Our Bodies Are Formed Streams
This is a preliminary draft of one chapter of a book-in-progress
tentatively entitled, “Evolution As It Was Meant To Be — And the Living Narratives That Tell Its Story”.
You will find
a fairly lengthy article serving as a kind of extended abstract of major
parts of the book. This material is part of the
Biology Worthy of Life
Project. Copyright 2017-2021
The Nature Institute.
All rights reserved. Original publication: August 27, 2019.
Last revision: August 27, 2019.
In this materialist era, we like our reality hard and our truths
weighty and rock solid. We may accept that there are states
of matter less substantial than rocks, but in our imaginations we turn
even fluids and gases into collections of tiny particles more or
less closely bound together. Similarly, in our reconstructions of
physiological processes, material structures come first, and only
then can movement, flow, and meaningful activity somehow occur.
How, after all, can there be movement without things to do the
moving? (It’s easy to forget that energy, fields, and forces are not
things!) Ask someone to describe the circulatory system, and you will
very likely hear a great deal about the heart, arteries, veins,
capillaries, red blood cells, and all the rest, but little or nothing
about the endless subtleties of circulatory movement through which,
for example, the structured heart first comes into being (see
Yet there is no escaping the fact that we begin our lives in a thoroughly
fluid and plastic condition. Only with time do relatively solid and
enduring structures precipitate out as tentatively formed “islands” within
the streaming rivers of cells that shape the life of the early embryo. As
adults, we are still about seventy percent water.
One might think quite differently based on the scientific rhetoric to
which we are daily exposed. This could easily lead us to believe that the
real essence and solid foundation of our lives was from the beginning
rigidly established inside those very first cells. There we find DNA
macromolecules that, in a ceaseless flood of images, are presented to us
as crystalline forms in the shape of a spiraling ladder — a ladder whose
countless rungs constitute the fateful stairway of our lives. So, too,
with the proteins and protein complexes of our bodies: we have been told
for decades that they fold precisely into wondrously efficient
molecular machines whose all-important functions are predestined by
the DNA sequence.
The trouble is, biological researches of the last few decades have not
merely hinted at an altogether different story; they have (albeit
sometimes to deaf ears) been trumpeting it aloud as a theme with a
thousand variations. Even the supposedly “solid” structures and molecular
complexes in our cells — including the ones we have imagined as strict
determinants of our lives — are caught up in functionally significant
movement that the structures themselves can hardly have originated. (See
“What Brings Our Genome Alive?”, and
“The Sensitive, Muscular Cell”.)
Nowhere are we looking either at a static sculpture or at controlling
molecules responsible for the sculpting. In an article in Nature
following the completion of the Human Genome Project, Helen Pearson
interviewed many geneticists in order to assemble the emerging picture of
DNA. One research group, she reported, has shown that the molecule is made
“to gyrate like a demonic dancer”. Others point out how chromosomes “form
fleeting liaisons with proteins, jiggle around impatiently and shoot out
exploratory arms”. Phrases such as “endless acrobatics”, “subcellular
waltz”, and DNA that “twirls in time and space” are strewn through the
article. “The word ‘static’ is disappearing from our vocabulary”, remarks
cell biologist and geneticist Tom Misteli, a Distinguished Investigator at
the National Cancer Institute in Bethesda, Maryland.
Everywhere we look, shifting form and movement show themselves to be the
“substance” of biological activity. The physiological narratives of our
lives play out in gestural dramas that explain the origin and significance
of structures rather than being explained by those structures.
Multiple, superimposed images from a movie, showing movements in a fruit
fly oocyte (a developing egg). Yolk granules are stained green, and tiny
red fluorescent polystyrene beads have been injected into the egg to show
the dynamism of flow in the egg body over
Hannah Landecker, a professor of both genetics and sociology at UCLA,
having looked at the impact of recent, highly sophisticated cellular
imaging techniques on our understanding, has written: “The depicted cell
seems a kind of endlessly dynamic molecular sea, where even those
‘structures’ elaborated by a century of biochemical analysis are
constantly being broken down and resynthesized.” And she adds: “It is not
so much that the structures begin to move, but movements — for example in
the assembly and self-organization of the cytoskeleton — begin to
And in a paper that appeared as I was writing this chapter, a team of
biochemists from Duke and Stanford Universities point out how inadequate
is our knowledge of the action of biomolecules when all we have is a
frozen structure of the sort commonly reported in the literature. “In
reality”, they say, “all macromolecules dynamically alternate between
conformational states [that is, between three-dimensional folded shapes]
to carry out their biological functions”:
Decades ago, it was realized that the structures of biomolecules are
better described as “screaming and kicking”, constantly undergoing motions
on timescales spanning twelve orders of magnitude, from picoseconds
[trillionths of a second] to seconds.
