The essential signaling pathways for animal development

The  essential signaling pathways   for animal development 1

https://reasonandscience.catsboard.com/t2351-the-essential-signaling-pathways-for-animal-development

Signalling pathways are essential for multicellular development 

The emergence of multicellularity was supposedly, a major evolutionary leap. Indeed, most biologists consider it one of the most significant transitions in the evolutionary history of Earth’s inhabitants. “How a single cell made the leap to a complex organism is however one of life’s great mysteries. ”

One of the far fetched and desperate pseudo-scientific attempts to explain how multicellularity emerged, can be read here.

Cell signaling is arguably the most important characteristic of multicellular organisms. 31 Without cell signaling, the different cells in the body of a plant or animal could not communicate with each other, and they could not coordinate their actions. Such coordination is essential: first, to build a complex body composed of thousands or millions of cells and second, for the correct performance of such a body in everyday life, whether acquiring nutrients, excreting toxins, or dealing with hostile or friendly interactions from other organisms. This coordination is corroborated by the many problems and diseases (such as developmental abnormalities and cancers) that arise from malfunction of the cellular machinery that deals with cell signaling and communication (1–3). Thus, the study of such cell signaling machinery is receiving a great deal of attention by biological and medical research. At the most basic level, any cell signaling process must involve a signal, synthesized or otherwise, generated by the sending cell and some kind of system to receive that signal and respond to it in the receiving cell. 

Less attention than this issue deserves,  has been given in the evolution/ID debate to elucidate  how cell signal transduction pathways function, what mechanisms, kind of molecules and proteins  are involved,, in what organisms they first emerged, and how these extremely complex and multifaceted  pathways could have possibly emerged, and what causes explain best their origins.  

Perhaps most surprising has been the finding that carbohydrates are also involved in the regulation of a number of signaling pathways. Genetic studies have  shown that proteoglycans/glycosaminylglycans play key roles in development, and, in Drosophila and Caenorhabditis elegans, they have been shown to be involved in regulating the fibroblast growth factor, Wnt, transforming growth factor-B, and Hedgehog signaling pathways. In vivo, oligosaccharides are synthesized by glycosyltransferases, each of which typically has a unique donor, acceptor, and linkage specificity. As such, a very large number of glycosyltransferases and related enzymes are required to generate the oligosaccharide diversity seen in nature. Although the basis for this diversity is not fully understood, general themes are beginning to emerge. The so-called terminal elaborations (e.g., sialic acid, galactose, and sulfate) typical of the N-linked oligosaccharides of multicellular organisms, for example, seem to have appeared as part of the machinery required to mediate cell–cell and cell–matrix interactions. 

Looking at how these pathways emerged might provide insights into how a few signalling pathways can generate so much cellular and morphological diversity during the development of individual organisms and the evolution of animal body plans.

If macroevolution involves changing morphological features, then the altering of signal transduction pathways becomes critical for any discussion of large scale evolution. 2 

Signalling pathways are  complex networks of interactions. Surprisingly, only a few classes of signalling pathways are sufficient to pattern a wide variety of cells, tissues and morphologies. The specificity of these pathways is based on the history of the cell (referred to as the ‘cell’s competence’), the intensity of the signal and the cross-regulatory interactions with other signalling cascades.

The origin,  formation and maintenance of  specialized tissues of multicellular organisms depend on the 

1. Coordinated regulation of cell size and number 
2. Cell morphology and shape
3. Cell location and migration 
4. Regulation and expression of differentiated functions

1. Coordinated regulation of cell size and number 
In the adult, homeostatic mechanisms maintain cell number and size to preserve organ size and function. However, this outward appearance of stability belies the complex balance of positive and negative regulatory stimuli required to maintain tissues with the differing proliferative and metabolic activities that make up a complex organism. 12 . In multicellular organisms, growth, proliferation, and survival need to be differentially regulated in different tissues, so additional levels of control are required. This is achieved by providing a more or less constant supply of nutrients systemically (by the bloodstream or its equivalent), but in addition, there is a requirement by each cell for an instructive signal to grow, proliferate, and survive. Thus, a combination of multiple growth, mitogenic, and survival signals with cell-specific responses provides the diverse signaling required to produce and maintain a complex adult organism.

Studies showing that cells require extracellular instructive signals to grow, coupled with the identification of key signaling pathways, have provided tractable systems for studying how cell growth is regulated. Moreover, the identification of abnormalities in these pathways in diseases as diverse as cancer, cardiac hypertrophy and neurodevelopmental disorders have highlighted the critical importance of the tight regulation of these pathways and have identified potential new therapeutic strategies.

The size of an adult organism is determined by both intrinsic developmental programs and by extracellular signals, which integrate to control cell number and cell size. 
Moreover, the water content of the cell must be controlled, requiring stringent controls of osmotic pressure (Koivusalo et al., 2009).
The Hippo pathway is also important in the control of tissue/organ size, mainly by regulating proliferation and apoptosis and thereby cell number (Tumaneng et al., 2012a). 

http://reasonandscience.heavenforum.org/t2350-the-hippo-signaling-pathway-in-organ-size-control-tissue-regeneration-and-stem-cell-self-renewal


2. Cell morphology and shape
depends on: 
(a) membrane targets and patterns 
(b) cytoskeletal arrays
(c) centrosomes 
(d) ion channels, and 
(e) sugar molecules on the exterior of cells (the sugar code)
(f)  Gene regulatory networks  19

3. Cell location and migration
Cell migration is a central process in the development and maintenance of multicellular organisms. 15 Processes such as tissue formation during embryonic development, wound healing, and immune responses, all require the orchestrated movement of cells in particular directions to specific locations. Errors during this process have serious consequences, including intellectual disability, vascular disease, tumor formation and metastasis. An understanding of the mechanism by which cells migrate may lead to the development of novel therapeutic strategies for controlling, for example, invasive tumor cells.

Cells often migrate in response to specific external signals, including chemical signals and mechanical signals. Due to a highly viscous environment, cells need to permanently produce forces in order to move. Cells achieve active movement by very different mechanisms. Many less complex prokaryotic organisms (and sperm cells) use flagella or cilia to propel themselves. Eukaryotic cell migration typically is far more complex and can consist of combinations of different migration mechanisms. It generally involves drastic changes in cell shape which are driven by the cytoskeleton, for instance a series of contractions and expansions due to cytoplasmic displacement. Two very distinct migration scenarios are crawling motion (most commonly studied) and blebbing motility.
The migration of cultured cells attached to a surface is commonly studied using microscopy. As cell movement is very slow (only a few µm/minute), time-lapse microscopy videos are recorded of the migrating cells to speed up the movement . Such videos reveal that the leading cell front is very active with a characteristic behavior of successive contractions and expansions. It is generally accepted that the leading front is the main motor that pulls the cell forward .

