Building a Cell: Staggering Complexity
“The living cell is a self-organizing, self-replicating, environmentally responsive machine of staggering complexity.” Thus began a special section on “Building a Cell” in Nature last week.1 The section with five papers explores what is known about gene regulation, cell organization and signalling. It’s an opportunity, as well, to see what scientists think about what they are seeing. “This Insight offers a hint of the most exciting research on the regulation of cellular organization and function,” the editors said, inviting the readers in for a look.
- Chromosome segregation: staggering machinery: Bloom and Joglekar started out the series with a look at how cells divide the daughter chromosomes during cell division.2 “All organisms, from bacteria to humans, face the daunting task of replicating, packaging and segregating up to two metres (about 6 x 109 base pairs) of DNA when each cell divides,” their attention-getting abstract began. “This task is carried out up to a trillion times during the development of a human from a single fertilized cell.” Scientists may understand the strategy for replication, “But when it comes to packaging and segregating a genome, the mechanisms are only beginning to be understood and are often as variable as the organisms in which they are studied.”
Yet the seemingly unlimited ways different organisms accomplish this must meet stiff requirements for precision: “chromosome segregation must be executed with high fidelity so that the mother cell and the daughter cell that arise from division receive precisely the same DNA content,” they said. Everything has to be done just right. The cell has to be able to tell the chromosomes apart: which ones are the copies, and which ones are just look-alikes? Where does each chromosome belong on the spatial template, like band members on a football field half-time show? And where is the drum major calling the signals? Here’s a take-home sentence: “Finally, the segregation machinery must function with far greater accuracy than man-made machines and with an exquisitely soft touch to prevent the DNA strands from breaking.”
Bloom and Joglekar talked “machine language” over and over. The cell has specialized machines for all kinds of tasks: segregation machines, packaging machines, elaborate machines, streamlined machines, protein translocation machines, DNA-processing machines, DNA-translocation machines, robust macromolecular machines, accurate machines, ratchets, translocation pumps, mitotic spindles, DNA springs, coupling devices, and more. The authors struggle to “understand how these remarkable machines function with such exquisite accuracy.”
The paper reads like a description of an alien spaceship filled with machinery carrying out amazing coordinated functions that visitors can only partially grasp, but know everything is obeying laws of physics: e.g., “Although DNA is not covalently linked to spindle microtubules or motor proteins, it may act as a spring in its capacity to absorb force and therefore prevent molecular motors from travelling too fast.” Another example: “A different way of organizing polymers is to anchor many chains to a substrate (Fig. 1c). In the field of polymer physics, this is an important strategy for regulating forces between polymers (for example in polymer brushes) and the environment, and for creating methods to switch rapidly from attraction to repulsion. One type of brush is a Velcro-like structure, in which a highly oligomerized protein is attached to a subcellular site.” Sure enough, such a strategy was discovered recently in a bacterium, with finesse: “Polymers of the C. crescentus protein PopZ assemble into a higher-order filamentous network that functions as an anchor for chromosome capture,” they said.
On two occasions they referred to evolution: (1) Speaking of how cells package the chromosomes to avoid breakage while making certain essential genes accessible during cell division, they said, “Several diverse protein machines have evolved to carry out these processes.” They did not say how they evolved. (2) Speaking of how certain genes are deactivated by histone modifications, they said, “DNA wrapping around the histone may impart a topological block to transcription. In this model, nucleosome chirality at the centromere, as well as the path of DNA as it enters and exits the nucleosome, may have evolved to inhibit transcribing polymerases from inactivating the centromere, which would otherwise lead to chromosome loss.” Presumably, if the cell had not “evolved” all this machinery “to” do these exquisite, coordinated functions, it would not exist today.