(Ganser et al. 2019)
Why, after all, should we ever have expected our physiology to be less a
matter of gesturings than is our life as a whole?
A long way from
According to the old story of the machine-organism, a protein-coding DNA
sequence, or gene, is not only mirrored in an exact messenger RNA (mRNA)
sequence, but the mRNA in turn is translated into an exact amino acid
sequence in the resulting protein, which finally folds into a fixed shape
predestined by that sequence. It was a picture of perfect, lawful,
lockstep necessity, leading from DNA through mRNA to a final, functional
“There is a sense,” wrote Richard Dawkins, “in which the three-dimensional
coiled shape of a protein is determined by the one-dimensional sequence of
code symbols in the DNA”. Further, “the whole translation, from strictly
sequential DNA read-only memory to precisely invariant three-dimensional
protein shape, is a remarkable feat of digital information technology”
(Dawkins 2006, p. 171).
And these proteins in turn were thought to carry out their functions by
neatly engaging with each other in a machine-like manner, snapping into
place like perfectly matched puzzle pieces or inserting into each other
like keys in locks.
We now know, and already knew when Dawkins published those words, that
everything about this narrative was wrong — and not only the parts about
DNA and RNA. Among proteins (those “workhorses of the cell”) every
individual molecule lives in transformational movement — as a dynamic
ensemble of rapidly “morphing”, or interconverting, conformations — and
therefore does not have a “precisely invariant three-dimensional shape”.
But there is much more that wholly escaped Dawkins’ computerized
Quite apart from the fact that each protein molecule rapidly shifts
between distinctly different, folded structures, we now know that
intrinsically disordered proteins — proteins that, in whole or in
part, have no particular, inherent structure at all — are crucial for much
of a cell’s functioning. Researchers refer to “fluid-like” and
(Grant et al. 2010;
Zhou et al. 1999).
This is why biophysicist Konstantin Turoverov and his Russian and American
colleagues tell us that “the model of the organization of living matter is
changing to one described by highly dynamic biological soft matter”. For
decades, they note, protein interactions were “considered to be rigid,
where, for a given protein, a unique 3D structure defined a unique
biological activity.” However,
it is now realized that many protein functions rely on the lack of
specific structure. This recognition has changed the classical
consideration of a functioning protein from a quasi-rigid entity with a
unique 3D structure resembling an aperiodic crystal into a softened
conformational ensemble representation, with intrinsic disorder affecting
different parts of a protein to different
(Turoverov et al. 2019, emphasis added)
Clearly, the finally achieved protein need not be anything like the
predetermined, inflexible mechanism with a single, well-defined structure
imagined by Dawkins. Proteins can be true shape-shifters, responding and
adapting to an ever-varying context — so much so that (as the noted
experimental biologist, Stephen Rothman has written) the “same” proteins
with the same amino acid sequences can, in different environments, “be
viewed as totally different molecules” with distinct physical and chemical
(2002, p. 265).
Many intrinsically unstructured proteins are involved in regulatory
processes, and often serve as Proteus-like hub elements at the center of
large protein interaction networks
(Gsponer and Babu 2009).
They also play a decisive role in molecular-level communication within and
between cells, where their flexibility allows them to modulate or even
reverse the typical significance of a
in effect transforming do this into do that
But the troubling question arises: if unstructured proteins, or
unstructured regions in proteins, are not “pre-fitted” for particular
interactions — if, in their “molten” state, they have boundless
possibilities for interacting with other molecules and even for reversing
their effects — how do these proteins “know” what to do at any one place
and time? Or, as one pair of researchers put it, “How is the logic of
molecular specificity encoded in the promiscuous interactions of
intrinsically disordered proteins?”