Cell migration directed by spatial cues, or taxis, is a primary mechanism for orchestrating concerted and collective cell movements during development, wound repair, and immune responses.  Mesenchymal cells possess a distinctive organization of the actin cytoskeleton and associated adhesion complexes as its primary mechanical system, generating the asymmetric forces required for locomotion without strong polarization. The emerging hypothesis is that the molecular underpinnings of mesenchymal taxis involve distinct signaling pathways and diverse requirements for regulation. 16

Cell migration is a fundamental process that occurs during embryo development. Classic studies usingin vitro culture systems have been instrumental in dissecting the principles of cell motility and highlighting how cells make use of topographical features of the substrate, cell-cell contacts, and chemical and physical environmental signals to direct their locomotion. 17 Motility bias relies on the induction of front-to-back cell polarity, which involves actin polymerisation at the cell front and the stabilisation of protrusion formation towards the signal. These events are frequently mediated by signal transduction events downstream of receptor activation that modulate the activity of small GTPases and actin dynamics. The transmission of membrane tension across the migrating cell also plays an instructive role in directing polarised motility. All the aforementioned processes show tight genetic regulation during development with respect to both the timing of cellular events and the spatial configurations of environmental signals. Such genetic control pre-configures the substrate landscape and determines the possible response mechanisms that cells can activate to direct their migration. However, migrating cells can also self-organise the chemical and physical substrate to which they will respond (e.g. by self-generating a chemoattractant gradient). In addition, cells can generate patterns of migration through interactions with other migrating cells (e.g. by means of contact inhibition of locomotion). The latter migratory events are not pre-configured and thus represent emerging properties of the system. 

4. Regulation and expression of differentiated cell functions
Developing animals face two main challenges. First, they must produce different types of proteins and cells and, second, they must get those proteins  and cells to the right place at the right time.  Davidson has shown that embryos accomplish this task by relying on networks of regulatory DNA-binding proteins (called transcription factors) and their physical targets.  18

The coordination of above mentioned points results partially from a complex network of communication between cells in which signals produced affect target cells where they are transduced into intracellular biochemical reactions that dictate the physiological function of the target cell 10 

The basis for the coordination of the physiological functions within a multicellular organism is intercellular signaling (or intercellular communication), which allows a single cell to influence the behavior of other cells in a specific manner. As compared to single-cell organisms, where all cells behave similarly within a broad frame, multicellular organisms contain specialized cells forming distinct tissues and organs with specific functions. Therefore, the higher organisms have to coordinate a large number of physiological activities such as:
 

Intermediary metabolism
 
Response to external signals
 
Cell growth
 
Cell division activity
 
Differentiation and development
Coordination of expression programs
 
Cell motility
 
Cell morphology

Properties of signalling pathways 
Cell–cell interactions through signal-transduction pathways are crucial in the coordination of embryonic development. Typically, signalling pathways are activated by the binding of a ligand to a transmembrane receptor, which in turn leads to the modification of cytoplasmic transducers. Subsequently, these transducers activate transcription factors that ultimately alter gene expression. One of the most surprising findings about signalling processes is that only a few pathways are involved in and are responsible for most of animal development

Signals generated during intercellular communication must be received and processed in the target cells to trigger the many intracellular biochemical reactions that underlie the various physiological functions of an organism. Typically, a large number of steps is involved in the processing of the signal within the cell, which is broadly described as intracellular signaling. Signal transduction within the target cell must be coordinated, fine-tuned and channeled within a network of intracellular signaling paths that finally trigger distinct biochemical reactions and thus determine the specific functions of a cell. Importantly, both intercellular and intracellular signaling are subjected to regulatory mechanism that allow the coordination of cellular functions in a developmental and tissue-specific manner.

Despite the bewildering number of cell types and patterns found in the animal kingdom, only a few signalling pathways are required to generate them.  One clear conclusion to be drawn from all these studies is that there is a rather limited number of signalling pathways to generate the remarkable variety and complexity of form and function that we see today, both across phyla and within the individuals of a given species. 26 Understanding how these pathways have emerged and function can thus illuminate the origin of morphological diversity, as well as the molecular and cellular basis of development and disease. Amongst the central canon of developmental signalling pathways are the 

Hedgehog (Hh) 
Wingless related (Wnt) 
Transforming growth factor-β (TGF-β)
Receptor tyrosine kinase (RTK) 
Notch
Janus kinase (JAK)/signal transducer  
Activators of transcription (STAT) protein kinases
Nuclear hormone pathways
Bone morphogenetic proteins (BMP)
Epidermal growth factor receptors (EGFR)
Fibroblast growth factors (FGF)
Inositol 1,4,5-trisphosphate/calcium (InsP3/Ca2) signaling pathway


Presence and absence of key signalling pathway components in Placozoans, Ctenophores, Sponges (Amphimedon and/or Oscarella) and non-metazoans (Monosiga and/or Dictyostelium).
White: absent, 
black: present, 
grey: not analysed, 
y: yes, 
n: no, 
y* indicates presence weakly supported by phylogenetic or domain composition analysis

                                                                               Trichoplax   Mnemiopsis  Amphimedon Monosiga 
                                                                                                                   (Choanoflagellate)








Schematic representations of the major metazoan developmental signalling pathways



Hedgehog
The  conserved Hedgehog (Hh) pathway is essential for normal embryonic development and plays critical roles in adult tissue maintenance, renewal and regeneration. 4 The Hedgehog (Hh) family of proteins control cell growth, survival, and fate, and pattern almost every aspect of the vertebrate body plan. 29 The Hh gradient is shaped by several proteins that are specifically required for Hh processing, secretion, and transport through tissues. The primary cilium is crucial for mammalian Hedgehog signaling 30
Germline mutations that subtly affect Hh pathway activity are associated with developmental disorders, whereas somatic mutations activating the pathway have been linked to multiple forms of human cancer. The misregulation or mutation of essential core components of the Hh pathway often result in congenital birth defects, such as polydactyly and holoprosencephaly. In adults, the inappropriate activation of Hh signaling leads to cancer, the most common type being basal cell carcinoma.  



