The morphogenesis of eukaryotic cells, structure, and shape is due to at least 38 different mechanisms. They are classified into two groups: The molecules that provide complex instructional cues of action based on information through signaling which is fundamental to coordinate any common behavior and organize the division of labor, and secondly by force-generating molecules that are directed through those signals, which are responsible for cell morphogenesis. On a grand scheme, there are four weblike networks, which form the scaffolds that give form to the cells: Spectrins, Actins, Microtubules, and the Extracellular Matrix. These scaffold networks are dynamic, not static, and can change sizes and forms, polymerize, and depolymerize filaments according to the informational cues received.
The following activities are performed by at least 36 different signaling molecules & mechanisms: 8 molecules signal, 4 orienting, 5 activate, 2 direct, 3 promote, 2 regulate, 1 guide, 3 organize, 1 inform, 1 coordinate, 1 specify, 1 modulating, 1 provide position cues, 2 mediate, 1 provoke change.
The molecules, acting upon the instructional signals received, form patterns, force change, stretch, change and induce cell shape, move positions, orient, provoke ingress, express, align, deform, accumulate molecules, invaginate, extend, form a web, concentrate, hold together, give mechanical support, stiffen, promote stabilization, form geometry, polarity, form division-plane positioning, phosphorylate, dephosphorylate, force transmission, couple molecules physically, form gradients, deform, pull forces, promote cell rounding, transduce, specify cell-fate, extend, provide structural links, form aspect ratio and size, form filament ends, etc.
Information is required to specify the making of the molecules that provide instructional information ( the engineers ) which are essential to direct the molecular actors to perform their actions in an orchestrated manner. But Information is also required to specify the making of the molecules and proteins that are the actors in this grand scheme ( the workers in the factory ). In cells, there are dozens of different engineers (signaling molecules ), which direct the factory workers ( actors ) in their job. In an engineer's department, the individual engineers must elaborate their instruction plans in harmony as a team and joint venture and orchestrate the plan of action, and coordinated instructions provided to the factory workers.
But while in human enterprises, in all steps, human intelligence is involved in a plan of action to achieve a specific goal, in cells, everything is pre-programmed and occurs without intelligent intervention. Cells are 100% autonomous interlinked factory parks with a director department, which also operates in a fully pre-programmed manner. Cell factories are not static. They work in a dynamic network together with their neighbor cells and even distant cell factory parks in a joint venture to form Tissues, Organs, Organ Systems, and Organisms, made of trillions of cells, all working together in a coordinated fashion. The placement of each of these cell factory parks is directed by bioelectric signaling.
The bioelectric code: An ancient computational medium for dynamic control of growth and form
In the same sense, as in human organization, there is the smallest nucleus of a society, the family, there is the district, the county, the region, the estate, and the country, so organisms are organized in hierarchies of organization: Cells, Tissues, Organs, Organ Systems, and Organisms. But rather than static, organisms adapt and react to the environment, food and energy supply, and a large variety of conditions.
In order for an organism to change from one species to another, the change must start at the smallest unit, which is the cell. The signaling molecules, and the language they operate upon, is not only stored in genes but in over 20 different epigenetic signaling codes. Any of those, if not working properly, can cause disease. This is a demonstration that the gene-centric view is false. It is based on a naive understanding of how biological systems work, going back to Darwins time. Today we know better.
The real mechanisms that explain biodiversity and complex organismal architecture are enormous amounts of data. Instructions, complex codified specifications, INFORMATION. Algorithms encoded in various genetic and epigenetic languages and communication channels and networks. Genes, but as well and especially various epigenetic signaling and bioelectric codes through various signaling networks provide cues to molecules and macromolecule complexes, and scaffold networks interpret and react in a variety of ways upon decoding and data processing of those instructions. Since signaling pathways work in a synergetic integrated manner with the transcriptional regulatory network and complex short and long-range cross-talk between cells, these instructions could not be the result of a random gradual increase of information. These information networks only operate and work in an integrated fashion, and had to be fully set up right from the beginning. Conveying codes, a system of rules to convert information, such as letters and words, into another form, and translation ciphers of one language to another, or are always sourced back to intelligent set-up. That is what we see in biochemistry. Complex instructional codified information is stored through the genetic code ( codons) in a storage medium (DNA), encoded ( DNA polymerase), sent (mRNA), and decoded ( Ribosome) That brings us unambiguously to intelligent design. To the origin by an intelligent designer.
With what I described above, I have elucidated just ONE of at least 17 different things that have to be specified in the formation of cells in a multicellular organism:
1. Morphogenesis of various eukaryotic cells, structures, and shapes
2. Cell fate determination and differentiation ( phenotype, or what cell type each one will become )
3. Cell growth and size
4. Development and cell division counting: cells need to be programmed to stop self-replicating after the right number of cell divisions
5. Mechanisms of pattern formation
6. Hox genes
7. Position and place in the body. This is crucial. Limbs like legs, fins, eyes, etc. must all be placed at the right place.