(Zhu and Brangwynne 2015).
In the next section we will look at one of the most recent and dramatic
developments in cellular physiology, which has seemed to many biologists
to offer an approach to this problem.
But first we should note the continuing mechanistic bias in the negative
descriptors, “disordered” and “unstructured”, which I have grudgingly
adopted from the conventional literature. Contrary to this usage, the
loose, shifting structure of a protein need be no more disordered than the
graceful, swirling currents of a river or the movements of a ballet
dancer. Given the many living processes these proteins harmoniously
support and participate in (including the movements of the ballet dancer),
it would be strange to assume that their performance is anything
less than graceful, artistic, purposive, and meaningful.
phases of life
It has become increasingly clear in recent years, that, quite apart from
its cytoskeleton and membrane-bound organelles (Chapter 4), the fluid
cytoplasm in each cell is elaborately and “invisibly” organized. Various
macromolecular complexes and other molecules, in more or less defined
mixes, congregate in specific locations and sustain a collective identity,
despite being unbounded by any sort of membrane. Here we’re looking at
significant structure, or organization, without even a pretense of
mechanically rigid form. How do cells manage that?
The problem was framed this way by Anthony Hyman from the Max Planck
Institute of Molecular Cell Biology and Genetics in Dresden, and Clifford
Brangwynne from the Department of Chemical and Biological Engineering at
Non-membrane-bound macromolecular assemblies found throughout the
cytoplasm and nucleoplasm … consist of large numbers of interacting
macromolecular complexes and act as reaction centers or storage
compartments … We have little idea how these compartments are
organized. What are the rules that ensure that defined sets of proteins
cluster in the same place in the cytoplasm?
Even more puzzling, a “compartment” can maintain its functional
(purposive) identity despite the rapid exchange of its contents with the
surrounding cytoplasm. “Fast turnover rates of complexes in compartments
can be found throughout the cell. How do these remain as coherent
structures when their components completely turn over so quickly?”
(Hyman and Brangwynne 2011).
Part of the picture that has recently come into focus has to do with the
phases of matter and the transitions between these phases. (Think, for
example, of the solid, liquid, and gaseous phases of water, or of
solutions and gels — matter in different states.) For example, it’s
possible for well-defined droplets of one kind of liquid to occur within a
different liquid, like oil droplets in water.
We now know that molecular complexes containing both RNA and protein often
gather together to form distinctive RNA-protein liquids that separate out
as droplets within the larger cytoplasmic medium. Like liquids in
general, these droplets tend toward a round shape, can coalesce or divide,
can wet surfaces such as membranes, and can flow. The concentration of
particular molecules may be much greater in the droplets than in the
surrounding fluid, conferring specific and efficient functions upon the
Enzymes and reactants can rapidly diffuse within the liquid droplet, while
also moving with relative ease across the boundary between droplet and
surrounding medium. Yet this boundary can remain distinct until
phase-changing environmental conditions occur — conditions that might
involve slight changes in temperature, pH, salt concentration, electrical
charge, molecular densities, the addition of small chemical groups to
proteins, degradation of proteins, the activity of gene transcription, or
still other factors.
In this way, a very subtle change — originating, say, from an
extracellular influence — can yield a dramatic transformation of
cytoplasmic organization, just as a slight change in the temperature or
salinity of water can shift an ice-forming condition to an ice-melting
one, or vice versa.
Moreover, these phase-separated droplets can be highly organized
internally: “multiple distinct liquid phases can coexist and give rise to
richly structured droplet architectures determined by the relative liquid
(Shin and Brangwynne 2017).
Also, some parts may become
and others may form more or less solid granules. Many such droplets may
pass through stages, from more liquid to more solid, before dispersing.
They form in response to particular needs, perform their work, and then
pass away. Others are more or less permanent. Phase separation has been
called “a fundamental mechanism for organizing intracellular space”
(Shin and Brangwynne 2017)
— one where “function derives not from the structures of individual
proteins, but instead, from dynamic material properties of entire [protein
aggregates] acting in unison through phase changes”
We also know now that weak, transient interactions among intrinsically
unstructured proteins and RNAs can result in crucial, flexible “scaffolds”
that help to assemble these phase-separated aggregates, drawing in a set
of functionally related molecules. “Weak”, “transient”, and “flexible” in
my description here might be taken as indicators of the living,
responsive, and non-machine-like character of the activity.