- Alternative splicing: staggering information and control: Nilson and Graveley contributed a review article for the series about how alternative splicing expands the genome.3 This refers to the fact that a compact library of genes can be read in different ways, to generate more information in less space. It would be like a software library with modules that can be joined in various ways to produce a variety of outcomes. Like the other papers, this one has plenty of “wow factor” –
The collection of components required to carry out the intricate processes involved in generating and maintaining a living, breathing and, sometimes, thinking organism is staggeringly complex. Where do all of the parts come from? Early estimates stated that about 100,000 genes would be required to make up a mammal; however, the actual number is less than one-quarter of that, barely four times the number of genes in budding yeast. It is now clear that the ‘missing’ information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene.
A realization has been growing that alternative splicing, once thought unusual, is common. Here’s a “spectacular example,” they noted: a gene in a fruit fly can produce 38,016 distinct messenger RNAs, “a number far in excess of the total number of genes (~14,500) in the organism.” This means that there is far more information encoded in the genome than earlier believed: “the number of functionally distinct proteins that could be encoded by the genome is staggering.” They said it now appears that “alternative splicing is one of the main sources of proteomic diversity in multicellular eukaryotes.”
This raises obvious questions about oversight and control. What tells the fruit fly which one of the 38,000 protein products is needed at a particular time from that particular gene? “The biochemical mechanisms that control splice-site usage, and therefore alternative splicing, are complex and in large part remain poorly understood,” they said. “It is clear that there cannot be specific and distinct factors dedicated to each of the more than 100,000 alternative splicing decisions that occur in human cells; several genomes worth of regulatory proteins would be required if this were the case.” Apparently, a small number of proteins are involved in alternative splicing events. But what regulates the regulators? “How can this handful of splicing regulators be responsible for controlling the plethora of alternative splicing events that occur?” Again, this is “far from understood.” The complexity truly is staggering when just the known mechanisms are listed:
The number of mechanisms that are known to be involved in splicing regulation approximates the number of specific splicing decisions that have been analysed in any detail. These mechanisms range from straightforward ones, such as steric blocking of splice sites or positive recruitment of the splicing machinery, to more complicated ones, such as formation of ‘dead-end’ complexes, blocking of splice-site communication or facilitation of splice-site communication. Even these mechanisms are poorly understood at a detailed biochemical level (for example, what distinguishes dead-end complexes from productive complexes remains unclear).
The picture becomes even cloudier when splicing (and alternative splicing) is viewed not as a static process but as a highly dynamic process encompassing a large (yet to be defined) number of kinetic steps. It is now clear that many factors can have marked effects on splicing patterns; these include transcription rate, core-splicing-machinery levels, intron size and competition between splice sites.
So the kinetic factors add another dimension to the effects of alternative splicing. Add to this the effects of chromatin structure (the “histone code”) and staggering seems an understatement. Had enough yet? “Last, before leaving the mechanistic aspects of alternative splicing, it should be noted that we have understated the complexity of the mechanisms involved.” At this point, when the reader is about to collapse from overload, they keep rubbing it in: “it is clear that context affects function, and this adds a layer of complexity to the already complex field of alternative and regulated splicing.”
Surely these authors would not think this all evolved, would they? Actually, they did. In a confusing section about “bioinformatics,” a word that connotes intelligent design, they suggested that alternative splicing provides “evolutionary plasticity” – a more fluid environment in which mutations could cause significant evolution over point mutations on a gene. But at the current time, these are only suggestions, if you can “envisage” them:
These examples show the high level of evolutionary plasticity that alternative splicing provides. Because small changes (that is, point mutations) in either exons or introns can create or destroy splicing control elements, it is easy to envisage that splicing patterns are constantly evolving: advantageous mutations would rapidly be selected for, and deleterious mutations would be selected against. Indeed, we speculate that ‘non-conserved’ changes in splicing patterns might underlie the observed phenotypic variations between species and between individuals within species. Recent studies have provided insight into the way in which human exons have evolved and the extent of alternative splicing differences between humans and chimpanzees. Additional studies along these lines are likely to improve the understanding of how alternative splicing contributes to speciation and phenotypic diversity.
Thus, the real “understanding” is only a promissory note dependent on future research. Will anyone remember to check back in a decade and see how the promissory note paid off? Or will this be an example of a misuse of the power of suggestion?
