, whereas the micronucleus is used for sexual reproduction with exchange of genetic material. Slime molds syncitia form from individual amoeboid cells, like syncitial tissues of some multicellular organisms, not the other way round. To be deemed valid, this theory needs a demonstrable example and mechanism of generation of a multicellular organism from a pre-existing syncytium.

The colonial theory Edit

The Colonial Theory of Haeckel, 1874, proposes that the symbiosis of many organisms of the same species (unlike the symbiotic theory, which suggests the symbiosis of different species) led to a multicellular organism. At least some, it is presumed land-evolved, multicellularity occurs by cells separating and then rejoining (e.g., cellular slime molds) whereas for the majority of multicellular types (those that evolved within aquatic environments), multicellularity occurs as a consequence of cells failing to separate following division. [35] The mechanism of this latter colony formation can be as simple as incomplete cytokinesis, though multicellularity is also typically considered to involve cellular differentiation. [36]

The advantage of the Colonial Theory hypothesis is that it has been seen to occur independently in 16 different protoctistan phyla. For instance, during food shortages the amoeba Dictyostelium groups together in a colony that moves as one to a new location. Some of these amoeba then slightly differentiate from each other. Other examples of colonial organisation in protista are Volvocaceae, such as Eudorina and Volvox, the latter of which consists of up to 500–50,000 cells (depending on the species), only a fraction of which reproduce. [37] For example, in one species 25–35 cells reproduce, 8 asexually and around 15–25 sexually. However, it can often be hard to separate colonial protists from true multicellular organisms, as the two concepts are not distinct colonial protists have been dubbed "pluricellular" rather than "multicellular". [5]

The Synzoospore theory Edit

Some authors suggest that the origin of multicellularity, at least in Metazoa, occurred due to a transition from temporal to spatial cell differentiation, rather than through a gradual evolution of cell differentiation, as affirmed in Haeckel’s Gastraea theory. [38]

GK-PID Edit

About 800 million years ago, [39] a minor genetic change in a single molecule called guanylate kinase protein-interaction domain (GK-PID) may have allowed organisms to go from a single cell organism to one of many cells. [40]

The role of viruses Edit

Genes borrowed from viruses and mobile genetic elements (MGEs) have recently been identified as playing a crucial role in the differentiation of multicellular tissues and organs and even in sexual reproduction, in the fusion of egg cell and sperm. [41] [42] Such fused cells are also involved in metazoan membranes such as those that prevent chemicals crossing the placenta and the brain body separation. [41] Two viral components have been identified. The first is syncytin, which came from a virus. [43] The second identified in 2007 is called EFF1, which helps form the skin of Caenorhabditis elegans, part of a whole family of FF proteins. Felix Rey, of the Pasteur Institute in Paris has constructed the 3D structure of the EFF1 protein [44] and shown it does the work of linking one cell to another, in viral infections. The fact that all known cell fusion molecules are viral in origin suggests that they have been vitally important to the inter-cellular communication systems that enabled multicellularity. Without the ability of cellular fusion, colonies could have formed, but anything even as complex as a sponge would not have been possible. [45]

The Oxygen Availability Hypothesis Edit

This theory suggests that the oxygen available in the atmosphere of early Earth could have been the limiting factor for the emergence of multicellular life. [46] This hypothesis is based on the correlation between the emergence of multicellular life and the increase of oxygen levels during this time. This would have taken place after the Great Oxidation Event (GOE) but before the most recent rise in oxygen. Mills [47] concludes that the amount of oxygen present during the Ediacaran is not necessary for complex life and therefore is unlikely to have been the driving factor for the origin of multicellularity.

Snowball Earth Hypothesis Edit

A snowball Earth is a geological event where the entire surface of the Earth is covered in snow and ice. The most recent snowball Earth took place during the Cryogenian period and consisted of two global glaciation events known as the Sturtian and Marinoan glaciations. Xiao [48] suggests that between the period of time known as the "Boring Billion" and the Snowball Earth, simple life could have had time to innovate and evolve which could later lead to the evolution of multicellularity. The snowball Earth hypothesis in regards to multicellularity proposes that the Cyrogenian period in Earth history could have been the catalyst for the evolution of complex multicellular life. Brocks [49] suggests that the time between the Sturtian Glacian and the more recent Marinoan Glacian allowed for planktonic algae to dominate the seas making way for rapid diversity of life for both plant and animal lineages. Shortly after the Marinoan, complex life quickly emerged and diversified in what is known as the Cambrian Explosion.

Predation Hypothesis Edit

The Predation Hypothesis suggests that in order to avoid being eaten by predators, simple single-celled organisms evolved multicellularity to make it harder to be consumed as prey. Herron et al [50] performed laboratory evolution experiments on the single-celled green alga, C. reinhardtii, using paramecium as a predator. They found that in the presence of this predator, C. reinhardtii does indeed evolve simple multicellular features.

Multicellularity allows an organism to exceed the size limits normally imposed by diffusion: single cells with increased size have a decreased surface-to-volume ratio and have difficulty absorbing sufficient nutrients and transporting them throughout the cell. Multicellular organisms thus have the competitive advantages of an increase in size without its limitations. They can have longer lifespans as they can continue living when individual cells die. Multicellularity also permits increasing complexity by allowing differentiation of cell types within one organism.

Whether these can be seen as advantages however is debatable. The vast majority of living organisms are single cellular, and even in terms of biomass, single cellular organisms are far more successful than animals, though not plants. [51] Rather than seeing traits such as longer lifespans and greater size as an advantage, many biologists see these only as examples of diversity, with associated tradeoffs.


Levels of Multicellular Organisms

Download the video from iTunes U or the Internet Archive.