When things happen in the cell, phase transitions often play
decisive roles, as a University of Colorado group discovered when looking
at phase transitions in a small roundworm. According to the researchers,
these transitions “are controlled with surprising precision in early
development, leading to starkly different supramolecular states” with
altered organization and dynamics. “Reversible interactions among
thousands of [these phase-separated] complexes”, the authors found,
account for “large-scale organization of gene expression pathways in the
(Hubstenberger et al. 2013).
How do you regulate flow and phases?
All this is, if you think about it, an amazing departure from the kind of
picture once burned into the minds of biologists such as Richard Dawkins,
from whom we heard some errant words above. Once there were dreams of
compelling digital instructions in DNA; of machine-like interactions
between molecules; of deterministic formation and functioning of proteins;
of the cell as a collection of cleanly separate, well-defined structures;
and of cellular processes with fully predictable outcomes. But this dream
has faded in the clear light of an entirely different reality where, among
many other things, we watch a subtle and almost incomprehensible play of
material changes of state.
These state changes can be affected by infinitely varying factors, such as
the momentary interaction between a few molecules of a particular sort,
the “minor” modification of a molecule, the increasing concentration of
molecules in a particular location, or the slight temperature change of a
degree or two — the kind of change that, in the larger world of nature,
can freeze the surface of a lake where, a few days previously, fish
routinely breached the surface to feed on insects.
Ice cools a drink, water carves a canyon, steam powers a locomotive
… But ice brings down power lines, water floods towns, steam scalds
skin. The context for these states matters, and there can be consequences
if the appropriate state is perturbed or dysregulated. Now more than ever,
we understand that physical states dictate biological function, and
… recent papers have highlighted, at the subcellular and tissue
levels, the importance of understanding those states and the conditions in
which they occur.
As an aside: Some researchers have applied the idea of biological phase
transitions in a novel way. Certain species of penguins huddle
tightly against the fierce cold of the sunless Antarctic winter (top
photo), or aggregate in somewhat looser clumps when it is a little warmer
(bottom photo), or move about more or less independently when it is warmer
still. So the different phases of their interaction are correlated with
temperature, just as water varies from solid to liquid to gas,
depending (among other things) on the
We heard it asked earlier how intrinsically unstructured proteins “know”
what to do at any one place and time. The old model assumed, rather
puzzlingly, that random encounters between freely diffusing molecules
accounted for many of the biological interactions we observe. But
numerous researchers are now embracing the emerging picture of biological
phase transitions as offering a very different understanding. Peter
Tompa, a structural biologist from Vrije Universiteit Brussel in Belgium,
sees certain phase transitions as directing “the movement of regulatory
proteins in and out of organized subcellular domains” — part of the
systematic maintenance of order in the
This is all well and good, but does it tell us (as is often implied) what
“controls” and “directs” molecular engagements in relation to the distinct
needs of the cell at different locations and times? If the organization of
phase-separated aggregates is what coordinates the activity of proteins,
then we shouldn’t have to ask, as researchers are now asking, “Why do some
proteins localize to only the nucleolus, while others can be found in both
the nucleolus and Cajal bodies?”
(Zhu and Brangwynne 2015).
(Cajal bodies, like the nucleolus, are non-membrane-bound organelles found
in the cell nucleus.) And, even if that question had a ready answer, the
more fundamental issue would remain: if we assume that phase-separated
droplets lead to properly coordinated protein interactions, then what
explains the well-timed and intricately organized formation, structuring,
and dissolution of the condensates?
This illustrates how (to get ahead of ourselves just a little bit) all
attempts to answer questions of regulation in strictly physical terms
never do really answer them. Rather, they lead only to an elucidation of
previous physical states that again raise the same broad questions. There
is no way to step outside the endlessly regressing physical explanations
except by truly stepping outside them — except, that is, by turning to the
play of intentions and end-directed activities that are implicit in the
stories we find ourselves looking at.
