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Difference between Engineering and Bio-processing
Physics of Cell Division
Spatial Cue in Cell Specialization
Symmetry Breaking and Body Plan, (2022, 2023 Updates)
Segmentation, Somitogenesis, and Hox Genes
Chemical Messages and Organogenesis
Cell Movement and Cell Migration
Vasculogenesis, Heart Tube Formation, and Angiogenesis
Development of the Organs
Determination of Sex
Development of Limbs
Formation of the Nervous System
2024 Update (curtesy of ChatGPT)

In his 2014 book "Life Unfolding", Jamie A. Davies explains the development of life from a single cell to a fully grown human via the mechanism of "self-organization". Following is a summary of the explanation.

Difference between Engineering and Bio-processing

Engineering vs Bio-processing While engineering relies on a blueprint, architect, engineer and construction workers - all of them outside the finished product and involving human intelligence; bio-processing includes self-assembly of components (such as protein, RNA, DNA) via interaction between residual charges and adoptive self-organization in response to external circumstances. It's a continuous process that would have problem with disruption, rearrangement or piecemeal implementation. The process occurs naturally without any cue from a human elaboration. Figure 01 illustrates the different processes pictorially.

Figure 01 Engineering vs Bio-processing


Physics of Cell Division

In multicelluar organisms, the egg is usually more than 10 times larger than normal cell. The initial stage of cell replication can therefore occur entirely within itself up to 32 cells. This phase is called cleavage. The division mechanism depends mainly on a special property of the microtubules which exist in one of two states - a fresh stage containing special "fresh molecule" at the end from which the tubule extends, and a stale state without the fresh molecules resulting in its gradual decimation. These tubules emanate from the centrosomes (composed of 2 orothgonally arranged centrioles, see Figure 02) which define the center of the normal cell or the opposite ends during cell division. Such remarkable features is caused by the imbalance of the number of long and short microtubules; the sum of the reaction forces create a net push toward the center when their far-ends hit the cell membrane (Figure 03, model a). The fundamental mechanism is just the physics of action and reaction from Newtonian mechanics in addition to the property of chemical bonds. In case of cell division, the same mechanism is involved.
Microtubule Microtubules in Action Both the centrosome and chromosome are divided into mother-daughter pair. The microtubules bind to a special site in the chromosomes and pull them apart (Figure 02). The binding of microtubules to the chromsomes and fresh molecules uses a trial and error approach in finding the right match. Therefore, it is expensive in terms of energy, but it is automatic. It seems to be very complicated, actually it is the feed back behavior of each individual component that gives rise to the complex from the simple. This process of first cell division is common to all cell replications by the name of mitosis. Meiosis involves further processing to produce gametes. See "Inner World of the Cell" for more information about "microtubule" and "molecular motors".

Figure 02 Microtubule [view large image]

Figure 03 Microtubules in Action [view large image]


Spatial Cue in Cell Specialization

The first 32 cells in the egg requires only the processing of division, there is no need to turn on the genes for additional tasks. The situation changes as soon as the egg runs out of space and material. the system has to acquire room and nutrients to grow. The necessary information is provided in the form of geometry. The genes are activated in those cells (about 1/6 of the total) facing clear space. These layer of very first specialized cells (together called tissue) is the trophectoderm, which pumps in fluid and forms a capsule. The clump of
Spatial Cue inner cell mass (ICM) moves to another end (Figure 04). The layer of ICM facing the fluid now receives another geometric cue to specialize into hypoblast cells, which spread around to form the yolk sac (providing nourishment and also functioning as internal circulation). The remaining ICM collaspes toward the hypoblast layer to form the epiblast, which is destinated to be the base of next life (Figure 04 which also shows some of the specialized cells from the stem cell). The process also creates the amniotic cavity, where fetal development occurs (see chicken egg in which the yolk sac and amnotic cavity are ready-made, and mammalian fetus which is the main subject of interest here).

Figure 04 Spatial Cue
[view large image]


Symmetry Breaking and Body Plan, (2022, 2023 Updates)

The initial embryonic cells has 3-D spherical symmetry until it reaches the 32 cells limit. The subsequent specialization reduces it to 2-D circular symmetry up to about 13 days (after fertilization). It is reduced further to 1-D axial symmetry when the body plan lays down the head and tail (posterior in human). Symmetry finally disappears altogether with the development of organs inside the body. In the parlance of "information", the sequence of development amounts to the acquisition of more and more information with the progression of time. It also means that the
Body Plan Body PLan 2 Germ Layers system is evolved further and further away from equilibrium in a state which requires energy infusion to sustain. It is not clear what triggers the expression of the genes that leads to all these changes. But the processes are well documented. Figures 05a and 05b depict the steps toward the laying down of the notochord from the two layers of epiblast and hypoblast (blast = form, epi = over, hypo = under). Figure 06 shows the body plan based on the three germ layers.

Figure 05a Schematic Body Plan Development [view large image]

Figure 05b Body Plan

Figure 06 Germ Layers

Followings are some elaborations on the 7 steps.

  1. The first change takes place in the hypoblast. The cells in its middle start to express a DNA-binding protein called Hex. Thes cells then move over to a point at the rim. It is not clear why they choose this particular point to congregate.

  2. The entire layer of the epiblast in the meantime receives signal to make structures characteristic of the posterior end of the body. While the Hex-expressing cells secrete proteins to suppress the formation of the posterior features.

  3. As a result, only those cells at the other end of the epiblast can escape the inhibition (because they are further away), and start making the tail end of the primitive streak.

  4. The center of the streak dips down to form a flat depression, to which other cells converge. This node grows clockwise rotating cilia to break the mirror symmetry inside the body.

  5. The converging cells have the cell-cell adhesion weaken and dive down one by one to the hypoblast. They push away the old residence of hypoblast to form the endoderm (inner skin).

  6. The cells that drop through later remain only loosely associated with one another to form the mesoderm (middle skin). Cells that never manage to drop throught and remain in the top layer (the epiblast) become the ectoderm (outer skin).