I am a professor in the Biology Department at MIT. And I will be co-teaching this course with Penny Chisholm who is a professor in the Department of Civil and Environmental Engineering, as well as a professor in the Biology Department. As well, Penny was recently featured in the journal Nature. She is a very well-known oceanographer who has become deservedly famous for discovering a very small bacterium that's capable of carrying out photosynthesis. For many years oceanographers used filters whose holes were big enough that this bacterium went through. And so when they were doing their studies of the ocean and how the biomass that was there and all the fluxes and so on, they didn't know this organism existed which can form up to 50% of the biomass in parts of the ocean. So Penny is really a wonderful lecturer, a wonderful person, and she'll be teaching the component of 7.014 which deals with ecology and the environment. And this is a section of 7. 14 that makes it different from the other two versions, 7.012 and 7.013. So for me personally this is an absolutely wonderful and exciting opportunity to be able to teach this Introductory Biology course. For some of you I know that biology is going to either be a major part of your career or quite possibly, even if you're in engineering or something else, you will find yourselves working with a biological system. You can see that happening all over campus these days that more and more engineering departments are finding that they're working on problems that come from biology or have a biological component. I'm sure there are at least a few of you here who are only here because it's a required course and you might well wish you were somewhere else. However, I will do my best to try to communicate to you why you need to know some biology, too. I think most of you know you can hardly pick up a newspaper these days without running into something that demands a knowledge of biology, something about stem cells, something about cloning humans, something about a new drug, lots of things having to do with biological affects on the environment and so on. You're also going to be confronted with decisions about your health, about the health of your loved ones concerning cancer, concerning whether a child might have birth defects, all sort of issues that will affect your personal lives that demand an understanding of biology. So I feel with some passion that whether you think you're going to need biology in your professional career or not, everyone in this institution needs some understanding of biology to just live their ordinary lives. I also think as MIT students you're going to be looked at, as you go through your lives, as people who are knowledgeable about science and engineering. And you'll be asked questions that go far beyond your immediate area of expertise. And again I think that's another reason for needing to know some of biology. Anyway, it's an absolutely wonderful time to teach biology because things have just been exploding over the last two or three decades and things are moving faster than ever. And another wonderful thing about teaching biology is that MIT is an absolutely marvelous place to teach it. Just to sort of drive this home, in the Biology Department alone there are four Nobel laureates who got honored for critical discoveries in biology. Gobin Khorana who is just down the hall from me synthesized the first gene. It was an extraordinary feat of synthesis of organic chemistry synthesizing DNA. When I was an undergrad I was a chemistry major but I had to take an introductory biology course. And at that point the DNA wasn't mentioned in the high school course. So the first time that I heard about DNA was in my introductory biology course. And that determined by career direction. I thought that was such an interesting molecule that I wanted to work on it and I talked myself into one of the labs in Ottawa, Canada where I grew up that was trying to synthesize DNA, synthesize pieces of the gene. And, as it turned out later, competing unsuccessfully with my now colleague Gobin Khorana. Susumu Tonegawa got a Nobel prize for discovering the amazing molecular operations that underlie the diversity of the immune system. Your immune system has the capacity to recognize viruses and bacteria, all sorts of different pathogens, including molecules. It can recognize molecules that haven't even ever been synthesized in the history of life. And we'll talk towards the end of the course about the way that happens. And you'll see why Susumu got his Nobel prize. Phil Sharp got his for discovering RNA splicing completely unanticipated component of the very heart of molecular biology. And then Bob Horvitz who was of pure mind when he started at MIT at the same time and our labs were side by side for many years, got his Nobel prize in 2002 for discovering a phenomenon, the general term is ìprogrammedî cell death. And it plays all sorts of important roles in biology from sculpting the shapes of organs and tissues. We initially have webs when we're developing between our fingers, and those go away because of the programmed cell death that the cells that were making the web disappear. And another role of that is prevent cancer. That if cells sense that something is very messed up they have a sort of suicide program that would make them destroy themselves. And if that doesn't happen those cells could go on and become more and more abnormal and eventually turn into an invasive cancer. Anyway, there's a picture of Bob when the institute was celebrating his Nobel prize. He was getting a congratulatory kiss from Martha Constantine-Paton, also a professor in the Biology Department who happens to be Bob's wife. Most of you know that the human genome has now been sequenced. That was one of the huge undertakings and most important undertakings in modern biology over the last while. It was an incredible feat. Each cell has, as most of you know, 46 chromosomes. And that's a total of about two meters of DNA in every human cell. And that two meters of DNA is composed of about 3 million DNA base pairs, these letters A, T, G and C that we'll be talking about as we go through the course. So to sequence the genome you had to work out the sequence of the exact run of these A, G, T and Cs along the backbone for 3 billion base pairs. And somewhere that genome encodes somewhere between 20,000 and 30,000 genes. And we'll be talking about the proteins that are encoded by most of those genes and their important roles as we go on in the course. What some of you may not know is the key role that MIT played in this. About a third of the genome was sequenced at the Whitehead MIT Genome Center. And here are some of the robots that were used to sequence that DNA. And that sequencing effort was led by Eric Lander whose name some of you may recognize because he teaches the fall version of 7. 12 along with Bob Weinberg. So here are just a few examples of why I think it's important for you to understand biology regardless of whether you're going to go on and use it professionally. Most of you know one of the biggest challenges we face on this planet is this AIDS epidemic. It's caused by a certain kind of virus called HIV-1 that gets into particular cells of your immune system that normally defends us against infection and destroys those. And then people die from infections by other organisms that normally you can fight off. It's a huge problem with vast societal and economic implications. And it's one that we're still, as a mankind still trying to deal with and grapple with. Here's another example. Just a couple of years ago there was the scar of anthrax. It's a bacterium that's very pathogenic and kills its host fairly easily. It does it by making particular toxins. The details shown here don't matter, but just reminding you that this is something that was in the front pages of the paper just a little while ago. A couple of years ago, when I was teaching this, we had the scare of the SARS virus that went all the way during the course when I was teaching it from the initial discovery of the virus to the actual sequencing of the genome which had happened by later on in this course. Smallpox was a disease we thought that we eliminated, but now it's come back as a bioterrorism treat and there is increased study of smallpox. It's something we have to worry about again. Here's another example. This is a picture showing the start of a transgenic animal. We'll talk about how this process goes later in the course. And it's related also to this whole issue of cloning, using the sense of the word such as in trying to clone a human or clone an animal to make a genetically identical copy. So you'll see there are a couple of different uses of the word cloning as we go through the course. There's a lot of fuss in the news and the newspapers about genetically modified food, and people have different positions on it. Here's a case where I think the benefit of a genetically modified food could hardly be argued with. About two-thirds of the world's population uses rice as their primary source of food. One of the problems with rice is that it doesn't make beta-carotene. And beta carotene is what our bodies take and use to make vitamin A. And if you have a vitamin A deficiency people are prone to infection. They have immune deficiencies in their immune system and blindness. And this deficiency of vitamin A caused by eating rice afflicts about 400 million people worldwide. Well, rice is only two chemical steps away from being able to make beta carotene. This is a genetically modified version of rice that has those two extra steps inserted in it. And you can see it's golden because it's making beta carotene. If people were to eat that form of rice then they wouldn't have this problem with vitamin A deficiency. Penny Chisholm in her part of the course will be considering things that are more global level. Here's a picture of our planet, and there are issues that you know about there. This is the carbon dioxide levels in the atmosphere rising. And because of the emission of fluorocarbons in the environment And that's a real phenomenon. This shows from 1960 to 1995. damage our cells if we were exposed to it. absorbs UV, a critical component of ultraviolet radiation that would This is associated with a global warming that again is undeniable this large hole developed over Antarctic. If that had spread, got a Nobel prize for that. Ozone is important because it that it's happening. You'll see stuff in the papers. Right here at MIT Mario Molina in EAPS discovered the ozone hole and And these gases, particularly carbon dioxide and methane, And Penny will talk to you a little more about