After all, questions about biological regulation are questions about the
significant patterning of living events, and these just are
questions about a story — about the relation of continually adjusted means
to the needs, strivings, and qualities of a particular life. It is no
surprise, then, that our answers must be gained in the way we come to
understand a story — not in the way we grasp the play of physical laws in,
say, the movements of walking or speaking. (See
And then there is water
— the mediator of flow
I have long thought that some day water will be seen as the single most
fundamental, “information-rich” physical constituent of life, and that
revelations in this regard will outweigh in significance even those
concerning the structure of the double helix. Not many biologists today
would countenance such a suggestion, and I am not going to mount a serious
defense of it here, if only for lack of ability. Time will decide the
matter soon enough. But I was particularly pleased to find that the
widely read and respected Nature columnist, Philip Ball, once
entitled a piece, “Water as a Biomolecule”. In it he wrote:
Water is not simply ‘life’s solvent’, but rather an active matrix that
engages and interacts with biomolecules in complex, subtle and essential
ways … Water needs to be regarded as a protean, fuzzily delineated
biomolecule in its own right.
In another paper, Ball
summarized some work bearing on the role of water in biological contexts.
The main topic had to do with the relation between water, the binding
cavity of an enzyme, and the substrate molecule to which the enzyme binds.
It turns out, according to the authors of a study Ball cites, that “the
shape of the water in the binding cavity may be as important as the shape
of the cavity”. Ball goes on to remark:
Although all this makes for a far more complicated picture of biomolecular
binding than the classic geometrical “lock and key” model, it is still
predicated on a static or quasi-equilibrium picture. That, too, is
Then he cites another paper on enzyme-substrate binding. There it is
revealed that, before the binding is complete, water movement near the
enzyme is retarded. “Crudely put, it is as if the water ‘thickens’
towards a more glassy form, which in turn calms the fluctuations of the
substrate so that it can become locked securely in place. It is not yet
clear what causes this solvent slowdown as a precursor to binding; indeed,
the whole question of cause and effect is complicated by the close
coupling of protein and water motion and will be tricky to disentangle.
In any event, molecular recognition here is much more than a case of
complementarity between receptor and substrate — it also crucially
involves the solvent”.
All this suggests to Ball that “changes in protein and solvent dynamics
are not mere epiphenomena, but have a vital role in substrate binding and
Structural biologists Mark Gerstein and Michael Levitt (the latter a 2013
Nobel laureate in chemistry) wrote a 1998 article in Scientific
American entitled “Simulating Water and the Molecules of Life”. In it
they mentioned how early efforts to develop a computer simulation of a DNA
molecule failed; the molecule (in the simulation) almost immediately broke
up. But when they included water molecules in the simulation, it proved
successful. “Subsequent simulations of DNA in water have revealed that
water molecules are able to interact with nearly every part of DNA’s
double helix, including the base pairs that constitute the genetic code”
(Gerstein and Levitt 1998).
A typical “ribbon” diagram of a protein, representing certain basic
Early attempts to simulate protein molecules rather than DNA produced an
analogous difficulty, with the same, water-dependent resolution. Gerstein
and Levitt concluded their article with this remark:
When scientists publish models of biological molecules in journals, they
usually draw their models in bright colors and place them against a plain,
black background. We now know that the background in which these
molecules exist — water — is just as important as they are.
A representation of a protein’s hydration shell, where the small,
red-and-white figures stand for water molecules. Of course, both this and
the preceding image represent almost nothing of the reality of the
molecules (whatever we might take that reality to be), but only certain
That was in 1998. More than twenty years later the background remains to
be filled in, even if we are now seeing signs of change. Philip Ball (who
likes to cite that Gerstein/Levitt remark, and who reproduces two images
like those to the right), has recently noted “an interesting sociological
question”, namely, “why certain communities in science decide that
particular aspects of a problem are worth devoting a great deal of
attention to while others become minority concerns, if not in fact
regarded as somewhat suspect and disreputable”. He adds:
Why should we place so much emphasis, for example, on determining crystal
structures of proteins and relatively little on a deep understanding of
the [water-related] forces … that hold that structure together and
that enable it to change and flex so that the molecule can do its job?