20

Wnt signaling pathway
The Wnt signaling pathway is an ancient and evolutionarily conserved pathway that regulates crucial aspects of cell fate determination, cell migration, cell polarity, neural patterning and organogenesis during embryonic development. 5

21

Transforming growth factor-β (TGF-β)
Transforming growth factor-β (TGF-β) superfamily signaling plays a critical role in the regulation of cell growth, differentiation, and development in a wide range of biological systems. 6

22

Receptor tyrosine kinase
Tyrosine phosphorylation is an essential element of signal transduction in multicellular animals. 7

23

Notch
Notch signaling is an evolutionarily conserved pathway in multicellular organisms that regulates cell-fate determination during development and maintains adult tissue homeostasis. 8

24

JAK/STAT 
Cell-cell signaling represents an essential hallmark of multicellular organisms, which necessarily require a means of communicating between different cell populations, particularly immune cells. Cytokine receptor signaling through the Janus kinase/Signal Transducer and Activator of Transcription/Suppressor of Cytokine Signaling (CytoR/JAK/STAT/SOCS) pathway embodies one important paradigm by which this is achieved. 9 

25

Nuclear hormone pathways
The nuclear receptor superfamily are ligand-activated transcription factors that play diverse roles in cell di erentiation/development, proliferation, and metabolism and are associated with numerous pathologies such as cancer, cardiovascular disease, infl ammation, and reproductive abnormalities. 

Bone morphogenetic proteins (BMP)
Bone Morphogenetic Proteins (BMPs) are a group of signaling molecules that belongs to the Transforming Growth Factor-β (TGF-β) superfamily of proteins. Initially discovered for their ability to induce bone formation, BMPs are now known to play crucial roles in all organ systems. BMPs are important in embryogenesis and development, and also in maintenance of adult tissue homeostasis. 27 



Since all seven signal transduction pathways are essential for multicellular development  : is it feasable to suppose that they were all co-opted or borrowed from uncellular organisms ? If so, they still need the information to direct new body plan development. Where did this information come from ? 



References
1) http://www.mun.ca/biology/desmid/brian/SignallingEvolution.pdf
2) Gilbert, S. F. & Bolker, J. A. in Homologies of Process and Modular Elements of Embryonic Construction (ed. Wagner, G. P.) 435–454 (Academic, San Diego, California, 2001).
3) Gerhart, J. 1998 Warkany lecture: signaling pathways in development. Teratology 60, 226–239 (1999).
4) http://www.cellsignal.com/contents/science-pathway-research-stem-cell-markers/hedgehog-signaling-pathway/pathways-hedgehog
5) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634250/
6) http://www.cellsignal.com/contents/science-pathway-research-stem-cell-markers/tgf-smad-signaling-pathway/pathways-tgfb
7) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3358447/
8  http://www.cellsignal.com/contents/science-pathway-research-stem-cell-markers/notch-signaling-pathway/pathways-notch
9) http://www.ncbi.nlm.nih.gov/pubmed/26897340
10) http://www.wiley-vch.de/books/sample/3527333665_c01.pdf
11) http://www.cellsignal.com/common/content/content.jsp?id=pathways-nuclear
12) http://www.sciencedirect.com/science/article/pii/S0092867413010842
13) http://phys.org/news/2012-10-factors-cell.html
14) http://www.the-scientist.com/?articles.view/articleNo/38404/title/Taking-Shape/
15) Source: Boundless. “Cell Migration in Multicellular Organisms.” Boundless Biology. Boundless, 26 May. 2016.  https://www.boundless.com/biology/textbooks/boundless-biology-textbook/gene-expression-16/regulating-gene-expression-in-cell-development-117/cell-migration-in-multicellular-organisms-467-13125/
16) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177959/
17) http://dev.biologists.org/content/141/10/1999
18) http://reasonandscience.heavenforum.org/t2194-control-of-gene-expression-and-gene-regulatory-networks-point-to-intelligent-design
19) http://reasonandscience.heavenforum.org/t2316-where-do-complex-organisms-come-from#4782
20) http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=04340&mapscale=&show_description=hide
21) http://www.genome.jp/kegg-bin/show_pathway?hsa04310
22) http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=04350&mapscale=&show_description=hide
23) http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=04012&mapscale=&show_description=hide
24) http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=04330&mapscale=&show_description=hide
25) http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=04630&mapscale=&show_description=hide
26) [url=http://zider.free.fr/papers/Paper (13).pdf]http://zider.free.fr/papers/Paper%20(13).pdf[/url]
27) http://www.sciencedirect.com/science/article/pii/S2352304214000105
28) http://www.genome.jp/kegg-bin/show_pathway?org_name=ko&mapno=04350&mapscale=&show_description=hide
29) http://genesdev.cshlp.org/content/22/18/2454.full
30) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882129/
31) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150914/
32) Handbook of Cell signaling, page 85

The  essential signalling pathways for animal development

https://reasonandscience.catsboard.com/t2351-the-essential-signaling-pathways-for-animal-development#4939

Cell signaling is arguably the most important characteristic of multicellular organisms.  Without cell signaling, the different cells in the body of a plant or animal could not communicate with each other, and they could not coordinate their actions. Such coordination is essential: first, to build a complex body composed of thousands or millions of cells and second, for the correct performance of such a body in everyday life, whether acquiring nutrients, excreting toxins, or dealing with hostile or friendly interactions from other organisms. This coordination is corroborated by the many problems and diseases (such as developmental abnormalities and cancers) that arise from malfunction of the cellular machinery that deals with cell signaling and communication. Thus, the study of such cell signaling machinery is receiving a great deal of attention by biological and medical research. At the most basic level, any cell signaling process must involve a signal, synthesized or otherwise, generated by the sending cell and some kind of system to receive that signal and respond to it in the receiving cell.

If macroevolution involves changing morphological features, then the altering of signal transduction pathways becomes critical for any discussion of large-scale evolution.

Less attention than this issue deserves,  has been given in the evolution/ID debate to elucidate  how cell signal transduction pathways function, what mechanisms, kind of molecules and proteins  are involved,, in what organisms they first emerged, and how these extremely complex and multifaceted  pathways could have possibly emerged, and what causes explain best their origins.  

Signalling pathways are complex networks of interactions. Surprisingly, only a few classes of signalling pathways are sufficient to pattern a wide variety of cells, tissues and morphologies. The specificity of these pathways is based on the history of the cell (referred to as the ‘cell’s competence’), the intensity of the signal and the cross-regulatory interactions with other signalling cascades.