that. it would have been a real disaster. And that seems to be, the efforts they're known as greenhouse gases are playing a role in that. gases and, hence, in global warming. And probably mankind is playing a role in the production of those to cut down the release of fluorocarbons seem to be helping with that. But, again, Penny will have more to say. Those of you who've lived around here for a little bit probably know that the fishing industry just locally has had a very hard time. There is a fishing boat just up in Gloucester, just up the coast less than an hour from here. And part of the problems, again, are caused by mismanagement of the resources where the fish have been, stocks have been over-fished so some of the fisheries have come to the point of collapse or near. Places such as the Grand Banks off of Newfoundland there has been a collapse, and it's not at all clear that it can be reversed and whether they'll be cod in large quantities every again there. OK. So there a variety of ways that we can study biology. And I think I'm going to begin by outlining how we do that. Biology is an experimental science and it's one of the really important themes that we'll run through in this course. You cannot study biology by just sitting down with a pen and paper in a room and thinking. You have to get out and find out what's there. You need to make observations. You need to try experiments. You need to formulate hypotheses and test them and either modify your hypothesis or reject it and so on. But it's a continual cycle of experimentation and making hypotheses and testing. It's the Scientific Method at work. But you can carry that out at different levels. The very highest level would be the biosphere. Here's one example. That's earth. It's here. There are many, many species of life that are on there. There are many more than a million. And the estimates of how many there are range from, in total, 10 to the 20 million estimated. And one of the big worries right at the moment is that as rain forests are being depleted, parts of the world that are a rich source of biological diversity, as those are disappearing we're losing diversity at quite a rate. Just a couple of years ago I had a chance to fly over a part of Brazil. And it was just scary to see from the plane how the rain forest was just being cut down. And you could just see how fast some of the rain forest was disappearing, and with it many different types of species that only can live there. One can look instead, going down a level, at an ecosystem which is a particular environment -- -- and the species of life found in it. And just to give you a couple of examples of that, it could be a salt marsh as shown here. Or here's an interesting environment that Penny Chisholm will tell you more about. This is a black smoker. There's a vent several miles deep in the Pacific Ocean. The water temperature that's gushing out of here is around 360 degree centigrade. And there's a particular community of life that's able to grow around these deep vents. And Penny will tell you more about that. Then going down yet another level you can come to a population. And this is interacting -- -- or interbreeding organisms. An example might be the fiddler crabs in a salt marsh. Or here we see an interesting population. These are tube worms that are up to a meter or more in length that you find down at these black smokers. If we move down yet another level -- -- we come to organisms. Organisms have three important sorts of characteristics that we'll talk quite a bit about in this course. They carry out metabolism which is the sum of all the different chemical reactions necessary for life. They undergo regulated growth -- -- and they reproduce. And the sort of fundamental unit of life that we will talk about over and over again in this course is known as a cell. And life comes in two kinds of species. There is unicellular life where the organism is just a single cell and multicellular forms of life that are made of many different types of cells. What's a cell? One of the secrets to life. It's a little tiny bit of the universe that's surrounded by a boundary. And it's given the special name of a membrane. It's selective, not very permeable to most things. And cells are able to put little importers and exporters and things that control the passage of things across the membrane by isolating the inside of a cell from all the rest of the universe. That is one of the principles that makes life possible. We have a couple of examples of organisms here. Here are some clams that grow down at those black smokers, and they can get pretty large. And, as I say, Penny will talk a bit more about this. And we have this really amazing diversity of life forms that we find on this planet. However, if we think about this division into unicellular and multicellular organisms. Unicellular organisms include things that you're familiar with. They're bacteria. There is a picture of just E. coli cells. And we'll be talking about E. coli quite a bit as a model organism as we go through the course. By studying E. coli, scientists have learned many important things that apply to all of life. Another kind of important single-celled organism, unicellular organism is yeast. Those are pictures of yeast saccharomyces that are used in baking bread or in brewing beer or making wine. And another one you're all familiar with are algae which are single-celled organisms that are able to carry out photosynthesis. And we'll be talking about that. If we think of an example of a multicellular organism then we see there are different levels at which we can think about this. We could take, for example, a picture of me, just an anatomically correct diagram here, that I'm made up, as you are, of about ten to the fourteenth human cells. We all started out as a fertilized egg, which is a single cell. And by the time we're grown up, where we have about ten to the fourteenth human cells. Just a tremendous amount of cell growth that had to happen and specialization. The other thing you may not appreciate is that we have an ecosystem inside us in our gastrointestinal tract. This part, the intestine having the highest concentration of microorganisms. But there are about ten to the fourteenth bacteria also inside of our gut. So we're actually almost the same number of human cells and bacterial cells. And if we don't have those bacteria then our digestive systems don't work well. So if we go down from a whole organism, a whole multicellular organism, a level, then we come to an organ. An example of that might be an eye. And I think we have a diagram of an eye which is made up of different parts. If we go down another level we come to a tissue. Which is now you can begin to see that tissue are made up of groups of specialized cells. An example might be the retina of an eye. And if we continue to go downwards we'll get to single cells. And at this point we're at the same level of the tail as when we're talking about a unicellular organism. If we continue down then -- -- we can get to organelles. These are involved in energy production, energy management. And mitochondrion and chloroplasts are the two principle examples of organelles that we'll talk about. And if we go down yet another level of organization we get to molecules. And part of the reason that biology has flourished so well over the last few decades at MIT is there has been a real emphasis on looking at things at a cellular and molecular level. So you're going to be hearing a lot about cells and a lot about molecules as we go through this course. Here's an example of rhodopsin. That's a protein. We'll be talking about what proteins are, but it's a very important class of molecule in nature. In this case, proteins involved in sensing light and play an important part in your vision. Here is another protein. You cannot really tell what it's doing by just looking at it, but in this case this is one of the lethal factors that is made by anthrax. It's one of the proteins that anthrax makes that's capable of killing you if you get infected with it. Here's another molecule we'll talk about in great detail. This is DNA. You probably all know it's a double helix, two strands of DNA that are held together by forces we'll be discussing. It's an absolutely beautiful molecule. It's fascinated me through all of my life. And we'll be talking quite a bit about that as the course goes on. OK. So if we're thinking about cells there are two important kinds of cells that one finds on this planet. Prokaryotic cells. Prokaryotic organisms and eukaryotic organisms. They each are made of cells that are distinguishable from each other. I've indicated that a cell is a little bit of the universe that's surrounded by a boundary or a membrane. But inside there, inside of this is the DNA which functions as the genetic material. It's the blueprint for everything that that cell is going to make and be able to do. Ultimately everything is encoded there. And in a prokaryotic cell the DNA is free within this membrane. The eukaryotic cell also has a membrane. But the DNA inside is inside another membrane compartment known as the nucleus. And this is the DNA. These prokaryotic cells tend to be of the order of a kilometer in length. And eukaryotic cells are usually larger, can be ten to a hundred kilometers. There's quite a bit of variation, but that gives you at least some sense of the range. Now, I've for years, when I did a diagram like this, I wanted to somehow be able to show you that these cells were impressive than just what's on the board. So here are a couple of pictures to try and do that. This shows a picture of E. coli swimming along. And the way this image is being taken lets you see what are called flagella but which are basically the propellers that E. coli have that let it swim through the water. These are long structures made of proteins that are several times the body length of the bacterium. And there's a molecular motor imbedded in the bacterium that whirls it around at about somewhere between 10,000 and 100, 00 RPM. And that's what drives the bacteria forward. So that was a prokaryotic cell. Here's a paramecium. This is a single-celled eukaryotic organism. And, as you can see here, it's capable of movement as well. In this case it has cilia along the outside that allow it to move. Here's an interesting one. I don't know if any of you can guess what these were. These were cells from the skin of a mouse. They're on an Auger surface. And, as you can see, they too can move. There are a couple of things that are important about this. I got this slide from Linda Griffith who is in the Biological Engineering Department. At the time I got it from her