Magic embryology: What guides cell development, placement? (Introduction)

by David Turell , Friday, March 15, 2019, 01:12 (1867 days ago) @ Balance_Maintained

There must be a blueprint, but where is it? Cells seem to make optimal decisions based on many stimuli that are chemical, physical force and positional:

https://www.quantamagazine.org/the-math-that-tells-cells-what-they-are-20190313/

"It’s now known that some form of positional information makes genes variously switch on and off throughout the embryo, giving cells distinct identities based on their location. But the signals carrying that information seem to fluctuate wildly and chaotically — the opposite of what you might expect for an important guiding influence.

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"The same precision and reproducibility emerge from a sea of noise again and again in a range of cellular processes. That mounting evidence is leading some biologists to a bold hypothesis: that where information is concerned, cells might often find solutions to life’s challenges that are not just good but optimal — that cells extract as much useful information from their complex surroundings as is theoretically possible.

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"For decades, scientists have been studying fruit fly larvae for clues about how development unfolds. Some details became apparent early on: A cascade of genetic signals establishes a pattern along the larva’s head-to-tail axis. Signaling molecules called morphogens then diffuse through the embryonic tissues, eventually defining the formation of body parts.

"Particularly important in the fly are four “gap” genes, which are expressed separately in broad, overlapping domains along the axis. The proteins they make in turn help regulate the expression of “pair-rule” genes, which create an extremely precise, periodic striped pattern along the embryo. The stripes establish the groundwork for the later division of the body into segments.

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"That prompted a group at Princeton University, led by the biophysicists Thomas Gregor and William Bialek, to suspect something else: that the cells could instead get all the information they needed to define the positions of pair-rule stripes from the expression levels of the gap genes alone, even though those are not periodic and therefore not an obvious source for such precise instructions.

"And that’s just what they found.

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"Even given the limited number of molecules and underlying noise of the system, the varying concentrations of the gap genes was sufficient to differentiate two neighboring cells in the head-to-tail axis — and the rest of the gene network seemed to be transmitting that information optimally.

"But new work shows if the cells can make optimal use of the information available, they can determine their location early, from the gap genes expression alone.

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"How the cells do it remains a mystery. Right now, “the whole thing is kind of wonderful and magical,” said John Reinitz, a systems biologist at the University of Chicago.

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'The findings provide a fresh perspective on Waddington’s idea of a developmental landscape. According to Gregor, their work indicates that there’s no need for 20 questions or a gradual refinement of knowledge after all. The landscape “is steep from the beginning,” he said. All the information is already there.

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"if these regulatory regions need to perform an optimal decoding function, that potentially limits how they can evolve — and in turn, how an entire organism can evolve. “We have this one example … which is the life that evolved on this planet,” Kondev said, and because of that, the important constraints on what life can be are unknown. Finding that cells show Bayesian behavior could be a hint that processing information effectively may be “a general principle that makes a bunch of atoms stuck together loosely behave like the thing that we think is life.”

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“'I don’t think optimization is an aesthetic or philosophical idea. It’s a very concrete idea,” Bialek said. “Optimization principles have time and again pointed to interesting things to measure.” Whether or not they are correct, he considers them productive to think about.

“'Of course, the difficulty is that in many other systems, the property being decoded is more difficult than one-dimensional position [along the embryo’s axis],” Walczak said. “The problem is harder to define.”

"That’s what made the system Bialek and his colleagues studied so tantalizing. “There aren’t many examples in biology where a high-level idea, like information in this case, leads to a mathematical formula” that is then testable in experiments on living cells, Kondev said."

Comment: Note the important use of information which is guiding the making of an embryo. A blueprint exists in an orchestrated mass of stimuli. As in a symphony, it has to written by a composer.