The authors are not ignorant of the questions this research raises about final causes. “Another crucial question is how many mRNA isoforms are functionally relevant? Teleology suggests that if an isoform exists, it is important (similarly to the way in which ‘junk’ DNA is now considered to be treasure),” they noted, as if smarting from the realization that the “junk DNA” paradigm has imploded. “But this idea [teleology] is hard to prove and is difficult for some to accept.” First of all, we don’t know how many isoforms [products of alternative splicing] are functional, and “the question of how many alternative splicing events are functionally relevant is destined to remain unanswered for some time.” A number of tantalizing possibilities appear on the horizon.
Another outstanding question is whether there is a decipherable ‘splicing code’. Will a computer be able to predict reliably the splicing patterns in a cell or organism? Despite the numerous variables (known and unknown) involved in splice-site choice, rapid progress has been made in this area. But it is not clear when or whether this Rosetta stone of splicing will emerge….
Much remains to be learned about the mechanisms of alternative splicing and the regulatory networks of alternative splicing. It is clear that researchers are only beginning to understand the diversity and details of the mechanisms that are used to regulate alternative splicing, as well as the factors involved. Recent technological advances, particularly in genomic analysis, suggest that the next few years are likely to be filled with many exciting and unanticipated discoveries that could rapidly reveal the mysteries of the field.
- Endocytosis: Master Plan Association: Cells are not isolated entities. They interact profoundly with their environment. One way they do this is through endocytosis: the orderly capture of material from outside the cell membrane to the inside. The authors of the third entry in Building a Cell4 wrote that endocytosis, long understood as mere intercellular trafficking, is being “integrated at a deeper level in the cellular ‘master plan’ (the cellular network of signalling circuits that lie at the base of the cell’s make-up).” By deciphering this level, the “endocytotic matrix,” scientists “might uncover a fundamental aspect of how a cell is built.”
Their are two major types of endocytosis. One uses clathrin (see 10/07/2003), the other does not. Clathrin is a unique 3-legged protein that links up to form a kind of geodesic-dome net around the cargo coming in through the cell membrane (watch the “Flight of the Clathrin Bumblebee” animation from Harvard). Other pathways envelop the cargo in lipids, without the clathrin. By containing the cargo in a vesicle, the cell can control it, like shipping containers arriving at a dock. The cargo can contain nutrients or signals from the environment. A new finding coming to light is that the signals are reciprocal. This hints that more is going on than once thought:
Recent studies, however, have uncovered a wealth of evidence that endocytosis has a much wider impact on signalling, including the finding that signalling pathways and endocytic pathways are regulated in a reciprocal manner, and the finding that several molecules have roles in both endocytosis and signalling (see refs 3, 4, 5 for reviews). The emerging model is that the net biochemical output of signalling pathways largely depends on topological constraints. These constraints are imposed by the association of signalling molecules with membranes, which in turn is regulated by endocytosis and by cycles of endocytosis and recycling to the plasma membrane (that is, endocytic and exocytic cycles (EECs)). This set-up allows signals to be decoded by the cell according to precise kinetics and at spatially defined sites of action. And, not surprisingly, it translates into endocytosis having a large impact on almost every cellular process. In addition, evidence is emerging that the endocytic machinery has molecular functions that are not immediately reconcilable with membrane trafficking, leading researchers to question whether these ‘non-canonical’ functions are ‘moonlighting’ jobs or whether they point to deeper levels of integration of the endocytic matrix within signalling circuitries and cellular programs.
Moonlighting jobs: what a suggestive analogy. But if the moonlighting is even part of a bigger master plan, that’s even more suggestive of unforeseen complexity at deeper levels. “Here we summarize the current understanding of how endocytosis is embedded in the cellular master plan, and more specifically its connections to signalling,” they said, launching into the discussion. They seem to like that “master plan” metaphor: “We review endocytosis at the level of the circuits involved, highlighting how the integration of endocytosis and signalling determines the net biochemical output of a cell. Then, we analyse how endocytosis affects the execution of complex cellular programs. And, last, we speculate on how endocytosis might have evolved to become a pervasive component of the cellular master plan.” How did the E-word evolved sneak into the master plan? We shall see.