8. What communication it requires to communicate with other cells, and the setup of the communication channels
9. Sensory and stimuli functions of cells
10. What specific new regulatory functions do cells have to acquire
11. When will the development program of the organism express the genes to grow the new cells during development?
12. Change regulation in the composition of the cell membrane and/or secreted products.
13. Specification of the cell-cell adhesion proteins and which ones will be used in each cell to adhere to the neighbor cells ( there are 4 classes )
14. Apoptosis: programming of the time period the cell keeps alive in the body, and when is it time to self-destruct and be replaced by newly produced cells of the same kind
15. Set up each cells specific nutrition demands
16. Cell shape changes
17. Cell proliferation which is the process that results in an increase of the number of cells, and is defined by the balance between cell divisions and cell loss through cell death or differentiation.
By design, or non-design?
Where Do Complex Organisms Come From?
How does biological multicellular complexity and a spatially organized body plan emerge?
How Systems Biology consolidates the inference of Creationism
Actomyosin mediates apical constriction which drives a wide range of morphogenetic processes.
Actin filaments, actin crosslinkers, and myosin motors form an intracellular-contractile network which provokes changes in cell shape.
Actin filaments in animal cells are organized into several types of arrays: dendritic networks, bundles, and weblike (gel-like) networks which permit the formation of different cell structures. The Arp 2/3 complex and formins contribute to these formations.
Arp2/3 complex is an essential organizer of treadmilling actin filament arrays.
Biochemical signaling directs the graded distribution of a morphogen across a tissue, which permits cells to interpret their position to make fate choices. The morphogen concentration, therefore, provides positional coordinates along the embryonic axis.
Centrosomes provide precise cell division positioning rules
Chemical signaling cascades bridge the plasma membrane and the nucleus. Focal adhesion proteins such as zyxin and paxillin shuttle between the cytoplasm and nucleus to modulate transcriptional activity.
Conserved geometrical features provided by cleavage patterns. The geometry of these patterns may specify developmental axes, germ layers, and cell fates.
Cortical force generators interact with spindle microtubules and are activated by cortical cues
Diverse sets of signaling pathways perform spatial-temporal coordination, regulation and control of actomyosin networks, co-responsible for morphogenesis, and cell shape change to get proper size and shape
Dynein force generators are employed to orient cell division axes at a specific angle. They work at the cell cortex and the cytoplasm.
Ezrin, radixin, and moesin proteins (ERM) help organize membrane domains through their ability to interact with transmembrane proteins and the underlying cytoskeleton. In so doing, they not only provide structural links to strengthen the cell cortex, but also regulate the activities of signal transduction pathways.
Extracellular matrix ECM stiffness directs differentiation or self-renewal of embryonic or somatic stem cells, and the ECM viscosity can also influence cell-fate specification. [/size
Filamins function as signaling scaffolds by connecting and coordinating a wide variety of cellular processes with the actin cytoskeleton.
Ga/LGN/NuMA complex binds to dynein, which then generates microtubule pulling forces toward the cell cortex
Gelsolin proteins break an actin filament into many smaller filaments, thereby generating a large number of new filament ends.
Intracellular modules such as the cytoskeleton inform and provide global and local cell geometry features, such as aspect ratio, size, or membrane curvature
Key regulator Rac activates the WAVE complex through coincident signals.
Lamellipodia permit the extension of sheetlike membrane projections that help cells to crawl across solid surfaces which is important for migration during early embryonic development.
Lamin A is a nuclear lamina component. In stiff tissue, tension from the ECM transmitted via the cytoskeleton to the nucleus can enhance lamin A transcription and stability of lamin A/C, leading to activation of Yap, serum response factor (SRF) and retinoic acid signaling pathways.
Mechanosensing and transduction employed by cells sense forces and mechanical cues, and subsequently, control cell differentiation and morphogenesis. How genetic cascades link cell-fate specification to tissue morphogenesis remains unclear.
Moesin also increases cortical stiffness to promote cell rounding during mitosis. ERM proteins are thought to bind to and organize the cortical actin cytoskeleton in a variety of contexts, thereby affecting the shape and stiffness of the membrane as well as the localization and activity of signaling molecules.
Morphogen-mediated chemical signaling induces cell shape, cell geometry, deformation, pulling forces of the extracellular matrix (ECM), and in the end, the architectural form of tissue.
Physical mechanotransduction relies on direct force transmission from the cell surface to the nucleus through physical coupling between the nuclear membrane and the extracellular space by cytoskeletal components.
Protein gradients that are mostly independent of DNA or any cytoskeletal structure
RhoGEFs of the small GTPase Rho1 activates ROCK, formin and formin-related proteins, such as Daam proteins, and they direct and regulate Myosin II motor protein phosphorylation and dephosphorylation
Signaling provides spatial information, guiding cellular geometry, conveys polarity, cell morphogenesis, and division-plane positioning.