  7. Middle of the endoderm layer rises up, invaginates and then detaches to form the notochord, which is used to stiffen the body in lower vertebrates. It is replaced by the bony skeleton in more advanced species. However, it is important in secreting proteins to organize the embryo. Eventually, it breaks up and is used to make inter-vertebral discs.

  8. [2023 Update]

    The subject of "Embryonic Model" (embryo made from pluripotent stem cell) suddenly become very popular in the middle of 2023. Followings are some of the news articles and scientific papers related to the subject :

    1. "Breakthroughs in race to create lab models of human embryos raise hopes and concerns"; CNN, October 26, 2023.
    2. "Stem cells used to model a two-week-old human embryo"; Nature, October 17, 2023.
    3. "Complete human day 14 post-implantation embryo models from naive ES cells"; Nature, September 06, 2023.
    4. "Self-patterning of human stem cells into post-implantation lineages"; Nature, June 27, 2023.
    5. "Pluripotent stem cell-derived model of the post-implantation human embryo"; Nature, June 27, 2023.
    6. "Scientists report creation of first human synthetic model embryos"; CNN, June 15, 2023
    7. "What are 'synthetic embryos' and why are scientists making them?"; New Scientist, June 15, 2023.

    Embryo Day 4-6 Embryo Day 6-13 Embryo Day 14 SEM Illustrations

    Figure 05d Embryo Day 4-6

    Figure 05e Embryo Day 6-13

    Figure 05f Embryo Day 14 [view large image]

    Figure 05g Immunofluorescence Images of SEM

    Figure 05g shows Immunofluorescence Images from Refs. 3, 4, and 5. Immunofluorescence gives microscopic high lighters to specific molecules in cells. It's a technique used in biology to visualize the location of proteins or other macro-molecules in a sample. Antibodies labeled with fluorescent dyes are used to bind to specific target molecules, and when exposed to light of a particular wavelength, they emit a colored glow. This allows researchers to see where those molecules are within a cell or tissue under a microscope. A corresponding image in schematic drawing can be found in Ref. 2.

    [End of 2023 Update]

    [2022 Update]

  9. By 2022, advanced technology has enabled determination of the type of cell (Pluripotent Stem Cells in this case) by examining the specific of various RNA transcriptions. As shown in Figure 05c, the specimen is a male human embryo that was estimated to be
    Embryo at 16-19 Days 16–19 days post-fertilization and that was undergoing a developmental process called gastrulation. During this process, a layer of cells called the epiblast gives rise to three 'germ' layers (the ectoderm, mesoderm and endoderm), establishing the body plan. At this stage, the embryo contains two cavities: a cavity formed by the amniotic ectoderm overlying the embryonic disc, and the yolk sac (surrounded by the extra-embryonic mesoderm) on the other side of the disc. The gastrulating embryo is dissected (by consent of its owner undergoing termination of her pregnancy) into three parts, a statistical analysis is used to ‘group’ the dissociated cells according to the similarity of their gene-expression profiles. Using this approach, the cell type that make up the various embryonic structures are identified, as well as the primitive haematopoietic cells that give rise to a rudimentary blood system, and Primordial Germ Cells (PGCs - future sperm cells; not shown in Figure 05c); but shown below by a mammalian equivalence :

    Figure 05c Embryo at 16-19 Days

    See original article : "A peek into the black box of human embryology", also
    "New guidelines for embryo and stem cell research", 2021 - no more 14-day limit?

    [End of 2022 Update]



Neural Tube Gut Tube The vertebrates have two important tubing inside the body. The neural tube that contains the nerves running from the brain to the tail end, and the gut tube that retrieves nutrient from food and repels the waste at the end. Their formation is achieved either from the local change of individual cell that propagates via a continuous mechanical network or just by the growth of the body. It is the microfilaments that helps to buckle the central axis of the ectoderm to form the neural tube. While the gut tube is formed by the overgrown of the endoderm. These processes are shown in Figures 07 and 08. A brief description is provided in the followings.

Figure 07 Neural Tube [view large image]

Figure 08 Gut Tube
[view large image]

    Neural Tube Formation (Figure 07) :

  1. At about 17 days after fertilization, signals from the notochord induce a form of curvature on the line of ectoderm cells immediately above as shown in Figure 07(1). The folding is caused by changing the cells (in the middle) into wedge-shaped pointing up. Since the cells are linked rigidly together by microfilaments (see Figure 07 insert at the lower left) the "chain reaction" makes the cells further away to become wedge-shaped in the opposite direction.

  2. The crests in the folding are pushed toward each others due to cell proliferation.

  3. The two sides of the folding fused to make a neural tube in the middle. At this stage there is nothing inside the tube - it is empty.

  4. The neural tube separates completely from the ectoderm layer that flanks it. The space in between is occupied by the neural crest cells. These cells are transient, multipotent, migratory cell population unique to vertebrates and gives rise to a diverse cell lineage that produces cartilage, bone, smooth muscle, and various types of nervous cells.
    Gut Tube Formation (Figure 08) :

  1. At about day 16 after fertilization, the endoderm is a flat plate at the bottom layer of the embryo, facing the open space of the yolk sac. See top view in Figure 07(1) and sagittal view in Figure 08(1).

  2. Elongation of the body pulls on the ends of the endoderm, causing them to overshoot the entrance to the yolk sac and to be drawn out to make short tube-like extensions into the growing head and tail ends of the embryo.

  3. The extensions become even longer as the embryo keeps growing.

  4. The opening to the yolk sac progressively becomes insignificaent. This branch is eventually closed off, leaving the gut as a tube fully enclosed within the body. The insert at the lower left of Figure 08 shows the location of the various organs corresponding to different section of the gut tube.