Despite the bewildering number of cell types and patterns found in the animal kingdom, only a few signalling pathways are required to generate them.  One clear conclusion to be drawn from all these studies is that there is a rather limited number of signalling pathways to generate the remarkable variety and complexity of form and function that we see today, both across phyla and within the individuals of a given species. Understanding how these pathways have emerged and function can thus illuminate the origin of morphological diversity, as well as the molecular and cellular basis of development and disease. Amongst the central canon of developmental signalling pathways are the :

The essential signalling pathways for animal 
development:


Hedgehog (Hh)
Wingless related (Wnt)
Transforming growth factor-β (TGF-β)
Receptor tyrosine kinase (RTK)
Notch
Janus kinase (JAK)/signal transducer  
Activators of transcription (STAT) protein kinases
Nuclear hormone pathways
Bone morphogenetic proteins (BMP)
Epidermal growth factor receptors (EGFR)
Fibroblast growth factors (FGF)

Hedgehog
The conserved Hedgehog (Hh) pathway is essential for normal embryonic development and plays critical roles in adult tissue maintenance, renewal and regeneration.  The Hedgehog (Hh) family of proteins control cell growth, survival, and fate, and pattern almost every aspect of the vertebrate body plan. The Hh gradient is shaped by several proteins that are specifically required for Hh processing, secretion, and transport through tissues. The primary cilium is crucial for mammalian Hedgehog signaling

Wnt signaling pathway
The Wnt signalling pathway is an ancient and evolutionarily conserved pathway that regulates crucial aspects of cell fate determination, cell migration, cell polarity, neural patterning and organogenesis during embryonic development.

Transforming growth factor-β (TGF-β)
Transforming growth factor-β (TGF-β) superfamily signaling plays a critical role in the regulation of cell growth, differentiation, and development in a wide range of biological systems.

Receptor tyrosine kinase
Tyrosine phosphorylation is an essential element of signal transduction in multicellular animals.

Notch
Notch signaling is an evolutionarily conserved pathway in multicellular organisms that regulates cell-fate determination during development and maintains adult tissue homeostasis.

JAK/STAT
Cell-cell signaling represents an essential hallmark of multicellular organisms, which necessarily require a means of communicating between different cell populations, particularly immune cells. Cytokine receptor signaling through the Janus kinase/Signal Transducer and Activator of Transcription/Suppressor of Cytokine Signaling (CytoR/JAK/STAT/SOCS) pathway embodies one important paradigm by which this is achieved.

Bone morphogenetic proteins (BMP)
Bone Morphogenetic Proteins (BMPs) are a group of signaling molecules that belongs to the Transforming Growth Factor-β (TGF-β) superfamily of proteins. Initially discovered for their ability to induce bone formation, BMPs are now known to play crucial roles in all organ systems. BMPs are important in embryogenesis and development, and also in maintenance of adult tissue homeostasis.

Above lists only the core pathways, but science has so far catalogized about sixty different signaling pathways, depending on area of biology:
https://www.thermofisher.com/br/en/home/life-science/antibodies/antibodies-learning-center/antibodies-resource-library/cell-signaling-pathways/view-all-pathways.html


Since all seven signal transduction pathways are essential for multicellular development: is it feasible to suppose that they were all co-opted or borrowed from unicellular organisms? If so, they still need the information to direct new body plan development. Where did this information come from?

Most signal-relay stations we know about were intelligently designed. Signal without recognition is meaningless.  Communication implies a signalling convention (a “coming together” or agreement in advance) that a given signal means or represents something: e.g., that S-O-S means “Send Help!”   The transmitter and receiver can be made of non-sentient materials, but the functional purpose of the system always comes from a mind.  The mind uses the material substances to perform an algorithm that is not itself a product of the materials or the blind forces acting on them.  Signal sequences may be composed of mindless matter, but they are marks of a mind behind the intelligent design.

Wanna Build a Cell? A DVD Player Might Be Easier 1
http://reasonandscience.heavenforum.org/t2404-wanna-build-a-cell-a-dvd-player-might-be-easier

The picture: 
bacterial chemotaxis signalling array
https://www.ndm.ox.ac.uk/principal-investigators/project/structure-and-function-of-bacterial-chemotaxis-signaling-array-by-cryo-electron-tomography

Transforming growth factor-beta (TGFβ)

The transforming growth factor-beta (TGFβ) receptor-catalyzed phosphorylation of Smad transcription factors, which permits their nuclear entry (which is crucial for pattern formation and cell-fate determination in metazoan embryonic development)

Overview  on Various Signaling Pathways

Estimating the number of signaling pathways in both eukaryotes and prokaryotes is a challenging task because "signaling pathway" can be defined and subdivided in various ways depending on the level of detail one considers. Additionally, the study of cellular signaling is a highly active area of research, with new pathways and details about existing pathways being discovered regularly.

Eukaryotic Signaling Pathways

There are dozens of primary, well-characterized signaling pathways in eukaryotes, especially in mammals. Many pathways can be further subdivided based on specific ligands, receptors, or downstream effectors. For example, the "MAPK pathway" is a general term, but there are several distinct MAPK pathways based on the specific MAPK involved (e.g., ERK, JNK, p38). Moreover, in multicellular eukaryotes, the diversity increases due to tissue-specific or developmental stage-specific signaling pathways. A rough estimate might be in the range of 50-100 major eukaryotic signaling pathways, but if we delve into more detailed categorizations, this number could easily be in the hundreds.

Prokaryotic Signaling Pathways

Bacterial signaling pathways differ from those of eukaryotes and are generally focused on environmental sensing, community behavior, and resource utilization.  Prokaryotes, especially bacteria, also have numerous signaling pathways that allow them to respond to environmental changes, interact with other cells, or regulate their metabolism. The Two-Component System (TCS) signaling is predominant, and there are potentially hundreds of unique TCSs even within a single bacterial species. Other systems like quorum sensing, various secretion systems, and metabolic regulatory pathways further add to the diversity. Given the vast number of bacterial species and the variety of environments they inhabit, the number of prokaryotic signaling pathways is likely in the thousands. However, not all of these are well-characterized or universally present across all bacteria. It's a bit challenging to provide a precise estimate, but we can say there are likely hundreds of eukaryotic pathways (when considering subdivisions and specific pathways) and thousands of prokaryotic pathways, considering the vast diversity among bacteria.

Signaling pathways play a pivotal role in ensuring cells respond appropriately to external stimuli, thus guiding processes like growth, differentiation, metabolism, and immune responses. These pathways are often intricate and intertwined, ensuring the coordinated functioning of cellular processes. Here's an overview of some notable signaling pathways. These pathways, among others, exemplify the intricate web of cellular communication governing our bodies. Understanding these pathways in depth offers insights into disease mechanisms, paving the way for targeted therapies and potential cures.