Certain peculiar historical episodes have contributed to the
disreputability of water as a “molecule of life”. (Too many researchers
have thought they glimpsed something about water that went beyond current
principles of understanding, so that work of this sort came to be seen as
mystically tainted or “on the fringe”.) But surely part of the answer to
Ball’s question has to do with the longstanding distortion of biology due
to the emphasis upon code and mechanism. It is much easier to imagine the
step-by-step execution of a computer-like code or the clean insertion of a
key into a lock than it is to come to terms with fluid transformations —
that is, with what is actually life-like.
The high era of molecular biology that followed upon discovery of “the”
structure of the double helix, was indeed the Age of Simplicity. We can
be thankful that the feverish enchantment of code and crystal is now
giving way to an increasing recognition of movement, flow, dynamically
flexible interaction, and the continual transfiguration of form — prime
narrative elements in the organism’s story.
Figure 5.1 credit: Copyright Margot Quinlan. Reproduced
“The Mystery of an Unexpected Coherence”
we will look at alternative splicing of RNAs, one of many ways the
DNA sequence is radically overridden by the larger purposes of the cell.
A terminological issue:
Turoverov and colleagues speak more specifically of “highly
dynamic biological soft matter positioned at the edge of chaos”. The
abstract and perhaps rather tiresome notion of “the edge of chaos” is
better captured in this context by a picture of lifelike processes —
but in a dynamic manner that continually adapts to circumstances from a
purposive, and therefore not physically predictable, center of
agency. The predictability, such as it is, lies in the reasonable
expectation of coherence in the interweaving meanings we observe. (See
“The Organism’s Story”,
“The Mystery of an Unexpected Coherence”, and
“Biology’s Missing Ideas”.)
Biologists often speak of communication in terms of signals and
signaling, where signal can hardly be distinguished in any
absolute way from cause. However, “signals” tend to be spoken of
where there are repeated, more or less stereotypical sequences
(“pathways”) of molecular interaction between different cells, leading to
more or less consistent consequences. This happens, for example, when a
gland secretes a hormone (“signal”) that subsequently has effects in other
parts of the body.
Wikipedia offered this definition of “cell signaling” in August, 2019:
“Cell signaling is part of any communication process that governs basic
activities of cells and coordinates multiple-cell actions. The ability of
cells to perceive and correctly respond to their microenvironment is the
basis of development, tissue repair, and immunity, as well as normal
tissue homeostasis.” This easy acknowledgment of “communication”,
“coordination”, “governance”, “perception”, and “correct response” — all
within a science that, on the surface, refuses the normal and unavoidably
immaterial meaning of these terms — illustrates the Biologist’s Blindsight
“The Organism’s Story”.
A sol-gel transition occurs when a solution (in which one substance is
dissolved in another) passes into a gel state. The latter consists of a
molecular lattice that is expanded throughout its volume by a fluid —
water, in the case of a hydrogel.
The fluid may constitute over 99% of
the volume of the gel, yet the solid lattice prevents the gel from flowing
like a liquid.
Figure 5.2 credit: Gerum, R. C., B. Fabry, C. Metzner et al. (2013).
“The Origin of Traveling Waves in an Emperor Penguin Huddle”, New
Journal of Physics vol. 15 (Dec.). Available at
under the Creative Commons Attribution 3.0 license.
Here is one of innumerable examples of the role of phase separation in
physiological processes: “Cells under stress must adjust their physiology,
metabolism, and architecture to adapt to the new conditions. Most
importantly, they must down-regulate general gene expression, but at the
same time induce synthesis of stress-protective factors, such as molecular
chaperones … [We] propose that the solubility of important translation
factors is specifically affected by changes in physical–chemical
parameters such [as] temperature or pH and modulated by intrinsically
disordered prion-like domains. These stress-triggered changes in protein
solubility induce phase separation into aggregates that regulate the
activity of the translation factors and promote cellular fitness”
(Franzmann and Alberti 2019).
Figure 5.3 credit: © Richard Wheeler (GNU FDL).
Figure 5.4 credit: From H. Frauenfelder et al. (2009).
PNAS vol. 106, p. 5129.
holism/organism as a “formed stream”
Ball, Philip (2008a). “Water as a Biomolecule”, ChemPhysChem vol.
9, pp. 2677-85.
Ball, Philip (2008b). “Water as an Active Constituent in Cell Biology”,
Chemical Reviews vol. 108, no. 1, pp. 74-108.