Segmentation, Somitogenesis, and Hox Genes


Chemical Messages and Organogenesis

Organogenesis A very important function of cells is the ability to secrete proteins to deliver chemical messages and to perform a task upon receiving such message, e.g., generating another chemical message or changing to another cell type. Since by the laws of physics, message from such small source as a typical cell (with a dimension about 0.001 cm) cannot go very far (with range ~ 0.005 cm), it is essentially a local action between adjacent blocks of cells. But the same kind of mechanism can be used repeatedly all over, the concentration gradient can also be used to induce different actions according to the amount. In organogenesis, different chemical message and different concentration would produce different type of cell or tissue as demonstrated in the following example in patterning the neural tube and somite to neuron, bone, muscle, and skin.

Figure 14 Organogenesis
[view large image]

  1. The notochord just below the ventral surface of the neural tube secrete a protein callec Sonic Hedgehog (SHH). The law of diffusion designates a higher concentration of SHH at the bottom of the neural tube (now called floorplate, which is now induced to produce SHH as well) and gradually fades away further up. At high concentration of SHH, the neural tube cells is committed to make motor neurons.

  2. The lower concentration of SHH further up the dorsal region triggers a reaction in those neural tube cells to commit to another type of neurons (the interneurons).

  3. Meanwhile the ectoderm immediately above the neural tube sends out signals by the names of BMP4 and WNT. These proteins with SHH and other activated genes conspires together in the formation of muscle, skin and bone (from the sclerotome cells which form the vertebral column) as shown in Figure 14.


Cell Movement and Cell Migration

Cell Movement Cell Movement - Normally, cells are tightly packed with adhesive protein E-cadherin. Cell migration starts by lowering the E-cadherin level in the EMT (epithelial-mesenchymal transition) process by which epithelial cells lose their cell polarity and cell-cell adhesion, and gain migratory and invasive properties to become mesenchymal stem cells; these are multipotent stromal cells that can differentiate into a variety of cell types. The reverse process, MET (Mesenchymal-epithelial transition) are critical for development of many tissues and organs in the developing embryo, and numerous embryonic events such as those in gastrulation (Figuge 15, left panel). EMT has also been shown to occur in wound healing, in organ fibrosis and in the initiation of metastasis for cancer progression.

Figure 15 Cell Movement [view large image]

    Once the cells are released from the packed arrangement, it can move by a mechanism similar to the cell division with unidirectional growth and the addition of anchors to absorb the reaction. The cells do not float in free space as portrayed in some illustrations. The process is outlined in the 4 steps below (also see Fiuge 15, right panel) :

  1. The cell movement is generated by the extension of the actin (a kind of molecular track). It grow only such protein filaments pointing to one direction. This particular region is populated by the lamellipodia ("thin sheet"-"foot") with a leading edge called filopdia (Figure 15, right panel).

  2. New adhesion complexes, which hold on to the substratum, are generated by the filopdia and left behind as the leading points move forward. The complexes are strongest just behind the filopdia and become progressively weaker further back.

  3. The actins together with the walking myosins at the bottom produce a forward pull.

  4. The pull is getting stronger as the active actins advance further and futher until it overcomes the adhesion at the rear, so the tail end let go and the cell as a whole moves forward.

Cell Migration - The mesenchymal cells do not move aimlessly. They are guided to a specific location to become a particular cell type. The navigation is provided by matching the receptors on the cell surface with the marker proteins on the substratum. This is something
Cell Migration like the GPS (Global Positioning System), which guides the vehicle through a network of streets to arrive at its destination. The neural crest cells migration to form various cell types is a good example to illustrate the process. Figure 16 right panel shows a few migration routes, more specific cell types or organs are displayed in the left panel, also see Figure 07.

Figure 16 Cell Migration
[view large image]

    There are many waves of migration of the neural crest cells, the following cases are just a few of them :

  1. The first wave of the migrating neural crest cells make receptors for the attractive surface proteins Laminin and Fibronectin (Figure 16L). They also carry another receptors, which is repulsive to the Ephrin molecules produced by the somite cells. Thus, the migrating cells can only move through the routes marked in green color (Figure 16L).

  2. Those cells attractive to the Laminin and Fibronectin settle down at the site near the somite and become the dorsal root ganglion.

  3. The other routes lead the cells to location next to the aorta. The tissues in there secrete a protein called Neuregulin, which matches yet another kind of receptor in the migrating cells. They are prevented to go further by strongly repulsive molecules down stream and have to stay there. Then the aorta secretes a protein that causes these neural crest cells to become the sympathetic ganglion.

  4. After a while, a third population of neural crest cells emerges from the neural tube. They still make receptors for Laminin and Fibronectin, but the receptors for Ephrin are now turned into attractive. Such combination forces them to stay just under the embryo's ectoderm to become the pigment cells of the skin.

The very complicated process of cell migration is illustrated above on only the neural crest cells of the main trunk. They can arise in the neck, head, and tail regions and will commit to different fates. These include making the nervous system of the gut, bony structures of the face, pigment cells of the iris, parts of the ear, parts of the heart, ... etc. All these migrating cells follow different routes and carry different receptors, but the organization principle is the same throughout.


Vasculogenesis, Heart Tube Formation, and Angiogenesis

The initial mass of the embryo is small enought (with few tens of cells) so that delivery of oxygen and nutrient by thermal motion is sufficient. About 17 days after fertilization, the embryo requires a more efficient mean to obtain the necessary supply. The new system is composed of a network of vessels and a rudimentary pump - the heart tube. The formation of this system can be separated into three steps as explained in the followings.

Vasculogenesis - The process starts from the heamangioblasts in the mesoderm (Figure 17a) and appear as blood islands at the edge of the embryo. These are multipotent cells activated by signals from the mesoderm and endoderm below them and can form into different components in the circulation system. Then the somites send out signalling proteins to urge these cells to migrate to the mid-line
Vasculogenesis (Figure 17b). The cells aggregate into two solid rods on each side. The rods become hollowed out later by cell-suicide. The SHH proteins secreted by the notochord prevent them from merging into one (Figure 17c). The process is applicable to the formation of both the arteries and veins. The only difference is that the veins has larger bore and thinner wall; the concentration gradient of the SHH proteins is responsible for the two types. Blood cells are made from some of the cells in the wall of the aorta on receiving signals from gut tube and neural tube. The signallings are combined in such a way that not all the cells in the wall are converted into blood cells. The actual blood cells are made in the newly developed liver.