I think it was in Chemical Engineering several years ago. And what was important about this, apart from it being a very nice little movie showing you a mammalian cell moving around, was that I saw Linda show this during one of her research seminars. So here is an engineer at MIT who was showing this picture as part of her research talk. And I think those of you who are going onto engineering, you may be surprised at the extent to which you need to know about biology as you go through your professional careers. OK. So one of the great discoveries that has happened over the last few years that came out of our ability to look at DNA and RNA was the discovery that the forms of life that are prokaryotic actually split into two distinct Kingdoms that are very, very different. The archaea and the bacteria. And just to give you a sense of the diversity of life, I'll just mention a couple of these. These archaea look like bacteria but they are diverged from the bacteria as they are from the eukaryotes. So there were sort of three really major Kingdoms of Life. And the archaea, many of them can live in specialized environments. For example, sulfolobus can live at about 90 degrees centigrade and a pH of somewhere between 1 and 2. So if you see something like a hot springs, there are organisms such as this that are able to grow in that environment. Or there are halophyes, salt-loving archaea that can grow, for example, in formula sodium chloride. And if you've, for example, ever flown into San Francisco airport coming up from the south over San Jose, you've seen things that look sort of like these pictures where seawater is being evaporated down to collect the salt. And you'll see they're colored, and the reason they're colored is that these halobacteria are photobacteria that are able to use light as an energy source. And they make pigments that absorb the light, and that's why these salt areas get colored. A third example would be methanogens. These are organisms that produce methane. If you've walked into a lake and stepped on the bottom and seen little bubbles come up, those are little bubbles of methane. Or another place where you find methanogens are inside of cows. Now, some of you may not know that the cow is more or less a walking anaerobic fermentor here. If we have an anatomically correct picture of a cow. The inside of the cow, there's a large chamber known as the rumen where there's no oxygen, and there's a culture of microorganisms there that include methanogens. And it's this combination of microorganisms that enables cows to each grass that we cannot manage to get energy from. And as a byproduct of this specialized type of metabolism produces methane. And a cow burps something of the order of 400 liters a day of methane. OK. So one last thing then just to kind of pull this all together is that these organelles that I mentioned, which are also membrane compartments that are found in eukaryotic cells, are the mitochondria -- coli or streptococcus that causes strep throat or the lactic acid you're more familiar with. Things like E. bacteria that causes the milk to turn into yogurt which some of you probably had for lunch today. That these organelles, the mitochondria and the chloroplast were derived from particular type of this point that these arose from bacteria that were things that bacteria that probably first got transiently associated with developing eukaryotic cells sometime back in evolution, and eventually became captured and became a permanent part of the eukaryotic cell. The mitochondrion is thought to have derived from something that looks like today's present day -- or chloroplast. There's pretty strong evidence at rizobia, which we'll talk about, that form an intracellular infection of plants, or rickettsia which is chronic intracellular pathogen. The mitochondrion look as though they came from something related to that. The chloroplasts look as though they came from a bacterium that was able to carry on photosynthesis which we'll also be talking about. I want to close by giving you just a quick little snapshot of evolution because I'm hoping this will maybe make some of the things that we talk about in this course clearer. So what we're going to do is we're going to look back from 4. billion years ago when the earth was just forming -- -- to now. I'm just going to try and give you a few key sort of landmarks as we go along. So about 4.5 billion years ago there was methane, carbon dioxide, ammonium, hydrogen gas, nitrogen gas, water, but importantly no oxygen at that point. There was a lot of debate as to how life initially came. One of the prevalent theories at this point is there's something called an RNA world. This is just a hypothesis in which it's thought that perhaps the molecule RNA, which we'll talk about, played role as both something that was able to catalyze chemical reactions and therefore did things actively and also stored information. But, in any case, the best guess is that the first life that was about 3. billion years ago, somewhere in that vicinity. It was something that probably resembled most closely a present-day bacterium, a single-celled organism, something like that. Now, initially when life got started it's thought that there were a lot of organic chemicals that had been made as a consequence of lightening strikes and all sorts of chemistry that had happened so there was sort of a soup of some kind, some molecules that could be used. So probably these first organisms where able to basically use some preformed nutrients. And then as the soup began to get depleted by using it they had to learn to synthesize, at least develop systems that would synthesize these building blocks. And they also had to begin to worry about what to use as energy. And so somewhere in here, something that I'll call, in a silly way, photosynthesis released number one. But this was a system that enabled the organism to capture energy from sunlight so that it wasn't now dependent on getting energy by eating some preformed ingredient. It was then able to take carbon dioxide and make it into forms that were useful, of carbon that were useful for life, and it produced molecules such as sulfur as a waste product. There was a bit later in evolution, somewhere in here, something we might think of as photosynthesis release two. This was an improved version of photosynthesis. It captured more energy, worked better, but it developed, it had a waste product which was oxygen. Well, oxygen hadn't been in our atmosphere. And the first thing that sort of happened was that the world started to rust. All the iron, a lot of the iron started to interact with the oxygen. And Penny will tell you that at the base of the sea there are huge beds of iron oxide that came from this slow rusting of the earth. And so it took many, many years before oxygen levels started to rise. As you know it's about 20% of our atmosphere now. Even at this stage it was only a few percent of our, made up a few percent of our atmosphere, even by here in evolution. The first eukaryotic cell is thought to have appeared somewhere here. Again, it was likely a single-celled organism like some of those pictures I showed you. And evolution continued to go. Somewhere around a billion years ago sex was evolved which enabled eukaryotic organisms to exchange genetic material, and therefore evolve at a fast rate than they could previously. The Cambrian Period was about a 0. billion to 0.6 billion years ago. And there was a veritable explosion of life forms. And you can still see in the fossil records how much diversity was generated at that point, some of which went on to become life forms and other which probably were more evolutionary dead ends. Finally we get to the dinosaurs that were about 245 to 65 million years ago which would place them somewhere here on this timeline. So in honor of this course, I've commissioned a full scale model of anatomically correct [NOISE OBSCURES]. So we'll put our dinosaur here, if I can get him to stay put for a minute. All right. And at this point in evolution things started to get interesting. So somewhere about here, 4 million years ago we've got the first evidence of hominoids. Maybe 20,000 years ago we found the cave paintings in France. And then there was the Roman Empire and Columbus discovered America. And you were born and the Red Sox won the World Series and the Patriots have just won the Super Bowl. And we are now here at the peak of evolution which is, as you all know, the MIT student. So we'll put our MIT student here, who I can probably not get to stay put because you can never get MIT students to stay anywhere. But, in any case, this is sort of a silly demonstration. But there is a very profound reason why I'm doing it. And I must say I don't think I'd ever fully appreciated it until I actually thought of doing this demo for the class. But what I think you can see is that evolution, for the most part, happened at the single cell level. Many people tended to think evolution, that was about dinosaurs and all that stuff. We can say that dinosaurs are, practically now, most of evolution occurred at the level of single cells, and that all this amazing diversity we see around us was very recent embellishments in evolution. So that means when you study biology at the cellular and molecular level you find tremendous commonalities. If you look inside a sulfolobus growing in hot spring, if you look inside an E. coli, if you look inside a yeast and you look inside one of our cells you find that, to a huge extent, many, many of the cellular components are common. They arose similarly in evolution that they're shared by all forms of life. Of course, there are some things that developed later and are different. But that's one of the reasons that you can learn so much by studying biology at the cellular molecular level and why we'll emphasize it a fair bit in this course. The other thing that I'd like to make out of this, a theme that you'll hear along is that organisms modify their environment. You can see that in the case of oxygen back when the earth formed. There was no oxygen in our atmosphere. Now we have a lot of it. The reason it's there is because it was generated by organisms carrying out photosynthesis and generating oxygen as a waste product. And that was an absolutely critical thing to enable creatures such as ourselves, which are dependent on oxygen for us just to be alive, if we hadn't had this change in environment things like us could have, organisms like us couldn't have evolved. So, anyway, I hope that will give you a little sort of snapshot of evolution and will help guide your understanding of this course. We'll see you at the next lecture.