Eukaryotic-Only Signaling Pathways

Adiponectin Signaling Pathway: Particularly significant in fat tissue, regulating glucose levels and fatty acid breakdown.
AHR (Aryl Hydrocarbon Receptor) Signaling: Response to environmental toxins.
Akt/PKB Signaling: Regulates cell survival and proliferation.
AMPK (AMP-activated Protein Kinase) Pathway: Energy sensor and cellular metabolism regulation.
Androgen Signaling: Central to male reproductive processes and other cellular activities.
Angiotensin II Receptor Signaling: Critical in blood pressure regulation.
Apelin Signaling Pathway: Influences cardiovascular development and angiogenesis.
Autophagy Signaling Pathway: Crucial for the degradation and recycling of cellular components.
BAK/BAX Pathway: Involved in mitochondrial-mediated apoptosis.
B Cell Receptor Signaling: Integral for B cell maturation and the production of antibodies.
BMP (Bone Morphogenetic Protein) Pathway: Involved in bone and cartilage formation.
cAMP-dependent Pathway: Utilizes cyclic AMP to activate protein kinase A.
Calcineurin-NFAT Signaling: Important for T cell activation and other immune responses.
Calcium Signaling: Uses calcium ions as intracellular messengers.
Cardiac Hypertrophy Signaling: Pathways leading to enlargement of the heart muscle in response to stress or injuries.
Caveolar-mediated Endocytosis Signaling: Focuses on the process where cells ingest external fluid, macromolecules, and large particles, including other cells.
cGMP-PKG Signaling Pathway: Important for regulating gene expression, cell proliferation, and apoptosis.
Chemokine Signaling Pathway: Involved in the directed migration of immune cells.
Cholinergic Receptor Signaling: Regulates the response to acetylcholine in various contexts, including muscle activation.
ChREBP (Carbohydrate Response Element-Binding Protein) Pathway: Modulates glycolysis and lipid synthesis in response to glucose.
Circadian Clock Pathway: Controls the daily rhythm of many physiological processes.
c-Met Signaling: Encodes the hepatocyte growth factor receptor involved in cell survival, embryogenesis, and cellular migration.
CRH (Corticotropin-Releasing Hormone) Signaling: Regulates the body's response to stress.
Cytokine Signaling Pathway: Critical for cell communication, especially in immune responses.
Delta-Notch Signaling Pathway: Regulates interactions between physically adjacent cells.
Dopaminergic Synapse Signaling: Important for several critical functions, including mood and motor control.
EGFR (Epidermal Growth Factor Receptor) Signaling: Plays a key role in the regulation of cell growth, survival, and differentiation.
Ephrin Receptor Signaling: Involved in developmental processes and in particular, in pattern formation.
ERBB Signaling Pathway: Important for cell growth and differentiation.
ERK/MAPK Pathway: Regulates cell proliferation, differentiation, and survival.
Estrogen Receptor Signaling: Mediates the effects of estrogen in various tissues, affecting growth, differentiation, and function.
FAK (Focal Adhesion Kinase) Signaling: Involved in cell movement and growth.
FGF (Fibroblast Growth Factor) Signaling: Plays critical roles in cell growth, embryonic development, and tissue repair.
FoxO Signaling Pathway: Involved in a variety of cellular processes, including cell cycle control, apoptosis, and oxidative stress resistance.
Frizzled Signaling Pathway: Critical for embryonic development.
GABA Receptor Signaling: Mediates the principal inhibitory neurotransmitter in the mammalian brain.
Gastrin-CREB Signaling Pathway: Plays a role in gastric secretion and gastric mucosal growth.
Ghrelin Signaling Pathway: Involved in the stimulation of growth hormone secretion and regulation of energy homeostasis.
Glioma Signaling Pathway: Pertains to the signaling involved in brain tumor formation.
GnRH (Gonadotropin-Releasing Hormone) Signaling: Controls the release of reproductive hormones.
Hedgehog Signaling Pathway: Important in embryonic development.
Hippo Signaling Pathway: Regulates organ size by controlling cell proliferation and apoptosis.
Histamine H1 Receptor Signaling: Involved in inflammatory responses and serves as a target for allergy medications.
HSP90 (Heat Shock Protein 90) Signaling: Plays a role in the folding, stability, and function of other proteins.
Huntington Disease Signaling: Pertains to the signaling defects associated with Huntington's disease.
IGF-1 (Insulin-like Growth Factor-1) Signaling: Important for growth and plays a key role in muscle repair.
IL-6 (Interleukin-6) Signaling: Plays a role in inflammation and the immune response.
Insulin Receptor Signaling: Critical for glucose uptake in response to insulin.
Integrin Signaling Pathway: Involved in cell adhesion and cell-extracellular matrix interactions.
Interferon Receptor Signaling: Plays a role in antiviral response and immune modulation.
JAK/STAT (Janus Kinase/Signal Transducer and Activator of Transcription) Signaling: Mediates responses to cytokines and growth factors.
JNK (c-Jun N-terminal Kinase) Signaling: Responds to stress signals.
KIT Receptor Signaling: Has a role in cell growth, survival, and differentiation.
Leptin Signaling Pathway: Regulates body weight by controlling appetite and energy expenditure.
mTOR (Mammalian Target Of Rapamycin) Signaling: Involved in cell growth and proliferation.
NF-κB (Nuclear Factor Kappa B) Signaling: A key regulator of immune responses, inflammation, and cell survival.
Notch Signaling Pathway: Regulates cell-fate determination during development.
p38 MAPK Signaling: Responds to stress signals and is involved in inflammatory responses.
p53 Signaling Pathway: A major pathway for detecting DNA damage and triggering apoptosis.
PACAP (Pituitary Adenylate Cyclase-Activating Polypeptide) Signaling: Functions in neuroprotection and neuromodulation.
Parathyroid Hormone Signaling: Regulates calcium balance within the body.
PCP (Planar Cell Polarity) Signaling: Essential for the polarization of cells within the plane of a tissue.
PDGF (Platelet-Derived Growth Factor) Signaling: Promotes cellular proliferation and differentiation.
PI3K (Phosphatidylinositol 3-Kinase) Pathway: Involved in cell survival, proliferation, and differentiation.
PPAR (Peroxisome Proliferator-Activated Receptor) Signaling: Plays a role in the regulation of lipid metabolism and inflammation.
PTH (Parathyroid Hormone) Signaling: Vital in bone remodeling and calcium homeostasis.
Ras Signaling: Regulates cell growth, survival, and differentiation.
Rho GTPase Signaling: Central to a variety of cellular processes including cell morphology and cell migration.
S1P (Sphingosine-1-Phosphate) Signaling: Involved in cell growth, survival, and immune cell trafficking.
Sonic Hedgehog Signaling: Essential for tissue patterning during development.
T Cell Receptor Signaling: Critical for T cell activation and adaptive immune response.
TGF-β (Transforming Growth Factor-beta) Signaling: Has roles in cell growth, differentiation, and tissue homeostasis.
Toll-like Receptor Signaling: Integral for innate immune response.
VEGF (Vascular Endothelial Growth Factor) Signaling: Prominent in angiogenesis, or the formation of new blood vessels.
Wnt Signaling Pathway: Important in embryonic development and tissue homeostasis.