Figure 17 Vasculogenesis
[view large image]

Heart Tube Formation - The process can be described in three steps :

Circulation System Circulation System
  1. The same vasculogenesis occurs in the head area.

  2. As shown in Figure 08, elongation of the embryo wraps its head downward. The two aortae facing the bottom merge into one during such manoeuvring.

  3. A heart tube has formed under the gut tube with 2 dorsal aortae and two veins joining on the other end to form a complete circuit.

Figure 18 Heart Tube
[view large image]

Figure 19 Circulation, Embryonic

Figure 18 shows the end result of the heart tube formation process, and Figure 19 depicts the complete embryonic circulation system.

The heart muscle cells have the special property that they can twitch all by themselves. When they join together, they communicate electrically so that their individual twitching is synchronized to beat in unison (see heart example in "Bio-electricity").

Angiogenesis (vessel-creation) - It is the process through which new blood vessels form from pre-existing ones. There are three ways to branch out as shown in Figure 20. At maturation, the pericytes (a kind of contractile cells) wrap around the vessels to perform many important functions. Arteriogenesis refers to an increase in the diameter of existing arterial vessels in cases such as narrowing or blocking
Angiogenesis of the vessel. The generation of capillaries is vital to the health of the embryo as well as to all adults. Whenever a cell is in need of oxygen or nutrient, it sends out a signal for help. Capillaries will grow to such location to deliver the supply. The capillary wall is a one-layer endothelium that allows lipophilic (oil loving), hydrophilic (water loving) molecules and gas to pass through without the need for special transport mechanisms. It allows bidirectional diffusion depending on osmotic gradients (diffusion of fluids through membranes or porous partitions). The capillaries can also repair themselves by the process of angiogenesis. The distressed cell eventually dies off if no capillaries come to its rescue.

Figure 20 Angiogenesis
[view large image]


Development of the Organs

The internal organs of the trunk can be divided into three main classes, according to its association with different tubular system. Theses classes include the heart and the vesseled system mentioned in the previous section. The other two related to the gut tube and the mesoderm will be discussed in the followings.

Gut Tube Organs - The organs attached to the gut tube include the thyroid, lungs, liver, pancreas, and gall bladder (Figure 21). They all develop as branches of the gut tube in a similar way as those branches from the arterial walls. Initial emergence of the bud from the gut
Gut Tube Organs Mesoderm Organs tube is controlled by signals coming from the surrounding, mesoderm-derived cells. For example, the lung buds start to form by pushing out from the gut tube. In fish, this gives rise to the swim bladder. In mammals it is heavily modified : it branches repeatedly to form a large tree-like structure. They eventually become the airways of the lungs. In all cases, it is the endoderm-derived cells, which make the tubes in the organ, while the mesoderm-derived cells compose into the rest of the solid tissue. Figure 21 also shows the beginning days for the development of the organs.

Figure 21 Gut Organs

Figure 22 Mesoderm Organs
[view large image]

Mesoderm Organs - The spleen, gonads, three pairs of kidneys (only one pair remains in adult), uterus, and variour tubes concerned with the plumbing of the urinary and reproductive systems are entirely derived from the mesoderm beyond the outer edges of the somites. As shown in Figure 22 in consecutive frames, the Wolffian duct generates three different pairs of kidney-like structures, which wither away progressively until only the real one left behind in the end. The Mullerian duct is responsible for generating the male and female reproductive systems. Lower animals have only one opening, the cloaca, at the end to excrete both urine and feces; while most placental mammals possess two or three separate orifices for evacuation.


Determination of Sex

Sex is necessary to refresh the genes. It is the germ cells that provide the raw material for reproduction. The germ line becomes identifiable when a group of around 50 cells is set aside in the epiblast at the posterior end of the primitive streak (Figure 08), just before gastrulation at about 13 days after fertilization. They proliferate to a population of thousands and crawl to the developing gonads (Figure 22), where they will
Sex Determination Difference of Genitals undergo the process of meiosis to become sperms (cells in haploid state with either X or Y chromosome) or eggs (cells in haploid state with only X chromosome) depending on whether further development is following the male or female path (Figure 23). In boys, meiosis does not begin until puberty but in girls all of the germ line cells begin meiosis almost as soon as the overy begins developing. Every egg that a woman can ever have is already in meiosis when she is born. The determination of sex is governed by the gonad, which begins to make a protein called WT1 at about day 42.

Figure 23 Sex Determination
[view large image]

Figure 24 Genitals, Difference

See "Sex and Death" for a philosophical discourse on mortal life.

    The process for the determination of sex can be separated into three steps or levels from the expression of triggering proteins, to the formation of the internal structures, then the different external appearances between male and female :

  1. Molecular Cascade - Release of the WT1 proteins triggers two difference pathways (Figure 23). If the SRY proteins secreted by the Y chromosome are presence, it induces the secretion of SOX9 (with the corresponding gene in chromosome 17), which opens the pathway to maleness. Otherwise, WT1 produces WNT4 leading to femaleness. SOX9 also cleans up any WNT4 residuals to make sure there is no mixture of maleness and femaleness - a transsexual. Obviously, the mechanism is not foolproof as about 3.5% of adults in the United States are identified as lesbian, gay, or bisexual.

  2. Internal Re-organization - The chemical avalanche of either pathway modifies the Wolffian and Mullerian ducts (Figure 22) to become male or female reproductive apparatus. The end result of the process is summarized in Table 01 below.