Sparing our overwhelmed readers the details of signalling, circuits and I/O, we note that the authors make “a plea for systems biology” to pull all this data together – i.e., a big-picture perspective. We note the authors mentioning “microtubule motors” that propel the vesicles along highways to their targets, such as the nucleus. Yet the average speed of the motors seem inadequate to explain how the signals traverse large distances to reach their targets as rapidly as experiments show. Are there “traveling waves” of protein activation? We don’t yet know. The system also has to account for degradation and recycling of some parts. Recent findings show endocytosis intimately involved in such diverse activities as mitosis, cell-cycle progression, and transcription, as well as in signaling. The roles for endocytosis described by the authors seems endless: asymmetrical cell division, cytokinesis (the last part of cell division), genetic reprogramming, tumor suppression, transcription. They wonder again whether the endocytosis mechanisms are “freelancing” these jobs or are part of a bigger picture.
Trying to get a grip on how all these roles might have evolved, they explored three analogies: (1) the moonlighting hypothesis (endocytic proteins carry on dual functions), the (2) autogenous hypothesis (it all started with membrane budding), and (3) the “Roman-road” hypothesis (it emerged for one function but found uses for others later, like Roman roads built to transport armies proved useful for commerce). The autogenous hypothesis imagines the nucleus evolving from an endosome (endocytotic vesicle). “Eukaryotic cells would thus have evolved as a consequence of the acquisition of a novel cellular property, the capacity to carry out endocytosis, putting this process at the centre of the eukaryotic cell master plan.” Putting have evolved and master plan in the same sentence seems strained. It gets even more strained when motors enter the picture: “As a consequence, several functions must have co-evolved with endocytosis,” they said: “For example, the evolutionary development of endocytosis must have co-evolved with that of the cytoskeleton, because membrane dynamics requires cytoskeletal scaffolds and molecular motors.” How that happened was left as an exercise. The Roman-road discussion became even more personified and mixed with intelligent-design lingo:
Different passengers can be envisaged on these endocytic routes: commuters, hitch-hikers, hijackers and ticket holders. Commuters are the regular passengers (cargo and associated machinery) for which the system was initially designed. Hitch-hikers are molecules that parasitize the system (that is, they hitch a free ride) for a purpose not associated with endocytosis, without altering the functioning of the system. Hijackers are hitch-hikers that sidetrack the system for their own purposes, causing it to malfunction, for example pathogens and, probably, cancer proteins. Ticket holders are hitch-hikers that have evolved to ‘pay the fare’, by acquiring a new endocytosis-associated role (and therefore contributing to the functioning of the endocytic system), while retaining their original role. Their new endocytic function might be unrelated to their original role to the extent that they seem to be moonlighting, thus bringing us back to the first proposed hypothesis [moonlighting].
How useful these metaphors are to really understanding the “master plan” of the cell is debatable. But it appears that intelligent design is the key to unlocking the mystery of endocytosis, regardless of what the authors think about evolution. Why? Because it is apparent there is a master plan:
The evidence that we have reviewed here clearly indicates that endocytosis and signalling are two sides of the same coin and should be conceptualized as a single cellular process that is central to the eukaryotic cellular master plan. Unravelling the logic of the ‘endocytic matrix’ therefore seems to be indispensable to any attempt to reverse engineer the cellular master plan in order to understand how a cell is ‘built’.
Remarkably, their concluding suggestions for further research incorporate both intelligent-design and evolutionary concepts. On the one hand, they recommended “complete understanding will be obtained only by integrating an additional level of complexity: information from ‘omics’ approaches and ‘top-down’ modelling,” as if there really is a master plan. But then they said we might be able to reproduce the evolutionary history of endocytosis. “Finally, scientists have traditionally devoted considerably more energy to understanding how things are than to how things came to be the way they are. Re-evolving an endomembrane system in vivo, starting from prokaryotes, is a formidable task, but if it is successful, it will enormously improve understanding of the master plan of eukaryotic cells.” Go figure. They used the phrase “master plan” eight times, but spoke of its antithesis, evolution, 14 times. We can only hope that with understanding – however scientists arrive at it – will come healthful benefits, like the ability to fight disease.