Creating an exhaustive list of all prokaryotic signaling pathways is quite extensive, especially given the vast diversity and the continual discovery of new pathways in the field of microbiology. However, I'll provide a list of some of the major and well-known signaling pathways/mechanisms predominantly found in prokaryotic cells, particularly in bacteria:

Crosstalk Among Signaling Pathways in Cellular Processes

Various signaling pathways frequently interact with one another, either through shared intermediates or through modulation of each other's functions. This "crosstalk" ensures that cellular responses are coordinated and appropriate for the given context. Here are several examples of how the signaling pathways you've listed crosstalk with each other:

EGFR and Ras Signaling

EGFR Activation: When EGFR (Epidermal Growth Factor Receptor) is activated by its ligand, it activates Ras, a small GTPase, which then initiates a cascade of phosphorylation events.
Ras and ERK/MAPK: Ras activates the ERK/MAPK pathway, which controls cellular proliferation, differentiation, and survival.

Hedgehog and Wnt Signaling

Coordination in Development: Both the Hedgehog and Wnt pathways play crucial roles in embryonic development, and they often work together to regulate processes like cell fate determination and tissue patterning.
Regulation of Gli Proteins: The Hedgehog pathway, through its effector Gli proteins, can regulate the expression of Wnt-related genes.

Akt/PKB and mTOR Signaling

Akt Activation and mTOR: Akt can activate mTOR (Mammalian Target Of Rapamycin), which then regulates cell growth and proliferation.
Insulin and Akt: The insulin receptor signaling pathway activates Akt, integrating metabolic responses with growth signaling.

TGF-β and Smad Signaling

TGF-β Activation: TGF-β activation leads to the phosphorylation of receptor-regulated Smads (R-Smads).
Smad and Wnt: Smad proteins can interact with components of the Wnt pathway to modulate responses, demonstrating crosstalk between these pathways in processes like embryonic development and tissue homeostasis.

JAK/STAT and Cytokine Signaling

Cytokine Receptors: Many cytokine receptors, upon ligand binding, activate the JAK/STAT pathway, which mediates responses to cytokines and growth factors.
Interferon and JAK/STAT: Interferon receptor signaling activates the JAK/STAT pathway, playing a role in antiviral responses and immune modulation.

PI3K and Akt/PKB Signaling

PI3K Activation: PI3K activation results in the production of phosphatidylinositol-3,4,5-trisphosphate (PIP3), a second messenger.
PIP3 and Akt: PIP3 recruits Akt to the plasma membrane, where it's activated, playing roles in cell survival, proliferation, and differentiation.

Notch and Delta-Notch Signaling

Direct Interaction: The Notch signaling pathway is initiated when a Notch receptor interacts with its ligand, Delta, on an adjacent cell, illustrating the direct interplay between these pathways in determining cell fate.

These examples represent just a fraction of the interactions and crosstalk that occur among the numerous signaling pathways in a cell. Each pathway can have multiple points of interaction with others, and their combined effects ensure that cells respond appropriately to a myriad of internal and external cues.

Decoding of Signaling Pathways in Cellular Processes

Cellular signaling pathways regulate essential processes such as growth, differentiation, and cell death. Understanding these pathways is fundamental for both basic biology and therapeutic applications. 

EGFR and Ras Signaling

Molecular Interactions: Scientists have detailed the sequence of molecular events that occur upon activation of EGFR, leading to Ras activation and its downstream effects.

Hedgehog and Wnt Signaling

Embryonic Development: Both pathways have been studied extensively for their roles in embryonic development. The molecular intricacies, such as how Gli proteins can influence Wnt signaling, have been revealed.

Akt/PKB and mTOR Signaling

Growth Signaling: Akt's role in activating mTOR and how this regulates cell growth and proliferation is well-understood.

TGF-β and Smad Signaling

Smad Activation: The process by which TGF-β activates receptor-regulated Smads is known.
Interplay with Other Pathways: Interactions of Smad proteins with components of other pathways, such as Wnt, have been elucidated.

JAK/STAT and Cytokine Signaling

Immune Responses: JAK/STAT's role in mediating responses to cytokines and growth factors is clear. The pathway's activation in response to interferons plays a role in antiviral and immune responses.

PI3K and Akt/PKB Signaling

Akt Activation: PI3K's role in producing PIP3, which then activates Akt, is known. This understanding is critical for realizing Akt's functions in cell survival, proliferation, and differentiation.

Notch and Delta-Notch Signaling

Cell Fate Determination: The interaction between Notch receptors and their ligands, like Delta, has been decoded. This direct interplay is essential for determining cell fate during development.

These decoded pathways offer valuable insights into normal cellular functions and the pathogenesis of diseases, opening doors for therapeutic innovations.

Interdependence, Irreducible Complexity, and Design in Cellular Signaling

The intricate network of cellular signaling pathways and their crosstalk presents an interesting argument when considering the origin of such systems. Considering the crosstalk and interdependencies among pathways, the absence of any single pathway would disrupt the entire signaling network, making the step-by-step evolution implausible. Many pathways do not operate in isolation but depend on signals from other pathways. This crosstalk ensures a harmonized cellular response. The deep integration of pathways suggests they must have appeared nearly simultaneously, which challenges the gradual development model. The intricacy and coordination of signaling pathways seems to be evidence for a designed system, where every component has a specific role and purpose.


Bacterial Signaling Systems and Adaptation Mechanisms

Bacteria, though microscopic in size, possess a plethora of signaling systems and mechanisms that enable them to adapt, thrive, and even dominate a myriad of environments. These systems provide bacteria with the ability to sense their surroundings, communicate with one another, and appropriately respond to environmental cues. This intricate network of signaling pathways and regulatory mechanisms plays a vital role in bacterial physiology, survival, and pathogenicity. The following list provides an overview of some of the most studied and understood bacterial signaling systems and their functions: Bacteria have a wide range of signaling systems to navigate and adapt to the myriad challenges they face in their environments. From simple chemotactic responses to complex quorum-sensing mechanisms, these systems underline the adaptability and resilience of bacteria. Understanding these systems is not only fundamental to microbiology but also has significant implications for human health, especially in the context of pathogenic bacteria and antibiotic resistance.