Spectrins are proteins that form a web. Spectrin is a long, flexible protein made out of four elongated polypeptide chains. In the red blood cell, spectrin is concentrated just beneath the plasma membrane, where it forms a two-dimensional weblike network held together by short actin filaments whose precise lengths are tightly regulated by capping proteins at each end. The resulting network creates a strong, yet flexible cell cortex that provides mechanical support for the overlying plasma membrane, allowing the red blood cell to spring back to its original shape after squeezing through a capillary. Close relatives of spectrin are found in the cortex of most other vertebrate cell types, where they also help to shape and stiffen the surface membrane. A particularly striking example of spectrin’s role in promoting mechanical stability is the long, thin axon of neurons
Static and pulsed mechanical deformations of mesodermal cells have been shown to promote Folded gastrulation (Fog) signaling and apical myosin II accumulation, which is required for mesoderm invagination prior to germband extension.
The mitotic spindle directs spatial cues for cytokinesis ( the physical process of cell division ). Septum ingression is pre-specified from the position of the nucleus, and the spindle usually aligns orthogonal to the septum.
The nucleus acts as a mechanosensor, whereby changes in nuclear shape can evoke transcriptional changes by locally altering the spatial accessibility of chromatin to transcriptional regulators. The physical links between the cytoskeleton and nuclear membrane proteins allow the entire cell to function as a single mechanically coupled system.
The dynamic orientation of nuclei and spindles, which are moved and oriented from the forces exerted by microtubules (MTs) and associated motors such as dynein.
Tissue-scale mechanical signals can confer positional information and control gene expression and fate at the cellular level, thereby allowing cells to coordinate embryonic patterning.
Twist, a transcription factor, and activation of Rho signaling direct ratcheting which is critical for the generation of tissue‐level tension and changes in tissue shape. That is provided by βH‐spectrin which forms a network of filaments which co‐localize with Medio‐apical actomyosin fibers.
Upstream developmental cues, downstream force generators that orient cell division and cue-dependent spatial control of the force generators generate diversity in division axis orientation
Yap/Taz signaling, where mechanical tension arising from physical stretching of cells or increased stiffness of the extracellular matrix (ECM) activates F-actin remodeling and Yap/Taz nuclear localization.
1. The grand overarching scheme of the morphogenesis and formation of single eukaryotic cell form, shape, architecture, function, structure, following the formation of tissues and higher order of biological structures is that information conveyed through codified signaling directs intracellular molecular actors. It is due to at least 36 different signaling molecules & mechanisms which direct at least 15 force-generating molecules, through least 38 different mechanisms. They are classified into two groups:
a) Semantophoretic molecules ( carry genetic and epigenetic information) that provide complex instructional cues of action through signaling which is fundamental to coordinate any common behavior and organize the division of labor. The following activities are performed in an integrated, orchestrated, interdependent manner by at least 36 different signaling molecules & mechanisms in the following different ways: 8 molecules signal, 4 orient, 5 activate, 2 direct, 3 promote, 2 regulate, 1 guide, 3 organize, 1 inform, 1 coordinate, 1 specify, 1 modulate, 1 provide position cues, 2 mediate, 1 provoke change.
b) At least 15 force-generating actors, molecules that are directed through those signals and instructions, are responsible for cell morphogenesis, that is: Filaments, microtubules, lamellopodia, crosslinkers, motors, protein complexes, the centrosome, adhesion proteins, force generators, the extracellular matrix, intra-cellular modules, key regulators, protein gradients, the mitotic spindle, mechanical signals which act in at least 38 different ways, to name: activating, binding, breaking, coordinating, conferring positional information, directing, forcing transmission, generating, guiding, helping to organize, inducing, informing, mediating, modulating, organizing, orienting, providing positioning rules, provoking changes, promoting, regulating, signaling, stretching, specifying.
2.The molecules, acting upon the instructional signals received, form patterns, force change, stretch, change and induce cell shape, move positions, orient, provoke ingress, express, align, deform, accumulate molecules, invaginate, extend, form a web, concentrate, hold together, give mechanical support, stiffen, promote stabilization, form geometry, polarity, form division-plane positioning, phosphorylate, dephosphorylate, force transmission, couple molecules physically, form gradients, deform, pull forces, promote cell rounding, transduce, specify cell-fate, extend, provide structural links, form aspect ratio, and size, form filament ends, etc.
3.Codified signals and information directing the making of machines ( proteins) and factories ( cells) have only been observed to come from intelligent minds. Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic codes, and upon it, instructional information, is like suggesting that a rainbow can write poetry... it is never going to happen! Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind. Life is no accident, the vast quantity of semiotic information in life provides powerful positive evidence that we have been designed.