  3. External Appearance - The development goes on to make male or female external genital as shown in Figure 24. The difference in appearance actually is based on the same starting tissues. All the three openings were developed from the cloaca (Figure 22) in the beginning. And then, there is the secondary sex characteristic, which is not directly related to reproduction; the traits are believed to be the product of sexual selection. Table 01 also shows some of those traits in human.
Substance (level) Male Female
Sex Chromosome Pair (1) XY XX
SRY Protein (1) Yes No
WNT4 Protein (1) No Yes
Mullerian Duct (2) Eliminated Develops to oviducts, uterus, upper vagina
Wolffian Duct (2) Becomes sperm transport duct Eliminated
Genital (3) Penis and scrotum Vagina and labia
Mammary Glands (3) Vestiged Presence
Bones and Muscles (3) Larger Smaller
Hair (3) More Less

Table 01 Differences between Maleness and Femaleness


Development of Limbs

Development of Limbs The two pairs of limbs start out as small projections underneath the ectoderm that covers the outside of the embryo. The proliferation is driving by signals from the mesoderm of the trunk. They switch on the production of the WNT proteins, which in turn induce the FGF signalling family. The FGF is the driving force to move the limb bud called "Progress Zone" outward (Figure 25a). Further development of the limb is explained by two different models as outlined below.

Figure 25 Development of Limbs [view large image]

Both models predict that only the upper arm will form if the progress zone or limb tip is removed (Figure 25d). Observations reveal that the process is more complicated than these simple minded models. There could be more signalling proteins involved. Abnormal growth of limbs is not limited to the temptation of the progress zone. Disruption of the capillaries to supply oxygen and nutrient to the growing cells could also arrest the formation of a proper limb. The adverse effect was demonstrated between 1958 and 1961 by babies with deformed limbs when their mothers took the tranquillizer thalidomide which inhibits outgrowth of new and immature blood vessels.


Formation of the Nervous System

The next phase after the formation of the neural tube at day 23 is dominated by cell proliferation. The cells navigate using the types of mechanism mentioned earlier in "Cell Movement and Cell Migration". As we have learned recently in the 2010's in the concept of "Connectome", the most important aspect of our mental capacity comes from the inter-connection of the neural cells. The task is achieved by sending out fine appendages from the cell body to seek out each other. The shorter ones are the dendrites for receiving bio-electrical signals while the very long axon is for transmitting sensory messages or relaying central commands. The axon can extend to nearly a meter long by
Growth Cone Meningeal Layers crawling with the growth cone (Figure 26). The direction of growth is specified by the adhesion of the substratum. The branching tends to follow a stickier path. Other guidance cues work by signalling to the molecular machinery that assembles the growth cone's leading edge. Since the movement of these migrating cells excesses the growth of the embryo, they all piled up at the wall to become the meningeal layers of the CNS (Figure 27).

Figure 26 Growth Cone
[view large image]

Figure 27 Meninges [view large image]

The brain grows at the head end of the neural tube with the development of three bulges - the prosencephalon (future forebrain), mesencephalon (midbrain), and rhombencephalon (hindbrain) as shown in Figure 28 at 4 weeks. Further development at 6 weeks shows more features (identified by numerals : 1. olfactory 2. optic 3. oculomotor 4. trochlear 5. trigeminal sensory 6. trigeminal motor 7. abducens 8. facial 9. vestibulocochlear 10. glossopharyngeal 11. vagus 12. cranial accessory 13. spinal accessory 14. hypoglossal 15. cervical I, II, III and IV); diencephalon refers to the posterior forebrain, and telencephalon the cerebrum at maturation. In simple vertebrate, such as fish, the brain remains as a straight tube with swellings. In mamals, and especially in humans, the process of formation involves bending and folding, and then go on to become furrowed
Embryo Brain Brain Development to cram even more surface area into the available space (Figure 29). The process follows the basic principle of chemical signalling over and over, getting more and more complicated. This is the physical base of mentality provided by nature, the owner of such system has much to learn to become a viable being after birth (see "Nervous System" for the mature version of CNS, PNS, ANS, ENS, etc.).

Figure 28 Embryo Brain at 4 and 6 Weeks
[view large image]

Figure 29 Development, Brain [view large image]

Similar to the wiring of the neurons, the immune system is developed after birth. The womb is sterile, the baby encounters the bacteria the very
Asthma first time at the birth canal. Delivery by caesarean section delays the contact until it is handled by the mother (see "Immune System" for the different forms of immunity). Since the adaptive immune system is acquired, the practice of good hygiene in developed countries has been accompanied by an increase in the incidence of diseases such as asthma, which reflect an immune system out of balance and inclined to be excited by harmless substances such as dust, animal hair, and pollen (Figure 30).

Figure 30 Asthma
[view large image]

BTW, It is found that infants delivered by cesarean section exhibit a distinct microbiome (the micro-ecosystems on and in our body) more colosely resembles the composition of the mother's skin.

It is not possible to describe the detail mechanism of growth as the embryo organizes itself into a very complicated system few weeks after fertilization. The two videos from YouTube below serve as supplements to the text in this topic. More details of the early embryonic development in the first 50 days can be found in the "Time Line".

Early Embryo Development General Embryo Development

Video 01 Early Development,
Embryonic [view video]

Video 02 General Development,
Embryonic [view video]

Final Step Finally, the the placenta and umbilical cord have delivered from the womb (Figure 31). When the umbilical cord is not cut, it naturally seals off about an hour after birth. The umbilical cord and attached placenta will fully detach from the baby anywhere from 2 to 10 days after birth. Modern practice ties off the cord tightly with heavy string after the cord has stopped pulsating. A clean shoelace, or sterile tape can be used about 4 inches from the baby; tie it again 2 to 4 inches from the first string, then cut between the two ties. It leaves a short piece of it, called a stump, attached to baby's belly button. The stump will naturally dry up and fall off within a few weeks after birth.

Figure 31 Disposal of Umbilical Cord


2024 Update (curtesy of ChatGPT)

Figure 32 Embryonic Development

    In spite of what has been said and done (about embryo) in previous sections, a "conversation" with ChatGPT provides a more comprehensive explanation into the subject. In very simple term, the vanilla version of ChatGPT consists of a database containing lot of information + a language model for input / output operation. The followings are mostly its views on various stages of embryonic development (in italic). Figure 32 helps to visualize the verbal comments.