- Chromatin remodelling: glimpses of a higher code: Combinatorial assembly is a key phrase in the fourth paper in the series.5 If that sounds like coding, that’s because it is. Ho and Crabtree wrote,
Before mammalian genomes were sequenced and genome-wide analyses of chromatin function became possible, ATP-dependent chromatin remodelling was thought to be largely a permissive mechanism that operates to allow the binding of general transcription factors. However, the discovery that a large number of non-redundant genes are involved in chromatin remodelling and the ability to carry out more rigorous genetic analyses is enabling the specialized and instructive functions of these complexes to be defined. These functions arise partly from the combinatorial assembly of the complexes. The assembly of complexes from products of gene families suggest that biological specificity is produced in much the same way that letters produce meaning by being assembled into words. But the mechanisms by which these chromatin-remodelling “words” are “translated” into specific biological functions are still unclear, and new ways to probe complex chromatin structure might be needed before we can improve our mechanistic understanding.
The authors did not use the phrase “histone code” but the concept is related. Apparently the combinatorial assembly of histone modifications is a means of storing cellular information independent of the genetic code. An important question is whether the code is heritable. The answer: we don’t yet know. They said, “At present it is not known whether chromatin remodelling can transmit the memory of cell fate from one generation to the next. With mounting evidence of the transience and reversibility of chromatin modifications (such as the presence of histone demethylases), the view that chromatin configuration is fixed after being established is giving way to the view that the chromatin landscape can be altered in response to both extrinsic signals and intrinsic signals, such that de-differentiation through nuclear reprogramming is possible.” That possibility is clearly of interest for stem cell research. On the other hand, “If their program of action is transmitted from one generation to another, then uncovering the mechanisms that direct remodellers back to their appropriate sites of action after each cell division will be crucial for understanding how the specificity and the memory of chromatin-remodelling action are achieved during development.” One thing is clear from recent research: “For these reasons, the roles of ATP-dependent chromatin remodelling may be wider, yet more precise and programmatic, than was previously thought.”
What did these authors think about evolution? All they said was brief and speculative. They assumed evolution without saying anything about how it took place.
ATP-dependent chromatin-remodelling complexes seem to have evolved to accommodate the major changes in chromatin regulation that occurred during the evolution of vertebrates from unicellular eukaryotes (Box 1). As an example, complexes of the SWI/SNF family, which is one of the most-studied families of chromatin-remodelling complexes, have lost, gained and shuffled subunits during evolution from yeast to vertebrates. In particular, the transition to vertebrate chromatin-remodelling complexes involved the expansion of several of the gene families encoding the subunits and the use of combinatorial assembly, which together are predicted to allow the formation of several hundred complexes. But what is the advantage of combinatorial assembly?
This statement says little more than “it evolved during the evolution of” this or that. Moreover, the wording that said evolution involved the expansion…and the use of combinatorial assembly, by using subjunctive and passive verbs, shields the statement from any explanatory utility. <1>Who</1> or <1>what</1> came up with “the use of combinatorial assembly” How? Why? Evolution, a mindless and passive process, cannot shed light on such questions.
Certainly, the authors avoided elaborating on what they meant. But they did elaborate on their last question, “what is the advantage of combinatorial assembly?” It’s much like the advantage of alternative splicing (see #2 above): it allows for orders of magnitude more information to be derived from the same compact code. It means that both alternative splicing and chromatin remodelling use the same strategy of combinatorial assembly to yield vast quantities of functional information. One of their figures illustrates how “Combinatorial assembly of chromatin-remodelling complexes produces biological specificity.” They said, “Current evidence indicates that many vertebrate chromatin-regulatory complexes are assembled combinatorially … thereby greatly expanding the potential for diverse gene-expression patterns compared with unicellular eukaryotes.”