RESULTS AND DISCUSSION

Enclosed ecosystems emerged in landscape of industrialized cities

In landscapes along rural-urban gradients, the identified entities are the industrial systems embedded in the matrix of ecosystems. In addition to the enclosed non-ecosystems (such as factories, which emerged three centuries ago), the remarkable thing is the recent emergence of enclosed ecosystems (Figure 1A, B). Both enclosed ecosystems and non-ecosystems are industrial systems, and their common features are the outer covers and internal industrial facilities (machines and apparatus). Enclosed ecosystems are unique because they rely on biological processes but are supported by industrial facilities. For example, greenhouses enhance plant production, livestock feedlots improve animal production, and wastewater treatment plants concentrate microorganism activities (Figure S2 Table S1). In contrast, factories, restaurants or banks have no biological components except the people working there. Non-ecosystem components can also provide “ecosystem services” such as cultural services provided by museums and theatres.

The outer membrane greatly increases the efficiency and productivity of enclosed industrial systems (Figure 1C), which yield 2–5 orders of magnitude higher goods and services per land area than open farmlands, and have become productivity hotspots in cities. Multiple types of enclosed ecosystems have emerged worldwide performing functions including food production (e.g., vegetables, meat, milk and eggs), decomposition (e.g., wastewater treatment, waste disposal) and other services (Figure S3 Table S1). In some regions they provide goods and services that cannot be provided by open ecosystems. For example, greenhouses can produce fresh vegetables in very cold areas (e.g., high altitude areas in Tibet, China), while the open farmlands cannot.

Similarities between an industrialized city and a eukaryotic cell

Industrialized cities have characteristics similar to living systems, but they are less similar to multicellular organisms than suggested by the super-organism hypothesis. This raises the question—to which living system in the biological hierarchy model are industrialized cities most similar? We analysed 15 traits of living systems and cities (see Table S2) to identify relatedness among living systems using a cluster analysis with the complete linkage method based on Gower distance. The clustering results show that industrialized cities are more similar to eukaryotic cells than to multicellular organisms (Figure 2A) in the hierarchy of living systems (Figure 2B). Although industrialized cities (10 5 m) are much greater in size than eukaryotic cells (10 –5 m), many traits, such as spatial functional structure, metabolism and regulation, are highly similar (Table S2).

A eukaryotic cell has thousands of organelles around the cell nucleus. Each type of organelle is distributed spatially along the centre (nucleus) to the edge (cell membrane) in a eukaryotic cell (Figure 3A). For example, mitochondria in a eukaryotic cell are concentrated near the nucleus while lysosomes are farther away, and many of organelles frequently move (Figure 3B, C). Similar to eukaryotic cells, there are a great number of enclosed systems around and within the urban centre in industrialized cities (Figure 3D). Enclosed non-ecosystems, such as banks, restaurants and hotels, are concentrated in the urban centre while factories are located on the urban fringe. Enclosed ecosystems, such as greenhouses and wastewater treatment plants, are located outside the urban fringe, while dairy farms are located in exurban areas (Figure 3E). Many studies focus on the two-dimensional pattern of cities, [ 5, 30 ] but some argue that living cells are three-dimensional objects and lack strong similarities with cities. In fact, industrialized cities have become increasingly spherical by expanding both above- and belowground, [ 9, 31 ] and developing into the third spatial dimension.

Enclosed ecosystems and enclosed non-ecosystems are frequently relocated for a variety of reasons (Figure 3F). They are moved directly, such as mobile restaurants and railway greenhouses, [ 32 ] or indirectly, such as a factory being dismantled in one place and reconstructed in another. For example, since the 1980s dairy farms in the Greater Shanghai Area have been pushed from the urban fringe to exurban areas many times because they produce high ecosystem disservices. Relocating enclosed systems in cities reflects the change in relative values for net goods and services of the enclosed systems and the changing costs of land leasing due to urban development.

From the perspective of physics, the allometric scale effect of components in response to system size is a general principle for both cities and eukaryotic cells. The number of chloroplasts and mitochondria in response to cell size (volume) is sublinear, with β = 0.51 for chloroplasts and β = 0.53 for mitochondria in our complied data (Figure 3G). Similar allometric scale effects are also found in many industrialized cities: the number of gasoline stations in response to city size (population) is β = 0.84 in China (Figure 3H) and 0.77 in United State of America [ 15 ] the number of wastewater treatment plants in response to city population are β = 0.77 on average across China, United State of America, France and Germany (Figure 3I). In contrast, an organism usually has a predetermined number of organs, indicating that there is no such scale effect in response to increased body size.

The metabolic flow and network characteristics of industrialized cities are also similar to those of eukaryotic cells. In eukaryotic cells, organelles are metabolic hotspots [ 33 ] similarly, enclosed systems are hotspots of biogeochemical metabolism in cities. The nitrogen fluxes passing through enclosed systems are up to three orders of magnitude higher on average than those in open systems (Figure S5a-c). Furthermore, the relationship between the rank of nitrogen pathways (P) and the nitrogen fluxes (F) in the metabolic networks of cities follows the power law F ∼ P β , and β = -3.5, indicating that the nitrogen fluxes in Shanghai City are centralized in a few hotspots, and that all of them are enclosed systems (Figure S5d). The nitrogen fluxes in cities have a steeper reduction (the exponent |β| > 3) than the food webs in natural ecosystem (|β| < 2 Figure S5d). This reveals that although the nitrogen fluxes (N fixation, N mineralization) in natural ecosystems are highly concentrated in root nodules, animal corpses, and faecal matter decomposition, [ 34 ] cities have a much higher concentration of nitrogen flux than ecosystems.