    But firstly, the three 2024 research's insights below would not be included in ChatGPT's January 2022 limitation of its data collection.

  1. Updates from 2024 Researches (on very early stage of embryonic development) :

    Very Early Embryo The May 13, 2024 study on "Human embryos embrace asymmetry to form the body" shows that most of the human body forms from only one of the 2 cells in conception (see Figures 33,a, and 32 at "starting"). The research discovers that one of the two cells would become a fetus that divided faster later. The other one divides more slowly tended to turn into the yolk sac regressed eventually.

    Figure 33 Very Early Embryo [view large image]

    Another research paper published a month earlier on "Colonies of single-celled creatures could explain how embryos evolved" discovers the single-celled organism, which could develop into multicellular structures with remarkable similarities to embryos.
    It seems to represent the stage of multicellular evolution earlier than 650 MYA before the development of troph-ectoderm (nourishing - outer layer, see Figures 33,b and 32). The zona pellucida (ZP), which is a relatively thick extracellular matrix (ECM) that surrounds all mammalian oocytes, eggs, and preimplantation embryos, from monotremes that lay eggs to placental mammals, is also absent.

    Surface Tension in Cleavage The research briefing article "Measuring the forces that shape early human embryos" reports that adequate surface tension is crucial for further embryonic development after the cleavage stage. Figure 34,a shows the degree of compaction as the C-M surface tension increase while the C-C's almost

    Figure 34 Surface Tension in Cleavage

    remains unchanged. The series of picutres on the top shows the change of compaction, i.e., C-M surface tension (in hours) during the experiment using a tiny glass tube (see top row in Figure 34,a).

    The physics of surface tension is explained graphically in Figure 34,b, which shows the inward force produced by the absence of interaction with the medium at the surface. Ultimately, the changing surface tension is related to chemistry via the change in organic substances within the cell (the molecules in the diagram should be replaced by the organic substances in the cell).

    Here's a list of the organic substances within the cell, courtesy of ChatGPT (in Italic) :

    Cells are composed of a variety of organic substances that are essential for their structure, function, and overall survival. The main categories of organic molecules found within cells include (also see pictorial illustration below and "ATP - Energy Supplier for Life") :

    1. Carbohydrates:
    " Monosaccharides: Simple sugars like glucose and fructose.
    " Disaccharides: Composed of two monosaccharides, such as sucrose (table sugar) and lactose (milk sugar).
    " Polysaccharides: Long chains of monosaccharides, such as starch (energy storage in plants), glycogen (energy storage in animals), and cellulose (structural component in plant cell walls).
    2. Lipids:
    " Fatty acids: Saturated and unsaturated fatty acids.
    " Triglycerides: Composed of glycerol and three fatty acids, used for energy storage.
    " Phospholipids: Major components of cell membranes, with hydrophilic heads and hydrophobic tails.
    " Steroids: Include cholesterol, which is a component of cell membranes, and steroid hormones like testosterone and estrogen.
    3. Proteins:
    " Amino acids: The building blocks of proteins.
    " Enzymes: Proteins that catalyze biochemical reactions.
    " Structural proteins: Such as collagen in connective tissues and keratin in hair and nails.
    " Transport proteins: Such as hemoglobin, which carries oxygen in the blood.
    " Antibodies: Proteins involved in the immune response.
    " Receptor proteins: Involved in cell signaling and communication.
    4. Nucleic Acids:
    " DNA (Deoxyribonucleic acid): Carries the genetic blueprint of the organism.
    " RNA (Ribonucleic acid): Involved in protein synthesis and gene regulation. Types include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA).
    5. Vitamins and Coenzymes:
    " Organic molecules that are essential for various cellular functions and enzyme activity.
    6. Small Organic Molecules:
    " Metabolites: Intermediates and products of metabolic pathways, such as pyruvate, lactate, and citric acid.
    " Signaling molecules: Such as hormones and neurotransmitters.

    These organic substances interact in complex ways to maintain cellular processes, including energy production, growth, and reproduction. Each category plays a crucial role in the cell's structure and function, and their precise composition and abundance can vary depending on the cell type and its specific functions. The zygote
    (see Figure 32) also contains these organic molecules needed to support its metabolism, growth, and the subsequent cellular divisions and differentiation that will lead to the development of a multicellular organism.

  2. Stem Cell Activation :

    The fate of stem cells, or their differentiation into various cell types, is determined by a combination of intrinsic and extrinsic factors. Here's an overview of the key factors involved:

    Intrinsic Factors:
    1. Gene Expression:
    " Stem cells have specific genes that, when expressed, influence their differentiation pathway
    (a series of actions among molecules in a cell that leads to a certain product or a change in the cell). The expression of these genes is regulated by various transcription factors and signaling pathways.
    2. Epigenetic Modifications:
    " Changes in DNA methylation and histone modification patterns can affect gene expression without altering the DNA sequence, guiding stem cells toward specific cell fates.
    3. Transcription Factors:
    " Specific transcription factors can activate or repress the expression of target genes that drive differentiation into specific cell types. For example, Oct4, Sox2, and Nanog are crucial for maintaining pluripotency in embryonic stem cells.