This expansion of compact information is particularly evident in the “diverse patterns of gene expression [that] occurs in the development and function of the brain,” they noted; therefore, “it may be no accident that an extraordinary diversity of neural phenotypes is emerging from genetic studies of the subunits of chromatin remodellers in the nervous system,” they said. No accident; does that comport with a blind Darwinian mechanism?
- Cell skeleton: epigenetic information: The final paper in the series concerns the cytoskeleton. Did you know those soft squishy entities we call cells have a skeleton? It’s true: “The ability of a eukaryotic cell to resist deformation, to transport intracellular cargo and to change shape during movement depends on the cytoskeleton, an interconnected network of filamentous polymers and regulatory proteins,” wrote Fletcher and Mullins,6 (see 01/14/2008). That’s old news. What’s new, they continued, is that “Attention is now focused on how cytoskeletal networks generate, transmit and respond to mechanical signals over both short and long timescales.” An important insight is emerging from this work, they said: “long-lived cytoskeletal structures may act as epigenetic determinants of cell shape, function and fate.” Not all the information about a living cell is stored in DNA. That’s what epigenetic (above the gene) means.
These authors put cell research into a historical context. Years of detailed research has brought us to a time when we need to step back and look at the big picture.
In a 1960 lecture, cell and developmental biologist Paul A. Weiss encouraged his audience to think of the cell as an integrated whole “lest our necessary and highly successful preoccupation with cell fragments and fractions obscure the fact that the cell is not just an inert playground for a few almighty masterminding molecules, but is a system, a hierarchically ordered system, of mutually interdependent species of molecules, molecular groupings, and supramolecular entities; and that life, through cell life, depends on the order of their interactions”.
This statement may be more relevant today than it was 50 years ago. Despite tremendous progress, fundamental gaps remain between our understanding of individual molecules and our understanding of how these molecules function collectively to form living cells. The sequencing of genomes outpaces characterization of the cellular components they encode and far exceeds our ability to reassemble these components into the types of complex system that can provide mechanistic insight into cellular behaviour. An even more difficult task is to connect the behaviour of cells in culture with that of more complex living tissues and organisms.
Notice how this statement relates to the quote by Dr. Daniel Robinson at the top right of this page. Understanding is not going to come merely from studying fragments; it’s going to require grasping the big picture of how all these hierarchical complex organizations fit together.
With that sermon in mind, Fletcher and Mullins delved into the details of the cytoskeleton. “The cytoskeleton carries out three broad functions: it spatially organizes the contents of the cell; it connects the cell physically and biochemically to the external environment; and it generates coordinated forces that enable the cell to move and change shape.” The word skeleton is a bit of a misnomer, they noted; “it is a dynamic and adaptive structure whose component polymers and regulatory proteins are in constant flux.”
Once again, the concepts of combinatorial assembly come to mind. They use a simple analogy that invokes images of intelligent design – more or less:
The proteins that make up the cytoskeleton have many similarities to LEGO, the popular children’s toy. Both consist of many copies of a few key pieces that fit together to form larger objects. Both can be assembled into a wide range of structures with diverse properties that depend on how the pieces are assembled. And both can be disassembled and reassembled into different shapes according to changing needs. But only the cytoskeleton fulfils all of these functions through self-assembly.
It appears that we are looking at a system that is both the toy and the player. From a few simple building blocks, many diverse structures and functions are built. The authors wonder “how molecules collaborate to form functional cytoskeletal structures” that both provide stability to the cell and response from the environment. Does “self-assembly” really explain such things? Or is it a place-holder for ignorance about processes beyond our comprehension?
Many wonders about the protein parts, like the microtubules, which form highways for intracellular traffic, are discussed in this paper, which space does not allow to recount. Here’s one sample: “A microtubule can switch between two states: stably growing and rapidly shrinking. This ‘dynamic instability’ enables the microtubule cytoskeleton to reorganize rapidly and allows individual microtubules to search the cellular space quickly, up to 1,000-fold faster than a polymer that is sensitive only to changes in the cellular concentration of its constituent subunits or to the actions of regulatory proteins.”