Agr System: A quorum sensing system in Staphylococcus aureus which controls virulence.
BvgAS System: Regulates virulence genes in Bordetella species.
CheA/CheY System: Central to chemotaxis, helping bacteria sense and respond to chemical gradients.
Chemotaxis Signaling: Directs bacterial movement towards beneficial environments and away from harmful ones.
Com System: Facilitates genetic competence in certain bacteria like Streptococcus pneumoniae, allowing DNA uptake.
c-di-GMP Signaling: Regulates the transition between motile and sessile states in bacteria.
CpxAR System: Responds to envelope stress in gram-negative bacteria.
DesK/DesR System: Enables bacteria to sense and adapt to temperature changes.
FixL/FixJ System: Important in nitrogen-fixation in symbiotic bacteria.
Iron-Uptake Regulation: Ensures bacteria maintain essential iron levels, often critical for pathogenesis.
LuxR/LuxI System: A quorum sensing system in Vibrio fischeri that regulates bioluminescence.
LytSR System: Responds to cell wall stress in certain gram-positive bacteria.
NarL/NarX System: Responds to nitrate and nitrite presence, helping in anaerobic respiration.
Nitrogen Fixation (Nif) Pathway: Allows some bacteria to convert atmospheric nitrogen into ammonia.
OmpR/EnvZ System: Responds to osmotic stress in gram-negative bacteria.
PhoP/PhoQ System: Helps bacteria sense and adapt to low-magnesium environments.
PmrA/PmrB System: Regulates resistance to cationic antimicrobial peptides in certain bacteria.
Pep/Pop System: Detects and responds to misfolded proteins in the periplasm.
QseC/QseB System: Responds to autoinducer-3 and epinephrine/norepinephrine, playing a role in virulence in E. coli.
Quorum Sensing (QS): Allows bacteria to sense and respond to cell population density.
ResDE System: Controls anaerobic respiration in Bacillus subtilis.
Rcs System: Regulates capsule synthesis in E. coli and other gram-negative bacteria.
RelA/SpoT System: Controls the stringent response, allowing bacteria to adapt to nutrient starvation.
Sporulation Signaling: Enables certain bacteria, like Bacillus subtilis, to form endospores.
Tad (Tight Adherence) System: Crucial for biofilm formation in bacteria like Aggregatibacter actinomycetemcomitans.
Two-Component System (TCS): A fundamental bacterial signaling mechanism with a sensor histidine kinase and a response regulator.
UhpA/UhpB System: Senses extracellular glucose-6-phosphate in E. coli.
VanR/VanS System: Regulates vancomycin resistance in Enterococcus faecium.
VieS/VieA System: Helps Vibrio cholerae adapt to varying viscosities in its environment.
Wsp System: Involved in the regulation of surface attachment and biofilm formation.

Archaeal Signaling and Regulatory Pathways

Archaeal signaling and regulatory pathways offer a fascinating insight into the ancient mechanisms that enable these microorganisms to thrive in diverse and often extreme habitats. Although archaea resemble bacteria in many aspects, their cellular and molecular strategies are distinct. Their signaling and regulatory pathways govern numerous functions, from communication to defense and from metabolism to adaptation. Understanding these mechanisms underscores the adaptability and resilience of archaea. Archaea, with their ancient lineage and unique cellular mechanisms, have evolved intricate signaling and regulatory pathways. These pathways play an indispensable role in their adaptation to diverse environments, from extreme temperatures to high salinity levels. By regulating their cellular processes, archaea can optimize their energy metabolism, maintain cellular integrity, and ensure their survival in challenging conditions. These mechanisms provide insights into the evolutionary strategies adopted by one of the oldest life forms on Earth.

Genetic Insights into Archaeal Signaling and Regulatory Mechanisms

The genetic makeup of archaea is a treasure trove of information, revealing the molecular intricacies of their signaling and regulatory pathways. Genes involved in these pathways encode a plethora of proteins, from sensors and receptors to transcription factors and effectors. By studying these genes, scientists can unravel the evolutionary history of archaea and gain insights into their adaptive strategies. Additionally, understanding the genetic basis of these pathways offers potential applications in biotechnology, where archaeal enzymes and systems can be harnessed for various industrial processes. The aforementioned pathways collectively highlight the remarkable adaptability and resilience of archaea, enabling their survival in diverse and often extreme habitats.

Agr-like Quorum Sensing System: Analogous to bacterial systems, controlling group behaviors in archaea.
Archaeal Chemotaxis System: Similar to bacterial chemotaxis but with unique features specific to archaea.
Archaeal Two-Component Signal Transduction: Systems enabling archaea to detect and respond to environmental changes.
Cas-Cascade Pathway: Part of the CRISPR-Cas system in archaea that defends against foreign DNA.
CheY-like Response Regulators: Used in archaeal chemotaxis.
DnaA-like Replication Initiators: Involved in the initiation of DNA replication.
eSTK/eSTP Signal Transduction: Encompasses the archaeal extracellular signal-regulated kinase pathways.
Gas Vesicle Synthesis Regulation: Controls buoyancy in some halophilic archaea.
Halocin Production and Sensing: Systems allowing haloarchaea to produce and detect proteinaceous toxins.
Histidine Kinase Signaling: Widespread among archaea to perceive environmental signals.
Lipid Biosynthesis Regulation: Maintains membrane fluidity and function.
Methanogenesis Pathways: Specific to methanogenic archaea for methane production.
NrpR Regulated Nitrogen Uptake: Pathway for nitrogen assimilation in some archaea.
Oxygen Sensing and Response: Mechanisms in aerobic archaea for sensing and responding to oxygen.
Pho4-like Phosphate Sensing: Regulates phosphate uptake in certain archaea.
Phototrophic Signaling: Allows certain archaea to respond to light, as seen in Halobacterium species.
Pilin-based Adhesion: Pathways facilitating archaeal adherence to surfaces.
Potassium Sensing and Transport: Mechanisms to maintain intracellular potassium levels.
Pyrococcus Furiosus Transcriptional Regulation: Pathways controlling gene expression in this hyperthermophilic archaeon.
Salt-sensing and Osmoregulation: Critical for halophilic archaea living in high salt environments.
S-layer Regulation: Governs the synthesis and maintenance of the protective S-layer in many archaea.
Sulfolobus Acidocaldarius DNA Repair: Mechanisms to repair DNA in this acid-loving, hot spring archaeon.
Thermosensory Pathways: Enables thermophilic archaea to respond to temperature changes.
TorRS-like Tolerance Response: Helps certain archaea sense and respond to toxic compounds.
Transmembrane Chemoreceptors: Involved in the chemotaxis of some archaea.
UV Radiation Response: Systems in some archaea to sense and repair UV-induced damage.
VNG117C Pathway: Involved in phototaxis in Halobacterium salinarum.
Zinc Homeostasis and Sensing: Regulates intracellular zinc levels in some archaea.
Archaeal Cyclic-di-GMP Signaling: Second messenger systems in some archaea for various processes.
Cdc6-1 Regulation in Sulfolobus: Control of cell cycle initiation in the archaeon Sulfolobus.