Similarities between enclosed industrial systems and organelles

The cluster analysis also demonstrates another closely related analogous pair (Figure 2A): enclosed systems are similar to organelles. The crucial feature of this pair is their enclosing structures. Many organelles, such as chloroplasts and mitochondria, have outer membranes to maintain their physical and chemical homeostasis similarly, enclosed systems are equipped with outer membranes (Figure 4A-C) to ensure the stability of internal physical and chemical conditions (Table S3). For example, air temperature variations within greenhouses, vertical farms and dairy feedlots are much smaller than ambient environmental variations (Figure 4D-G). With outer membranes, dairy feedlots can keep cooler or warmer and producing milk in extreme climate zones such as subtropical regions and cold-temperate areas that were previously unattainable. In addition, the outer membranes mitigate pollutant leakage, in much the same way as the membranes of organelles play a role in reducing the release of “intermediates” (such as ketones, metal ions) to the cytoplasm. More importantly, organelle membranes have a great number of small “facilities”, [ 35 ] such as channels, ion pumps, glycoproteins, ATPase and receptors, to regulate the physical and chemical conditions. Similarly, the outer membranes of enclosed industrial systems are increasingly fitted with small facilities such as sensors, monitors, air-conditioners, solar batteries, fans, and so on (Figure 4A-C) to improve the conditions for plants, animals and microorganisms. It stands to reason that the development of these fine-scale structures should greatly improve the functions of the enclosed systems.

The internal structures of enclosed systems have also acquired fine structures similar to organelles. For example, a vertical farm uses multi-layer planting to centralize cultivation with 20 to 100 tiers, and uses technology and automation to achieve high yields throughout the year. [ 12, 36 ] Similarly, a chloroplast has a multi-layer thylakoid structure that improves photosynthetic efficiency. [ 37 ] Like the fine structure formed by the inner membrane of a mitochondrion, [ 38 ] a cowshed has many stalls, hence efficiently using space and avoiding crowding by designing a trough configuration that gives each cow an equal chance of getting feed: these measures increase the feed utilization efficiency and dairy productivity (Figure S3). Yet, human design of such fine structures is in its infancy compared with organelles, suggesting exciting possibilities for further development.

Another similarity between enclosed systems and organelles lies in their information systems. The enclosed non-ecosystems (factories) only have human cultural information systems, such as technology, management and standards. However, the enclosed ecosystems have dual-information systems, that is, human cultural information and biological genetic information. For example, industrial dairy feedlots have biological information systems including the age, sex and genetic structures of cattle populations. [ 39 ] The information collected in enclosed ecosystems and non-ecosystems ensures their self-organization, including technology innovations and updates, in a manner similar to the semi-autonomous DNA genetic of mitochondria and chloroplasts. [ 40 ] For human information, a new field, “culturomics”, has recently emerged as an analogy to genomic research in biology. [ 41, 42 ] It has been found that word frequency changes in history also follows rules similar to biological genetics rules. For example, the process of naming a newborn is similar to the process of infinite allele replication of random genetic drift [ 43 ] the evolution of English grammar is influenced by random drift and selection, [ 44 ] and the evolutionary rate of language can be predicted by population genetic models. [ 45 ] Of course, the evolution of human culture information—whether at the city level or at the enclosed system level—has its own unique characteristics, and requires additional research.

A conceptual super-cell city model

The results of our analysis encouraged us to develop a new hypothesis: an industrialized city is analogous to a eukaryotic cell with respect to component composition, spatial pattern, and metabolic processes. We henceforth propose a conceptual super-cell city model in which an industrialized city is a “eukaryotic city” or a “eukarcity”, the urban area is “citynucleus”, the enclosed system is “organara”, and the rural ecosystems and open farmlands is “cityplasm” (Figure 5). The term “organara” is similar to “organelles” in etymology, for the suffix “-elle” in means small (via French, from Latin “ella”), while “-ara” means big (from Greek -ar / -ara / -aros). The processes in the super-cell city model mimic the biological processes of eukaryotic cells. Organaras provide major goods, such as food production corresponding to “synthesis” in organelles, and they provide services, such as garbage disposal (corresponding to “degradation” in organelles), corresponding to “decomposition” by lysosomes and catalases in eukaryotic cells. The emergence of organaras led to the transformation of traditional cities to eukarcities, just as organelles substantially transformed prokaryotic cells to eukaryotic cells. The “citynucleus” regulates the whole city and integrates urban and rural areas, as well as the number of organaras and their spatial distribution, through policies, science, technology, culture, markets and finance. The cityplasm provides regulating and supporting services such as maintaining air quality, water cycling, soil and biodiversity. Eukarcities and organaras also have many “grey” infrastructures (such as cement, metal, glass, and synthetic plastic polymers) (Table S3) that are non-living materials just as eukaryotic cells have non-living materials such as calcified microtubules, interior materials of some vacuoles, and vacuoles, [ 46 ] as well as collagen. This suggests that non-living components within a living system are a common feature.

The basic processes of a eukarcity couple the ecosystem-based loop with the organara-based loop (Figure 5). The flows of artificial goods, services and cultural information based on organaras are much greater than those based on cityplasm. Organaras interact with the city core frequently by providing goods and services for people and by receiving feedback from people. Organaras also exchange goods and services, as well as information with other organaras. A eukarcity interacts with other eukarcities and is also constrained by upper organizational level systems (such as province/state and nation). The constraints include policy, culture, economic and environmental standards proposed by provincial or national central governments.

The super-cell city model informs a new management approach

The new principles revealed by the super-cell city model also require new rules to adapt to these new systems, from ecosystem management to organara management. In view of the “super-cell city” model, the new management approach mainly includes three aspects:

(1) Improving organaras following the optimized principles of organelles in terms of structure and function. [ 38 ] First, more tightly closed ecosystems would be expected to increase efficiency and reduce the influence of climate, as well as reduce pollutant leakage. For example, air filters installed on the walls of livestock farms can prevent virus entry. [ 47 ] Of course, closed ecosystems may also bring risks, such as facilitating disease spread and concentrating soil pollution from fertilizer and pesticide use. [ 48 ] Moreover, further development of membrane structures by learning from organelle membranes that have complex structures and important functions [ 49-51 ] could also be envisaged. For example, air temperature sensors, monitors and air-conditioners on the outer membranes of greenhouse improve the production efficiency of vegetables. Internal structures also need to be advanced by learning from organelles such as mitochondria and chloroplasts in which the inner membrane is divided into distinct regions to constitute separate functional domains. [ 37, 38 ] Inspired by these traits, organaras can also be compartmentalized by internal membranes into specialized subunits to increase efficiency, such as the multi-layers of vertical farms. [ 12, 36 ] The outer membranes and internal structures of organaras are preliminary, and it can be expected that increasing the structural similarities between organaras and organelles will greatly improve organara supply capacity of goods and services.