Microtubules, intermediate filaments, and actin filaments with their cross-bridges form intricate, dynamic networks that give spatial organization to the cell interior. The pieces are not independent: “the polymers of the cytoskeleton are intricately linked together,” they said. “The organization of these links and the resultant architecture of the cytoskeletal networks has a central role in transmitting compressive and tensile stresses and in sensing the mechanical microenvironment. On the hubs and highways of this network, motor proteins do their work – carrying cargo, pulling, harnessing, constructing, and responding to signals. Interestingly, “Some cytoskeletal structures can span distances much larger than that of the typical cell,” such as in filopodia, forming communication channels between cells. The same physical constraints must be obeyed that engineers consider when building bridges:
Microtubules are the stiffest of the three polymers and have the most complex assembly and disassembly dynamics. The persistence length of microtubules, a measure of filament flexibility that increases with stiffness, is so large (~5 mm) that single microtubules can form tracks that are almost linear and span the length of a typical animal cell, although microtubules are known to buckle under the compressive loads in cells. During interphase, the part of the cell cycle during which cells prepare for division, many cells take advantage of this stiffness by assembling radial arrays of microtubules that function as central hubs and ‘highways’ for intracellular traffic. During mitosis, the part of the cell cycle during which cells separate chromosomes into two identical sets, the microtubule cytoskeleton rearranges itself into a high-fidelity DNA-segregating machine called the mitotic spindle. The ability of the mitotic spindle to find and align chromosomes depends, in part, on the complex assembly dynamics of individual microtubules.
Another example shows that biology speaks the same language as engineering:
When shear stresses are applied to actin-filament networks, as well as to networks of intermediate filaments or extracellular-matrix filaments such as collagen and fibrin, the networks stiffen and resist additional deformation, as a result of filament entanglement (in which the displacement of one filament is impeded by another filament) and the entropic elasticity of individual filaments. When a rigid crosslinker such as scruin is added to randomly organized actin filaments and shear stress is applied, the magnitude of the elastic modulus (a measure of the resistance of the network to deformation) increases significantly, and the network retains the stress-stiffening behaviour attributed to the entropic elasticity of individual filaments. When the more flexible crosslinker filamin A is added to randomly organized actin filaments together with the molecular motor myosin, the rigidity of the network increases to more than that of an entangled filament network, and the network stiffens nonlinearly as though it were subject to external stress. These studies demonstrate the importance of the entropic elasticity of filaments in the mechanical properties of networks without specific filament orientation.
You get the idea. Young’s modulus, compressive forces, shear stresses and other physics terms pervade the paper – as if we were reading a treatise on architecture. But it’s not just the architecture. These systems are integrated with other systems in a hierarchical, unified whole – the living cell. When things go wrong, the results can be as catastrophic as an earthquake. “And mutations in the genes encoding intermediate filament proteins are associated with many diseases in humans … including a predisposition to liver disease in the case of some keratins, amyotrophic lateral sclerosis (also known as Lou Gehrig’s disease) in the case of a neuronal class of intermediate filament called neurofilaments, and progeria (a hereditary form of premature ageing) in the case of improperly assembled nuclear lamins.”
The authors commented on one other interesting and important development: epigenetics. Evidence is emerging that the cytoskeleton determines part of a cell’s “memory” that is inherited through cell division. “Given that cytoskeletal structures are often highly dynamic, with specific factors that promote disassembly and recycling of the cytoskeletal building blocks competing with factors that assemble and stabilize them, is it possible for mechanical inputs to be recorded?” they asked. Because the time lag for disassembly of a network exceeds the cell cycle, it appears that a hysteresis signal persists through the division: “the result can be a persistent structure that affects the behaviour of a cell over a longer timescale than the initial signal.” It can provide a memory independent of DNA. But this memory is not in the particulars, but rather than in the interactions: “In contrast to molecular motors, for which the relationship between force and velocity is immediately reversible, the observation that there is more than one growth velocity for a given force suggests that actin-filament network growth depends on history. The cytoskeletal structure and the process by which it is built can record mechanical interactions, whereas a single filament could not.” What are the implications? A cell’s fate will depend not only the DNA it inherits, but on the structure of the parent cells: “To the extent that the cytoskeleton is intricately involved both mechanically and biochemically in cellular processes such as cell division and motility, long-lived cytoskeletal structures could create variability in cell behaviour and may guide variation towards certain phenotypes,” i.e., cell fate. The details of this idea have “just begun to be explored in detail.”
The authors ended by noting that, “Until not long ago, eukaryotic cells were thought to be distinguished from bacteria and archaea by the presence of a cytoskeleton. But the discovery of cytoskeletal polymers even in comparatively simple cells of small size and genome are revealing the central importance of internal organization for cell function.” They speculated briefly on the origin of the polymers of the cytoskeleton, but the description was only about possible homologous structures in bacteria. “More than 35 actin-like proteins have been identified in bacteria, but most remain to be characterized,” they said. This begs the question about where the bacteria got their cytoskeletons. They must do a good job, because we still have them with us.
The authors of the last paper concluded with another quote from Paul Weiss’s lecture in 1960: “Life is a dynamic process. Logically, the elements of a process can be only elementary processes, and not elementary particles or any other static units. Cell life, accordingly, can never be defined in terms of a static inventory of compounds, however detailed, but only in terms of their interactions” (italics in original). This realization reverberates throughout all the sciences. The more we focus on reducing biology to chemistry, and chemistry to physics, and physics to fundamental particles, the more we risk missing the real story.
1. Deepa Nath, Ritu Dhand and Angela K. Eggleston (Editors), “Building a Cell,” Nature 463, 445 (28 January 2010); doi:10.1038/463445a.
2. Kerry Bloom and Ajit Joglekar, “Towards building a chromosome segregation machine,” Nature 463, 446-456 (28 January 2010); doi:10.1038/nature08912.
3. Timothy W. Nilsen and Brenton R. Graveley, “Expansion of the eukaryotic proteome by alternative splicing,” Nature 463, 457-463 (28 January 2010); doi:10.1038/nature08909.
4. Giorgio Scita1 and Pier Paolo Di Fiore, “The endocytotic matrix,” Nature 463, 464-473 (28 January 2010); doi:10.1038/nature08910.
5. Lena Ho and Gerald R. Crabtree, “Chromatin remodelling during development,” Nature 463, 474-484 (28 January 2010); doi:10.1038/nature08911.
6. Daniel A. Fletcher and R. Dyche Mullins, “Cell mechanics and the cytoskeleton,” Nature 463, 485-492 (28 January 2010); doi:10.1038/nature08908.
We hope you have enjoyed this tour inside the cell. Review articles like those in this series, unlike single papers that focus on one detail, are valuable for pulling together many recent findings into a coherent picture. And what a picture! Systems upon systems, structures upon structures, codes upon codes: the language of networks, signals, responses, interactions, and communication – the details of which underscore the complexity of the whole. Whoever described a cell as an “undifferentiated blob of protoplasm” should be placed in the Dodo cage. Dr. Mullins sure knows better now. His paper was the least concerned about evolution. We hope he will smell the coffee, trust his instincts, and wake up to thoughts of design (10/21/2008).
Evolutionists have to be the most incorrigible ideologues that ever walked this planet. No one else in the history of mankind has had this much access to the details of life’s complexity. Yet despite staring at this complexity with the highest resolution ever attained, and despite employing the language of engineering to describe it, they continue to say “it evolved.” They attribute “machinery [that] must function with far greater accuracy than man-made machines” to blindness and accident. To add insult to injury, some of them forbid anyone from thinking anything else!
This is one area where the Master Plan has broken down. The broken parts require complete overhaul, wipe, reinstall of new software, and reboot. It was costly to provide that overhaul, but it can be downloaded free. In the big picture, though, we can see that, all along, it was the Master Plan behind the Master Plan.