Which signaling pathways are shared among all three domains of life and were probably extant in LUCA?

The Last Universal Common Ancestor (LUCA) represents the shared ancestor of all extant organisms on Earth. Identifying the signaling pathways that are shared among Bacteria, Archaea, and Eukarya can provide insights into the ancient cellular processes that were likely present in LUCA. Several signaling mechanisms and pathways are believed to be evolutionarily conserved across these domains:

Two-Component Systems (TCS)

Presence Across Domains: While this signaling mechanism is predominant in Bacteria and Archaea, rudimentary forms of two-component signaling have also been identified in Eukarya, particularly in plants.
Function: Two-component systems involve a sensor histidine kinase and a response regulator. Upon sensing an environmental cue, the histidine kinase autophosphorylates and subsequently transfers the phosphate to the response regulator, initiating a cellular response.

ATP-binding Cassette (ABC) Transporters

Presence Across Domains: ABC transporters are found in all three domains of life.
Function: These transporters move a variety of molecules across cellular membranes. In some instances, they can sense specific ligands and might change cellular behavior in response.

Protein Phosphorylation

Presence Across Domains: Protein phosphorylation is a universal method of signal transduction.
Function: While Eukaryotes primarily use Ser/Thr and Tyr kinases, Bacteria and Archaea often employ histidine kinases within the two-component systems.

Small Molecules as Messengers

Presence Across Domains: Molecules such as cAMP and ppGpp are utilized across all three domains.
Function: These small molecules serve as intracellular signal carriers in various pathways. Their synthesis and recognition can induce changes in cellular behavior.

Ion Concentration Gradients

Presence Across Domains: Utilization of ion gradients is a universal cellular strategy.
Function: These gradients, especially those involving protons, are crucial for processes like ATP synthesis in cellular energy metabolism.

These conserved pathways offer a glimpse into the ancient cellular machinery of LUCA and how life's fundamental processes have been retained and diversified over billions of years.

How does the lack of homology among certain signaling pathways challenge the concept of universal common ancestry?

The idea of universal common ancestry posits that all living organisms on Earth descended from a single common ancestor, referred to as the Last Universal Common Ancestor (LUCA). This concept suggests that the evolutionary trajectories of life should exhibit certain shared features, or homologies, in fundamental processes and structures. However, the lack of homology among certain signaling pathways challenges this concept. 

Signaling Pathway Diversity

Absence of Shared Pathways: Despite the existence of some universally shared signaling pathways, a significant number of them appear to be domain or lineage-specific. If all organisms arose from a universal common ancestor, one might expect to see more conservation and less divergence in these core cellular processes.
Domain-Specific Complexity: Each domain of life—Bacteria, Archaea, and Eukarya—possesses numerous unique signaling systems. For example, quorum sensing is specific to bacteria, and certain intracellular signaling pathways are more prevalent in eukaryotes. This degree of complexity suggests the independent origins of these systems.
Lack of Intermediate Forms: Universal common ancestry would anticipate the existence of transitional or intermediate forms of signaling pathways that bridge the differences among the domains of life. However, for many pathways, these intermediate forms are absent or not easily identifiable.

Functional Necessity vs. Evolutionary Legacy

Functional Constraints: Some argue that the presence of a signaling pathway in one organism but not in another is due to the specific functional requirements of that organism, rather than an evolutionary legacy. In other words, organisms developed these pathways out of necessity, not because of shared ancestry.

While the lack of homology in signaling pathways provides a line of argument against universal common ancestry, it's worth noting that evolutionary biology considers various mechanisms, like horizontal gene transfer, loss of function, and the aforementioned convergent evolution, to explain these discrepancies. Thus, while these arguments are thought-provoking, they form only one part of a much larger and complex discussion about the origins  of life and biodiversity on Earth.

Convergent Evolution vs. Convergent Design: Insights into the Origins of Similar Signaling Pathways in Different Domains of Life

The observation of similar signaling pathways in different domains of life can be interpreted from various perspectives. While convergent evolution posits that similar features arise independently in separate lineages due to similar environmental pressures, the idea of convergent design suggests an intentional design principle behind these similarities. 

Convergent Evolution

Environmental Pressures: Similar environmental challenges can lead organisms from different lineages to develop similar solutions. For example, wing structures have evolved independently in birds, bats, and insects as a response to the need for flight.
Independent Origins: In the context of signaling pathways, convergent evolution implies that some pathways, though appearing similar, might have originated independently in different domains of life. This is often driven by the organisms' need to respond to similar cellular or environmental cues.
Natural Selection: Over time, natural selection might favor certain traits or pathways that offer a competitive advantage in a particular environment. As a result, similar pathways can emerge in entirely unrelated lineages.

Convergent Design

Intentional Similarities: Convergent design implies that the similarities observed are the result of an intentional design or pattern, rather than random evolutionary events. This interpretation often aligns with certain philosophical or theological views that believe in a designer or higher power.
Functional Optimization: From a design perspective, the repetition of certain pathways across domains might be seen as an optimization of function. Just as engineers might reuse effective design patterns across different projects, nature might "reuse" effective signaling pathways across different organisms or domains of life.
Shared Blueprint: The idea of convergent design can also suggest that there's a shared blueprint or template that different domains of life follow, leading to the emergence of similar pathways or structures.

While convergent evolution and convergent design offer different explanations for the presence of similar signaling pathways across life's domains, both perspectives highlight the intricate and fascinating nature of life. The decision to adopt one view over the other often depends on a combination of scientific evidence and personal beliefs.


Signal transduction listed at Keggs


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