Cells work automatically with molecular actions in sequences. One such sequence is being worked out now:-http://phys.org/news/2015-10-scientists-essential-amino-acid-sensor.html-"Whitehead Institute scientists have at last answered the long-standing question of how the growth-regulating pathway known as mechanistic target of rapamycin complex 1 (mTORC1) detects the presence of the amino acid leucine—itself a key player in modulating muscle growth, appetite, and insulin secretion. Through a series of protein-mediated signals, mTORC1 interprets cues in the cellular environment, including nutrient availability, and instructs the organism to react accordingly. mTORC1 is apt to trigger growth during abundant times and slow metabolism when food is limited. Over the past several years, researchers in the lab of Whitehead Member David Sabatini have been identifying the many key components of the pathway—whose deregulation is associated with diseases ranging from diabetes to cancer to epilepsy—moving ever closer to finding precisely how mTORC1 actually senses the presence of amino acids.-"Earlier this year, Sabatini's group identified the transmembrane protein SLC38A9 as a putative sensor for arginine, but the sensor for leucine had remained elusive. Now, however, the lab has discovered that Sestrin2—one of a three-member protein family Sabatini previously implicated in amino acid detection—is a highly specific leucine sensor. The finding is reported online this week in the journal Science.-"'We finally have the sensor," says Rachel Wolfson, a graduate student in the Sabatini lab and co-first author of the Science paper. "We've always wanted to find it because we've known that leucine is one of the most important amino acids for the (mTORC1) pathway."-"Wolfson and co-first author Lynne Chantranupong, both of whom were involved in the earlier Sestrin research, found that in the absence of amino acids, Sestrin2 interacts with a protein complex known as GATOR2 to inhibit the mTORC1 pathway, thereby reducing cell growth. They then discovered that leucine binds directly to Sestrin2, disrupting the interaction and activating the mTORC1 pathway.-"'This was a big surprise for us, that there's an amino acid interaction with GATOR2 that's specific for leucine," says Chantranupong, also a graduate student in Sabatini's lab. "This is the first instance of a sensor for leucine, and there may be ways we might be able to take advantage of Sestrin2's leucine binding properties.'"-Comment: And all of this is run by information in the genome. See the video I presented today

A newer article with new discoveries:

https://www.quantamagazine.org/

"Think of liquids with different properties that don’t really mix but, under specific circumstances, cluster and separate like the shifting blobs in a lava lamp. That phenomenon, also known as liquid-liquid phase separation, was once considered to be an exclusively chemical process. But less than a decade ago, Brangwynne became one of the first to observe it happening inside cells as well, and ever since then, biologists have been trying to learn its significance.

"Now scientists are beginning to understand that evolution has tuned certain proteins to act in aggregate like liquids. Through phase separation, they spontaneously self-assemble into dynamic, membrane-free, dropletlike structures that can perform needed tasks in cells.

***

"One of the latest findings is that phase separation allows certain types of cells to cheat death when they are deprived of nutrients or otherwise put under stress. Phase separation enables the cells to turn a large part of their cytoplasm from a liquid to a solid — essentially putting themselves into a hardy condition of stasis until the nutrients return.

***

"That initial work by Brangwynne, Eckmann and Hyman triggered an avalanche of papers investigating the assembly and dispersal of various cytoplasmic proteins under various conditions. The evidence was getting stronger that cells had evolved a fine-tuned mechanism for organizing some of their internal structure and processes through phase separation — that is, letting proteins self-assemble into structures that could perform distinct functions.

***

"Zaburdaev and several of his colleagues, including Alberti, decided to check what happens to proteins when cells are subjected to stresses such as falling temperatures and the sudden disappearance of nutrients. The surprising result they uncovered was that phase separation can be part of a cell’s survival mechanism.

"The cells’ behavior could be likened to hibernation for bears. The animal lays still in a dormant state for weeks, minimizing its expenditure of energy. At a cellular level, phase separation helps the gelatinous cytoplasm make a protective transition into something more solid. “In this ‘solidified’ state, a cell can survive starvation,” Zaburdaev said.

***

"Simply by varying the acidity of the [yeast] cells’ environment, the scientists could induce them to switch into this survival state, even without taking away the cells’ nutrients. The cells could rest this way for hours or even days. “We found that the cells are so rigid that they keep their shape” instead of being deformable, Alberti said. They “transition into a completely different material state.”

"When their normal pH was later restored, the cells returned to normal, “dividing and living happily,” Zaburdaev said.

***

"The team found that when a protein has a certain identifiable domain or region, the protein will form easily reversible gels. In the absence of this domain, the protein forms an irreversible type of assembly — permanently removing it from further use.

"In effect, this domain modifies the protein’s phase behavior and keeps it reusable. “The domain provides a new possibility, for that protein to assemble into a benign kind of gel and not something from which you cannot come back,” Alberti said.

***

"Such results imply that nature has designed the domain sequences to tune the proteins’ material properties.

***

"Recently, for example, the neuroscientist Pietro De Camilli at Yale University and his colleagues found evidence that phase separation might be involved in the controlled release of neurotransmitters at synapses. It had been observed that vesicles containing neurotransmitters routinely hover in clusters near the presynaptic membrane until they are needed. De Camilli’s team showed that a scaffolding protein called synapsin 1 condenses into a liquid phase, along with other proteins, to bind the vesicles into these clusters. When the synapsin is phosphorylated, the droplet rapidly dissipates and the vesicles are freed to spill the neurotransmitters into the synapse."

Comment: Other than the neurological finding directly above, this is yeast research, and how it applies to multicellular organisms is not known. But what is seen at the single cell stage is usually finally found in complex organisms. Too complex for any mechanism than design of specific proteins with this property .

The method used to analyze these chemical processes is through mathematics:

https://www.sciencedaily.com/releases/2018/05/180502094636.htm

"'I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation. (my bold)

"'Essentially we are now discovering the needles in the haystack in terms of the network constructions that can actually exist in nature.

"'Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to 'think' -- essentially giving the cell a 'cognitive' ability, or a 'brain'," she said. "It has been a longstanding mystery in science how this cellular 'brain' works.

"'We could never hope to measure the full complexity of cellular networks -- the networks are simply too large and interconnected and their component proteins are too variable.

"'But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.

***

"An example of perfect adaptation is our sense of smell," she said. "When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present.

"'Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very feint and very strong odours.

"'This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals -- hormones, growth factors, and other chemicals -- and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there.

"'I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.

"'Essentially we are now discovering the needles in the haystack in terms of the network constructions that can actually exist in nature.'"

Comment: this study fits exactly my concept of automatic molecular activity. The limited number of a 'rigid set of mathematical principles' describes this to a 'T'. this is like a cellular brain, as the author states, but because of superior design it becomes a brain equivalent. This is an answer to the Shapiro approach, and fits my knowledge of biochemistry.