(2) Optimizing the number of organaras following the scale effects in response to the population size in cities for rational cost and benefit, [ 5 ] which is similar to the number of organelles allocated in eukaryotic cells. [ 52 ] As part of this larger process, the optimization of spatial pattern of organaras by learning from organelles can improve yields and reduce pollution. For example, the intense industrialization of dairy feedlots increases the pollution intensity per unit area of land and increases ecological risk. [ 53 ] Building artificial wetlands near dairy feedlots can recycle and capture waste nutrients and greatly mitigate pollution. [ 29 ] By analysing optimization principles of organelles in eukaryotic cells and by diagnosing existing problems, city functional and spatial structure can be improved to reduce pollution and optimize the spatial distribution and functionality of future cities.

(3) Increasing supply efficiency and robustness by regulating the metabolic networks of organaras according to the high metabolic efficiency and robustness of eukaryotic cells. [ 54 ] The principle of bionic approaches is generally superior to “trial and error” methods [ 55 ] because they are guided by natural selection, and can reduce trial times while increasing efficiency.

There has been much evidence that supports the utility of the super-cell city model in urban design and management. One successful case occurred in Lake Taihu in southeast China, where over the past 30 years water quality deteriorated and then recovered as a result of increasing the number of organaras (Figure 6A-C). The lake had relied on its abundant wetlands for wastewater purification for over 4000 years. After the 1980s, however, industrial waste and farmland fertilization exceeded the purification capacities of the natural ecosystem, and water quality rapidly declined. In Wuxi city, which draws its drinking water from Taihu, a famous drinking water interruption event occurred in 2007, when the water became non-potable. Since the economic upturn (Figure 6D), the number of wastewater treatment plants in all cities around Lake Taihu increased from 5 in 1985 to 331 in 2014 (Figure 6E), and water quality improved even though the population continued to increase (Figure 6F). This case clearly illustrates that optimizing the number of decomposition organaras has been a crucially effective strategy for mitigating environmental pollutions in industrialized cities. Together with industrial non-ecosystems, the industrialization of ecosystems increases the supply of goods and services, and reduces the ecological footprint per unit product. [ 56 ] In China, greenhouse area is increasing while open farmland area is decreasing (Figure 6G). Industrial dairy feedlots are increasing while pasture areas are declining (Figure 6H). In contrast, forests and wetlands are continually being restored as economic development progresses (Figure 6I). These examples suggest that the information provided by the super-cell city model can guide the sustainable development of industrialized cities.

Despite the increasing role of organaras, the cityplasm is crucial in keeping the balance of energy fluxes, material, biological productivity and waste decomposition. The quality of the cityplasm, such as quality of air, water bodies, soil, and ecosystem health is mainly affected by organaras. For example, restaurants and dairy feedlots discharge wastewater causing water pollution. [ 29 ] Now the cityplasm is frequently monitored by people and the data collected are fed back to the citynucleus which then modifies the institutions and policies for optimizing the city through regulating organaras as units. A considerable area of pasture and farmland may be converted into organaras in many cities as populations grow and space becomes scarce and more expensive. However, a substantial portion of land will remain as open farmland and pasture, just as much of the space in most eukaryotic cells is still cytoplasm. [ 57 ] The cityplasm will continue to provide key ecosystem services and some goods in future eukarcities. For example, open farmlands, pastures and forests will continue to provide grain, fibre and raw materials [ 58, 59 ] ocean, forest and wetland provide clean air, water and biodiversity etc. Therefore, the super-cell city model requires serious collaborative management between natural ecosystems and organaras in order to realize city sustainability. Furthermore, the idea that “cities can save the planet” has enjoyed a recent boon, [ 60 ] and it could be realized though the cooperation of all cities worldwide.

Theoretical significance of the super-cell city model

Filling the gap in the model hierarchy of living systems by adding new living systems

A hierarchical living system model was built from the bio-macromolecular scale to the entire globe but left a sizable gap several orders of magnitude large between ecosystems (∼10 3 m in size) and the biosphere (∼10 8 m). [ 61 ] The super-organism hypothesis [ 15, 17 ] placed “urban systems” into the hierarchical model at a point that filled the gap between ecosystems and the biosphere (Figure S6). However, sustainable development requires the coupling of urban with rural areas, [ 60 ] , and a coupled urban-rural system (a city) averages ∼10 5 m in size and forms an arithmetic sequence, 10 3 m, 10 5 m and 10 8 m, between ecosystems and global scale (Figure S6). Based on the evidence that we have presented here, we suggest that the super-cell city model should replace the super-organism model. The emergence of organaras forms the basis for eukarcities just as organelles are the basis of eukaryotic cells, revealing that the shared features between cities and cells can be scaled up and down in the hierarchy of living systems (Figure S6). We further suggest that, following the origin of life, the emergence of eukaryotic life [ 62 ] and the appearance of humans, the emergence of the eukarcity is the latest evolutionary event.

Extending endosymbiosis theory from eukaryotic cells to the city level

The super-cell city model extends endosymbiosis theory from eukaryotic cells to the city level. According to endosymbiosis theory, eukaryotic cells were “big vacant cells” that assumed prokaryotic cells, such as cyanobacteria and spirochetes, to form a symbiotic fusion. [ 63 ] There is evidence that some organelles retained their own genes, which can self-duplicate and interact with genes in the nucleus to achieve semi-autonomous regulation. [ 40 ] For example, chloroplasts and mitochondria—besides being controlled by nuclear genes—also have their own DNA. [ 63 ] Inspired by the endosymbiosis theory, we hypothesize that the origin of the eukarcity is a symbiotic fusion of organaras (enclosed ecosystems and enclosed non-ecosystems) with pre-industrial traditional cities. Like organelles, some organaras are also semi-autonomous in that in addition to being controlled by the citynucleus, they also have their own “genetic information” for duplication and operation. [ 58 ] For example, wastewater treatment plants’ information systems include libraries, laboratories and offices that contain technology, records and management files (Figure S3). Cultural information is interpreted, copied, transmitted and modified, and constantly evolves. [ 64 ] The internal structure becomes complex and some organaras start to manifest multi-component nature in their structure: for example, greenhouses have bees that live in symbiosis with crops. In sum, the super-cell city model adopts endosymbiosis theory to explain the evolution of the industrialized city, and also provides a theoretical basis for city research, design and management.


Model of development reveals shapes of cell lineages and links to regeneration

Figure 1 (A): An example generative model showing an organism with N = 3 genes and two cell types. Circles represent all possible cell types. The organism is composed of cell types represented by white circles and does not contain the gray cell types. Binary strings written inside the circles represent the presence (1) or absence (0) of determinants in those cell types. (B) Schematic of “organismal development” in the model. All cell types synchronously undergo cell division, exchange signals, and respond to signals through gene regulation until reaching a steady state. (C) Lineage graph of the homeostatic organism in A. Credit: Institute for Basic Science

Various forms of complex multicellular organisms have evolved on Earth, ranging from simple Volvox carterii, which possess only two cell types, to humans, with more than 200 cell types. All originate from a single zygote, and their developmental processes depend on switch-like gene regulation. These processes have been studied in great detail within a few model organisms such as the worm C. elegans, and the fruit fly D. melanogaster. It is also known that the key molecules and mechanisms that are involved in the development of multicellular organisms are highly conserved across species.

What is also remarkable is that only a handful of molecules and mechanisms that go into the development of a multicellular organism can generate such a huge diversity of forms and complexity. Recently, researchers from the Center for Soft and Living Matter within the Institute for Basic Science investigated how this is possible using a simple mathematical model. Through this work, they sought to answer two seemingly opposite questions: what are the limits of diversity that can be generated through development, and what common features are shared among all multicellular organisms during their development.

Three processes are common to biological development in all multicellular organisms: cell division, cellular signaling, and gene regulation. As such, this study's model generated millions of these rules and explored them in an unbiased way. The mappings generated by the model represent how one cell type converts into another during the lifetime of the organism. Traditionally, previous cell type maps based on single-cell transcriptomics are biased to be tree-like, with stem cells sitting at the root of the tree, and increasingly more specialized cells appearing downstream along the branches of the tree. However, the cell-type maps produced by the new mathematical model were far from tree-like it was found that there were many cross-links between different branches of the cell types. These resulted in directed acyclic graphs, and tree lineages were found to be the least prevalent. This means that it is possible for multiple developmental routes to converge on the terminal cell type in the maps generated by the model.

Figure 2: (A) Lineage graph from real organisms. (B) Examples of unicellular, cyclic, chain, tree, and directed acyclic lineage graphs generated from the mathematical model. Credit: Institute for Basic Science

Surprisingly, it was also found that many organisms produced by the mathematical model were endowed with the ability to regenerate lost cells, without any selection imposed by the authors. When a single cell type is isolated from the adult organism, single cell could transform into and replenish all the other cell types. This ability to generate all the cells of the body is called pluripotency, and these cells granted the organisms in the model the ability of whole-body regeneration. Interestingly, most tree-type lineages contained few pluripotent cells, in comparison to other graph types.

While mammals, including humans, are especially bad at regenerating damaged parts, many animals such as worms and hydra, are exceptionally good at this ability. In fact, whole-body regeneration occurs widely across the multicellular animal tree of life, and therefore it has been hypothesized that whole-body regeneration could be an epiphenomenon of biological development itself. The fact that pluripotency occurred in this very simplified model suggests that this trait is indeed likely to emerge due to the process of development itself, and no special extra components are required to put it in place.

Figure 3: (A) Schematics of regeneration trajectories from the root and non-root pluripotent cells. (B) Proportion of pluripotent and non-pluripotent cells in organisms with different cell lineage graph types. Credit: Institute for Basic Science

In addition to these results, it is anticipated that the framework of this model can be used to study many more aspects of development. This generative model is simple and modular, and it can be easily expanded to explore important processes which were not included in the present study, such as the effect of the spatial arrangement of cells and the effect of cell death. The researchers further described some possible real-life experiments to test some of the predictions made by their mathematical model. It is hoped that the framework of this model will prove useful for uncovering new features of development, which may have a wide range of implications in developmental biology and regenerative medicine.


A unicellular organism is an organism that is made of up of a single cell and the life processes such as reproduction, feeding, digestion, and excretion occur in one single cell. There are some examples of unicellular organisms like Amoeba, bacteria, and plankton. These unicellular organisms are typical microscopic which cannot be seen with the naked eyes. Unicellular organisms are of different types including bacteria, protozoa, and unicellular fungi. Asexual reproduction is famous among unicellular organisms. To make you more understanding, below are the details of types of bacteria.

This organism is unique because it can be both unicellular and multicellular. To fit this category, a cell must have membrane-bound organelles. These cells have a nucleus that consists of DNA, mitochondria for energy and other organelles to carry out the cell functions.

On the other hand, prokaryote consists of a single cell with no membrane-bound organelles. This organism has to adopt other ways of carrying out reproduction, feeding and waste excretion.

The structure of bacteria is too tiny and every bacterial cell id different from an animal and plant cell. The size of bacterial cell is about micrometers across. Even bacteria are of a single cell but it consists of different parts like Chromosomal DNA, Plasmid DNA, Cell Wall, Cell Membrane, and Flagellum.

It is a type of unicellular organism that lives in water or in damp places. Protozoa have adaption that it behaves like an animal a bit. It produces pseudopodia that let it move to surround food and let it take inside the cell. Once the process of taking food inside is done, contractile vacuoles appear inside the cell then combine with the surface to remove waste.

Yeast is another type of unicellular fungi. It may be possible you are familiar from seeing mushrooms and toadstools. Yeast has cell walls like plant cells and no chloroplasts that mean sugar is the main nutrition for them as they are not able to make their own food by photosynthesis.

The cyanobacterium is also known as Blue-Green Algae (BGA). It is the process of characteristics of both bacteria and algae. It resembles algae as photosynthesis for food production whereas the prokaryotic nature of BGA forms it similar to bacteria. Other than this, diatoms, euglena, chlorella, and Chlamydomonas includes in the example of cyanobacteria.

There are many unicellular organisms that live in extreme environments like hot springs, thermal ocean vents, polar ice, and frozen tundra. These unicellular organisms are called extremophiles. This unicellular organism is specially adapted to live in places where multicellular organisms cannot survive because they are resistant to extremes of temperature or pH. Although, not every unicellular organism are extremophiles because many live under the same range of living condition as multicellular organisms, but still necessary things to all life forms on earth. For instance, phytoplankton is a type of unicellular that lives in the ocean.

A multicellular organism, tissue or organ is organisms that are made up of many cells. Animals, plants, and fungi are multicellular organisms. Multicellular organisms are much bigger in size and are very complex and intricate in their composition along with structure. Human beings, animals, plants insects are the example of a multicellular organism.


Multicellular organism

Our editors will review what you’ve submitted and determine whether to revise the article.

Multicellular organism, an organism composed of many cells, which are to varying degrees integrated and independent. The development of multicellular organisms is accompanied by cellular specialization and division of labour cells become efficient in one process and are dependent upon other cells for the necessities of life.

Specialization in single-celled organisms exists at the subcellular level i.e., the basic functions that are divided among the cells, tissues, and organs of the multicellular organism are collected within one cell. Unicellular organisms are sometimes grouped together and classified as the kingdom Protista. See protist.

The Editors of Encyclopaedia Britannica This article was most recently revised and updated by Adam Augustyn, Managing Editor, Reference Content.