    Extrinsic Factors:
    1. Growth Factors and Cytokines :
    " Proteins such as growth factors and cytokines in the cellular microenvironment can bind to receptors on stem cells and activate signaling pathways that promote differentiation. For instance, bone morphogenetic proteins (BMPs) and fibroblast growth factors (FGFs) play critical roles in stem cell fate determination.
    2. Cell-Cell Interactions:
    " Direct interactions between stem cells and their neighboring cells can influence differentiation. Notch signaling is a well-known pathway mediated by cell-cell contact that regulates stem cell fate.
    3. Extracellular Matrix (ECM):
    " The composition and stiffness of the ECM can impact stem cell behavior. Integrins and other receptors interact with ECM components, triggering intracellular signals that affect differentiation.
    4. Mechanical Forces:
    " Physical forces such as tension, compression, and shear stress can influence stem cell differentiation. Mechano-transduction pathways convert these physical cues into biochemical signals that guide cell fate decisions.
    5. Nutrient Availability:
    " The availability of nutrients, oxygen, and metabolic substrates
    (a substance or surface which an organism grows and lives on and uses as food) in the microenvironment can influence stem cell differentiation. Hypoxia, for instance, can promote the maintenance of stemness or direct differentiation toward specific lineages.
    Combinatorial Effects:
    " Often, it is the interplay between multiple intrinsic and extrinsic factors that ultimately determines the fate of stem cells. The specific combination and timing of these signals are crucial for directing stem cell differentiation accurately.
    Niche Influence:
    " The stem cell niche, the specialized micro-environment where stem cells reside, plays a pivotal role in regulating their fate. The niche provides a dynamic and supportive environment, offering the necessary signals to maintain stem cells in an undifferentiated state or to prompt their differentiation as needed.

    The fate of stem cells is a result of complex and tightly regulated interactions between their intrinsic properties and the external cues they receive from their environment. Understanding these factors and their interplay is crucial for advancing stem cell therapies and regenerative medicine.

  3. See previous version.

  4. Blastocyst Stage :

    The blastocyst stage is crucial for several reasons, including the establishment of a selective barrier that can interact with the maternal environment while providing protection and support to the developing embryo. Here's a detailed look at why the blastocyst stage is important in terms of its structural and functional developments:

    Key Developments at the Blastocyst Stage
    1. Formation of the Trophectoderm (TE):
    " Selective Barrier: The trophectoderm, which forms the outer layer of the blastocyst, develops into the first cellular interface with the maternal endometrium (the lining of the uterus). This layer is essential for implantation and establishing the placenta.
    " Tight Junctions: Trophectoderm cells form tight junctions, creating a barrier that regulates the passage of substances between the external environment and the inner cell mass (ICM). This helps protect the developing embryo from potential external influences.
    2. Creation of the Blastocoel:
    " Cavity Formation: The blastocoel is a fluid-filled cavity within the blastocyst, providing a controlled environment for the ICM to further differentiate and develop.
    " Ion and Water Transport: The trophectoderm cells actively transport ions and water to create and maintain the blastocoel, which also helps in nutrient distribution and waste removal.
    3. Differentiation of the Inner Cell Mass (ICM): " Embryo Proper: The ICM will give rise to the embryo proper and some extraembryonic structures. This differentiation is tightly regulated and sheltered by the trophectoderm layer. " Pluripotency: The ICM cells retain their pluripotent nature at this stage, which means they have the potential to develop into any cell type of the body.

    Interaction with Maternal Environment
    1. Implantation:
    " Attachment and Invasion: The blastocyst attaches to the uterine wall, and the trophectoderm cells invade the endometrium to establish a connection with the maternal blood supply. This step is critical for obtaining nutrients and oxygen from the mother.
    " Placental Development: The trophectoderm eventually forms part of the placenta, an organ that facilitates nutrient and gas exchange between the mother and the developing embryo while also serving as a selective barrier.
    2. Protection from External Influences:
    " Immune Modulation: The placenta and the surrounding maternal tissues create an immunologically privileged site that protects the embryo from the maternal immune system.
    " Selective Transport: The placental barrier selectively transports nutrients, hormones, and waste products between the mother and the fetus, filtering out potentially harmful substances.

    Importance of the Blastocyst Stage
    " Critical Milestone: The blastocyst stage is a pivotal developmental milestone that sets the stage for successful implantation and subsequent embryonic development.
    " Establishment of Lineages: Differentiation of the ICM and trophectoderm marks the beginning of the establishment of distinct cell lineages that will give rise to different parts of the embryo and supporting structures.
    " Environmental Control: By forming a protective barrier, the blastocyst ensures that the developing embryo is exposed only to the regulated maternal environment, minimizing external disruptions during a critical period of development.

    The blastocyst stage is essential for mammalian development because it establishes the initial structures that facilitate interaction with the maternal environment while protecting and nurturing the inner cell mass. The formation of the trophectoderm and the blastocoel, along with the initiation of implantation, are key processes that ensure the embryo can proceed with proper development in a controlled and supportive environment provided by the mother.

  5. Differentiation into Different Types :

    Inner Cell Mass (ICM) vs. Trophectoderm (TE) Differentiation -

    1. ICM Differentiation:
    " Transcription Factors: Oct4, Sox2, and Nanog are critical for maintaining pluripotency in the ICM cells.
    " Hippo Signaling Pathway: Active Hippo signaling in the inner cells leads to phosphorylation and cytoplasmic retention of YAP, preventing the expression of TE-specific genes like Cdx2.
    2. TE Differentiation:
    " Transcription Factor: Cdx2 is essential for TE development. In the outer cells, inactive Hippo signaling allows YAP to enter the nucleus and promote the expression of Cdx2.
    " Polarization: The establishment of apical-basal polarity in outer cells also supports the differentiation into the TE.

    Further Differentiation of ICM -

    The ICM can differentiate into two primary cell types: epiblast (which will form the embryo proper) and primitive endoderm (which will contribute to extraembryonic tissues like the yolk sac).
    1. Epiblast:
    " Transcription Factors: Continued expression of Oct4, Sox2, and Nanog maintains the pluripotent state.
    " Signaling Pathways: FGF/Erk signaling is involved in maintaining pluripotency and guiding further differentiation.
    2. Primitive Endoderm:
    " Transcription Factors: Gata6 is crucial for the differentiation into primitive endoderm.
    " Signaling Pathways: FGF signaling promotes the expression of Gata6 and other endoderm markers.