Ball, Philip (2011). “More Than a Bystander”, Nature vol. 478
(Oct. 27), pp. 467-8.
Ball, Philip (2013). “Concluding Remarks: Cum Grano Salis”,
Faraday Discussions vol. 160, pp. 405–14.
Dawkins, Richard (2006). The Blind Watchmaker, third edition. New
York: W. W. Norton. First edition published in 1986.
Franzmann, Titus M. and Simon Alberti (2019). “Protein Phase Separation
as a Stress Survival Strategy”, Cold Spring Harbor Perspectives in
Biology vol. 11, no. 6 (June).
Ganser, Laura, Megan L. Kelly, Daniel Herschlag and Hashim M. Al-Hashimi
(2019). “The Roles of Structural Dynamics in the Cellular Functions of
RNAs”, Nature Reviews Molecular Cell Biology (Aug).
Gerstein, Mark and Michael Levitt (1998). “Simulating Water and the
Molecules of Life”, Scientific American vol. 279, no. 5 (Nov.), pp.
Grant, Barry J., Alemayehu A. Gorfe and J. Andrew McCammon (2010). “Large
Conformational Changes in Proteins: Signaling and Other Functions”,
Current Opinion in Structural Biology vol. 20, pp. 142-7.
Gsponer, Jörg and M. Madan Babu (2009). “The Rules of Disorder Or Why
Disorder Rules”, Progress in Biophysics and Molecular Biology 99,
no. 2-3 (Feb.-May), pp. 94-103.
Halfmann, Randal (2016). “A Glass Menagerie of Low Complexity Sequences”,
Current Opinion in Structural Biology vol. 38, pp. 18-25.
Hilser, Vincent J. (2013a). “Structured Biology: Signalling from
Disordered Proteins”, Nature vol. 498 (June 20), pp. 308-10.
Hyman, Anthony A. and Clifford P. Brangwynne (2011). “Beyond
Stereospecificity: Liquids and Mesoscale Organization of Cytoplasm”,
Developmental Cell vol. 21 (July 19), pp. 14-6.
Hubstenberger, Arnaud, Scott L. Noble, Cristiana Cameron and Thomas C.
Evans (2013). “Translation Repressors, an RNA Helicase, And Developmental
Cues Control RNP Phase Transitions during Early Development”,
Developmental Cell vol. 27 (Oct. 28), pp. 161-73.
Landecker, Hannah (2012). “The Life of Movement: From Microcinematography
to Live-Cell Imaging”, Journal of Visual Culture vol. 11, pp.
Pearson, Helen (2003a). “Beyond the Double Helix”, Nature vol. 421
(Jan. 23), pp. 310-12.
Rothman, Stephen (2002). Lessons from the Living Cell: The Limits of
Reductionism. New York: McGraw Hill.
Shin, Yongdae and Clifford P. Brangwynne (2017). “Liquid Phase
Condensation in Cell Physiology and Disease”, Science vol. 357, no.
6357 (Sep. 22).
Szewczak, Lara (2019a). “Just Solid or Liquid Enough”, Cell vol.
178, no. 4 (Aug. 8), pp. 763-4.
Tompa, Peter (2013). “Hydrogel Formation by Multivalent IDPs: A
Reincarnation of the Microtrabecular Lattice?”, Intrinsically
Disordered Proteins 1:e24068 (January–March).
Turoverov, Konstantin K., Irina M. Kuznetsova, Alexander V. Fonin et al.
(2019). “Stochasticity of Biological Soft Matter: Emerging Concepts in
Intrinsically Disordered Proteins and Biological Phase Separation”,
Trends in Biochemical Sciences vol. 44, no. 8 (Aug. 1), pp. 716-28.
Zhou, Yaoqi, Dennis Vitkup and Martin Karplus (1999). “Native Proteins
Are Surface-Molten Solids: Application of the Lindemann Criterion for the
Solid versus Liquid State”, Journal of Molecular Biology vol. 285,
Zhu, Lian and Clifford P. Brangwynne (2015a). “Nuclear Bodies: The
Emerging Biophysics of Nucleoplasmic Phases”, Current Opinion in Cell
Biology vol. 34, pp. 23-30.
Steve Talbott :: Our Bodies Are Formed Streams