Bottom-up biology

By: James V. Kohl | Published on: November 19, 2018

A special issue of Nature extends examples of human idiocy touted by biologically uninformed theorists to claims about: Bottom-up biology

How is that a multitude of different molecules within a lipid envelope all come together to carry out the basic functions required to sustain organisms? Conventionally, biologists have worked from the top down to dissect how components in cells interact in their natural environment. But now technical advances are allowing researchers to take a different tack: using engineering principles to reconstruct biological processes from the bottom up. This special issue explores the potential and possible limits of bottom-up cell biology.

The special issue obfuscates the fact that the creation of energy must be linked from top-down causation to energy-dependent bottom-up cause and effect.
Focus on the benefits of building life’s systems from scratch (11/7/18)

Top down involves a decomposition process. So although a researcher can make a career out of unpicking the workings of a cellular machine such as a ribosome or mitochondrion, the starting point for such projects has always been the role of these structures in existing cells. The work is directed by the context in which it originated and into which it will fold back once complete.

No serious scientist starts with the role of these structures in existing cells. Serious scientists link energy as information from the physiology of reproduction to biophysically constrained cell type differentiation via feedback loops.
How biologists are creating life-like cells from scratch (11/7/18)

Almost anything life-like requires cellular energy, usually in the form of ATP. And although this can be added from the outside to feed a synthetic system, many biologists working on bottom-up approaches argue that a true synthetic cell should have its own power plant, something similar to an animal cell’s mitochondrion or a plant’s chloroplast, both of which make ATP.

Cytosis for ages 10+ starts with ATP and links the creation of energy to the creation of RNA and all biodiversity via claims from 1964.
Dependence of RNA synthesis in isolated thymus nuclei on glycolysis, oxidative carbohydrate catabolism and a type of “oxidative phosphorylation”

The synthesis of RNA in isolated thymus nuclei is ATP dependent.

Which biological systems should be engineered?  (11/6/18)

Engineering a ‘minimal chassis’ that is capable of sustained gene expression and functional homeostasis would be an invaluable starting point for building synthetic cells that produce proteins, form tissues and remain viable for months to years. This would require detailed understanding and incorporation of metabolic pathways, trafficking systems and nuclear import and export — an admittedly tall order.

Order Subatomic and Cytosis
Learn what others ages 10+ have learned about metabolic pathways, trafficking systems and nuclear import and export.
Cell parts to complex processes, from the bottom up  (11/6/18)

…changes in the size and shape of encapsulated compartments — manipulations that are easy in microfabricated systems, but not in living cells — have revealed roles for these parameters in controlling the oscillatory behaviour of proteins involved in cell division2 and the sizes of organelles3.

The oscillatory behavior of proteins is energy-dependent and it has been linked from olfaction to the physiology of reproduction and all biophysically constrained biodiversity in: Olfaction Warps Visual Time Perception
Cellular stretch reveals superelastic powers  (10/31/18)

Latorre and colleagues’ work has revealed a more complex relationship between cell size and the forces that cells experience than was previously appreciated. Future studies should attempt to unravel the mechanisms that enable cells to enter a state of superelasticity and to recover from high levels of deformation. Now that we know cell shape is not an appropriate proxy for assessing cellular tension, it will be crucial to develop ways to accurately monitor tension levels in tissues, so as to better understand the factors that influence tissue shape.

Cellular stretch must be viewed in the context of energy-dependent supercoiled DNA and the virus-driven degradation of messenger RNA that links negative supercoiling to mutations and all pathology.
Active superelasticity in three-dimensional epithelia of controlled shape

Fundamental biological processes are carried out by curved epithelial sheets that enclose a pressurized lumen. How these sheets develop and withstand three-dimensional deformations has remained unclear. Here we combine measurements of epithelial tension and shape with theoretical modelling to show that epithelial sheets are active superelastic materials

See: MicroRNA-based regulation of epithelial–hybrid–mesenchymal fate determination (2013)
Reported as MicroRNA

The researchers discovered that there was an intermediate function, which is termed a “ternary,” or three-way switch. This function relates to the fact that ZEB has the ability to turn itself on due to a positive feedback system. This allows a cell to keep intermediate levels of all four proteins required for the switch. Ben-Jacob notes that the hybrid, or partially on-off state, also supports cancer metastasis by enabling collective cell migration and by imparting stem-cell properties that help migrating cancer cells evade the immune system and anticancer therapies.


Subscribe
Notify of
guest
0 Comments
Inline Feedbacks
View all comments

Want more on the same topic?

Swipe/Drag Left and Right To Browse Related Posts: