Physics of Life (2022) / Chapter Skim
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Pages 215-237
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From page 215... ...
The mechanism of such cellular mechanosensation from the atomic to the tissue scale is a major thrust in the fields of cell and developmental biology. Physicists have applied the concepts of fluid dynamics to the study of developmental cell migration and tissue movement during morphogenesis, similarly to how fluid dynamics has been applied to the epithelial-to-mesenchymal transition (EMT)
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From page 216... ...
All living cells have a voltage difference across their membrane, and the dynamics of voltage changes are crucial to the functioning of muscles, the nervous system, and the heart. As explained in Chapter 2, the elucidation of the basic mechanisms of this electrical signaling, through a combination of theory and quantitative experiment, forms a classical chapter in the emergence of biological physics.
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From page 217... ...
Neuroscience as a field was actively constructed from multiple more wellestablished biological disciplines -- physiology and pharmacology, anatomy and cell biology, biochemistry, and more. Perhaps because of this history, there has been a relatively rapid absorption of ideas from the biological physics community into the mainstream of neuroscience.
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From page 218... ...
The physics community's interest in human perception was especially strong, and productive. It is not only that physicists were interested in the mechanics of the ear or the optics of the eye, they also were interested in the inferences that the brain draws from these raw sense data.
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From page 219... ...
This chapter explores some of this infrastructure, how parts of it emerged from the biological physics community, and how it has influenced the progress of human health, medicine, and technology more generally; an overview is given in Table 7.1. The practice of medicine has been revolutionized by our ability to see what is happening inside the body and in isolated cells, on scales from single molecules to whole organs.
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From page 220... ...
Neural networks and artificial Emulate human and animal performance Ongoing revolution in intelligence at challenging tasks, ranging artificial intelligence. from walking on rough terrain to understanding language.
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From page 221... ...
was evident. A generation of work that connects the biological physics community with ecology and epidemiology resulted in the rapid development of effective models for spread of the virus, within which the impact of different public health measures could be assessed.
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From page 222... ...
The impact of biological physics on human health can be discerned even before a baby is born, when a fetal heartbeat is detected by Doppler sonography and the fetus is imaged by ultrasound tomography. If the parents' fertility has been examined, then sperm motility will likely have been assessed with technologies such as microfluidic methods.
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From page 223... ...
Further development and refinement of X-ray–based medical imaging continues to the present day. The invention of tomographic three-dimensional X-ray imaging, now widely known as X-ray computed tomography (CT)
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From page 224... ...
. FIGURE 7.2 X rays are not the only portion of the electromagnetic spectrum with an important role in medical imaging; gamma ray cameras are also used for imaging and diagnosis.
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From page 225... ...
Today, PET imaging is a workhorse technique for cancer diagnosis. Moreover, thanks to its ability to target specific biological processes of interest -- often limited only by the ability of radiochemists to produce a suitable tracer -- PET also has a forefront role in the growing radiological subfield of molecular imaging.
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From page 226... ...
These are the methods that have been pushed to the point of counting single molecules and surveying the expression of many genes, as in Figure 2.6. Unlike H&E, these fluorescence-based methods in pathology have the advantage of revealing specific proteins or RNA sequences in the tissue specimen, which can enable more pre cise diagnoses.
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From page 227... ...
These develop ments depend both on advances in technology and on theoretical ideas about the representation of information in the brain. Some sense for the liveliness of this enterprise comes from the continued emergence of startup companies based on technologies that have emerged from the biological physics community, as described in Box 7.1.
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From page 228... ...
By the early 2000s, single molecule approaches to DNA sequencing, which had emerged from the biological physics community, were becoming industrialized. Technologies based on optical methods for single molecule fluorescence detection, zero-mode optical wells, and intellectual property licensed from biological physics groups led to companies that now are publicly traded, and competing commercial approaches based on nanopores had a similar origin.
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From page 229... ...
In a startling develop ment, the problem of predicting protein structure from the amino acid sequence has inspired the development of a direct machine learning approach, "AlphaFold," which achieves a precision close to that of experimental structure determination by X-ray crystallography. A corollary of the ideas mentioned above is that the number of protein se quences seen in nature today is much larger than the number of protein folds, or folding motifs, that have been found by studying protein structures.
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From page 230... ...
Purple arrows are hydrogen bonds. The amino acids shown are the designed RMSD of from 0.79 x-ray Å and pro-Stereorepresentation crystal structures can a backbone ular replacement searches RMSD of thefail.
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From page 231... ...
Research in synthetic biology is powered by technological advances in genetic engineering, live cell imaging, sequencing, protein engineering, and so on, and often pursued in interdisciplinary teams that bring together physicists, engineers, biochemists, and cell biologists. As with almost every other scientific discovery, the discovery of gene regulation provided the means and impetus to assert human control over nature, in this case the genetic networks in cells.
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From page 232... ...
Antecedents to the synthetic biology revolution are biofuels produced from starch, sugar, animal fats, and vegetable oils, which are playing an increasingly large role in our energy landscape. Ethanol, a first-generation biofuel made primarily from corn, is one of the main biobased products produced worldwide and is present in more than 98 percent of the gasoline sold in the United States.
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From page 233... ...
To fashion synthetic biology into a true engineering discipline will require under standing the quantitative relationships between the microscopic interactions of the molecular parts and the emergent, cell-scale properties of the network. Again, basic scientific questions in biological physics are linked closely to opportunities for new technologies.
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From page 234... ...
One excellent example of the contribution of biological physicists to this endeavor is in the development of Nextstrain, a widely used analysis and visualization tool (see Figure 7.5)
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From page 235... ...
Theoretical work from the then nascent biological physics community showed that, combining these observations, es sentially all single- and double-point mutations were accessible to the virus on time scales that matter for treatment, but triple mutations are not. This means that there are almost no paths for the virus to evolve resistance to three different drugs simultaneously.
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From page 236... ...
Perhaps surprisingly for those outside the field, some of the biggest challenges are with everyday tasks, such as walking or running over complex, real world terrain. For the biological physics community, trying to understand why these problems are so hard is part of making precise what is meant by biological function, or specifying the physics problems that organisms must solve in order to survive (Chapter 1)
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From page 237... ...
If walking is complicated, perhaps it would be easier to move without legs at all. Several groups in the biological physics community have focused their attention on the mechanisms of locomotion in snakes.
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