    Mesoderm, Endoderm, and Ectoderm Differentiation
    Once the ICM cells form the epiblast, they undergo gastrulation to give rise to the three germ layers: mesoderm, endoderm, and ectoderm. Each layer gives rise to different cell types, influenced by specific factors and signaling pathways.
    1. Mesoderm (e.g., muscle, bone, blood):
    " BMP Signaling: Bone Morphogenetic Proteins (BMPs) promote mesoderm differentiation.
    " Transcription Factors: Brachyury (T) is a key factor for mesoderm formation.
    2. Endoderm (e.g., liver, pancreas, lungs):
    " Nodal/Activin Signaling: These pathways are crucial for endoderm specification.
    " Transcription Factors: Sox17 and Foxa2 are important for endoderm differentiation.
    3. Ectoderm (e.g., skin, nervous system):
    " Wnt and BMP Inhibition: Inhibition of BMP signaling is essential for ectoderm formation.
    " Transcription Factors: Sox2 and Pax6 are important for neural ectoderm development.

    Hematopoietic Stem Cells (HSCs) Differentiation
    HSCs give rise to various blood cell types and are influenced by specific growth factors and cytokines.
    1. Erythrocytes (Red Blood Cells):
    " Erythropoietin (EPO): Promotes differentiation into erythrocytes.
    " Transcription Factors: GATA1 is crucial for erythroid differentiation.
    2. Myeloid Lineage (e.g., macrophages, neutrophils):
    " Growth Factors: Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) and Macrophage Colony-Stimulating Factor (M-CSF) guide myeloid differentiation.
    " Transcription Factors: PU.1 and C/EBP? are key for myeloid lineage specification.
    3. Lymphoid Lineage (e.g., B cells, T cells):
    " Cytokines: Interleukin-7 (IL-7) is important for lymphoid differentiation.
    " Transcription Factors: E2A and Pax5 are crucial for B cell development; GATA3 and T-bet are important for T cell differentiation.


    Stem cell differentiation into specific cell types is a highly regulated process involving a combination of transcription factors, signaling pathways, and external cues such as growth factors and cytokines. These factors work together to guide stem cells along specific developmental pathways to produce the diverse cell types necessary for proper organismal function and development.

  6. See previous version.

  7. Time Line :

    The differentiation and development of an embryo follow a specific schedule where various factors and cues are activated sequentially, and sometimes simultaneously, to ensure proper timing and coordination of development. This tightly regulated process ensures that cells differentiate into the correct cell types at the right time and place. Here's a more detailed look at how these factors are evoked during embryonic development:

    Pre-implantation Development

    1. Fertilization to Zygote (1 day) :
    " Maternal mRNA and Proteins: Control early cell divisions and initial cellular functions.
    2. Cleavage Stages (2-cell to Morula, 4 days) :
    " Zygotic Genome Activation (ZGA): Occurs around the 4- to 8-cell stage in humans. This is when the embryo begins to transcribe its own genes.
    " Compaction: At the 8-cell stage, cells increase their adhesion to form a more compact structure.
    " Polarization: Begins during compaction, leading to the formation of apical
    (apex) and basolateral (base) domains.
    3. Morula to Blastocyst (5 days) :
    " Inner Cell Mass (ICM) vs. Trophectoderm (TE) Differentiation:
    " Hippo Signaling Pathway: Active in inner cells to promote ICM fate and inactive in outer cells to promote TE fate.
    " Cdx2 Expression: Initiates in the outer cells to drive TE formation.
    " Oct4, Sox2, and Nanog: Maintain pluripotency in the ICM.

    Post-implantation Development

    1. Blastocyst Implantation (6 - 8 days) :
    " Adhesion Molecules: Allow the blastocyst to adhere to the uterine wall.
    " ICM Differentiation: Further differentiation into epiblast and primitive endoderm (10 - 14 days).
    2. Gastrulation (15 days) :
    " Formation of Germ Layers (Ectoderm, Mesoderm, Endoderm):
    " Nodal/Activin Signaling: Promotes mesoderm and endoderm formation.
    " BMP and Wnt Signaling: BMP inhibition is crucial for ectoderm formation, while BMP signaling is important for mesoderm differentiation.


    1. Neurulation (Formation of the Neural Tube, 18 - 28 days):
    " Neural Induction Signals: Inhibition of BMP signaling and activation of FGF signaling promote neural ectoderm differentiation.
    " Sox2 and Pax6: Important for neural progenitor specification.
    2. Somitogenesis (Formation of Somites, 20 - 35 days) :
    " Notch and Wnt Signaling: Regulate the periodic formation of somites from the presomitic mesoderm.
    " Mesp2 and Pax3: Critical for somite formation and differentiation.
    3. Hematopoiesis (Blood Cell Formation, 17 - 84 days):
    " Hematopoietic Stem Cell (HSC) Specification:
    " Runx1 and GATA2: Important for HSC emergence.
    " Erythropoietin (EPO): Drives erythroid lineage differentiation.
    " GM-CSF and M-CSF: Guide myeloid lineage differentiation.

    Tissue and Organ Development

    1. Limb Development (26 - 56 days) :
    " FGF and Sonic Hedgehog (Shh) Signaling: Critical for limb bud formation and patterning.
    " HOX Genes: Provide positional information for limb patterning.
    2. Heart Development (15 - 49 days) :
    " NKX2-5 and GATA4: Important transcription factors for cardiomyocyte differentiation.
    " Wnt and BMP Signaling: Regulate early heart field specification and differentiation.

    Sequential and Overlapping Activation

    " Sequential Activation: Some factors are activated in a clear sequence. For instance, ZGA occurs before the major differentiation events like compaction and ICM/TE segregation.
    " Overlapping Activation: Many signaling pathways and transcription factors operate concurrently and interact with each other to refine the developmental processes.

    Embryonic development follows a precise timeline where specific factors and cues are evoked in a regulated manner. This sequential and sometimes overlapping activation ensures that stem cells differentiate into the correct cell types at the appropriate stages, leading to the proper formation of tissues, organs, and the overall organism. Understanding this timeline and the interplay of various factors is crucial for developmental biology and can have important implications for regenerative medicine and developmental disorder research.

    See previous version from "Symmetry Breaking" ... to Formation of the Nervous System.

  8. Also see "organogenesis" by courtesy of ChatGPT for more detail on the subject + some images inserted by Yours Truly.