Biological Physics with New Art by David Goodsell: Errata
"The laws of nature will defend themselves;--but error--(he would add,
looking earnestly at my mother)--error, Sir, creeps in thro' the minute
holes and small crevices which human nature leaves unguarded." -- Laurence
Sterne, Tristram Shandy
The current version of the book is the 8th printing (2017). Very soon I will release a completely revised Student Edition.
I'll be grateful to hear of any errors not already on this list.
Thanks, Philip Nelson
Errata to the 8th printing:
Pages 64-65: The Protein Database continually evolves. Most of the requested tasks can now be done in a Web browser directly from the PDB, without installing any standalone application.
Page 406: The discovery of kinesin in 1985 did not involve single-molecule motility assays, which were developed much later.
Clarifications and small corrections:
Color Figure 2: Caption should say, "antibodies labeling both kinesin (red) and tubulin (green).... the yellow color where fluorescence
from the two kinds of antibodies overlap."
Figure 3.7: The axis label should say "speed" not "velocity."
Figure 7.3: The gray rectangles represent the actual extent of the large objects. The dashed lines indicate the larger extent of the depletion zone(s).
Page 523: More modern measurements show sodium conductance increasing even more than 500-fold. At the action potential peak the enhancement factor is at least 2000. Moreover, even at this point not all channels are open; the conductance per area with all channels open is larger still.
Appendix A: The SI was revised in 2018:
Errata to the 5th printing:
Page 40, footnote 2: Prokarya and Eukarya are now called "domains" (not "kingdoms"). A domain may contain multiple kingdoms.
Figure 7.10: Both in the figure and in the caption, the curve that rises on the left involves the charge density divided by the proton charge e, not the permittivity epsilon, as seen from eq 7.29.
Clarifications and small corrections:
Page 23: The definition of the mole was changed in 2019: https://en.wikipedia.org/wiki/Mole_(unit) . (The coulomb was also changed: https://en.wikipedia.org/wiki/2019_redefinition_of_SI_base_units .)
Chapter 1 further reading: the web site www.biopyhsics.org/btol/ has been discontinued.
Fig 2.8: For a recent discovery about the structure of chromatin see Ou, H. D., Phan, S., Deerinck, T. J., Thor, A., Ellisman, M. H., & O’Shea, C. C. (2017). ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science (New York, N.Y.), 357(6349), eaag0025–15. http://doi.org/10.1126/science.aag0025
Fig 2.24: The caption states that initiation and elongation factors are not shown. Actually, they are visible flanking the tRNA at the lower left of the figure.
Problem 2.4: The web site listed has been discontinued. Use http://ligand-expo.rcsb.org .
Problem 2.5: The web site persweb.wabash.edu/facstaff/fellers/ has been discontinued.
Page 83, Fig 3.7: The horizontal axis should be labeled u-bar, not u.
Example solution on page 209: In part (b),
The temperature T should be replaced by the larger final temperature T_eq. Moreover, the force f should be replaced by the smaller f_eq (force decreases as the spring extends).
Problem 7.7 is stated in a potentially misleading way. You are to expand each of the exponentials on the right side of the Poisson-Boltzmann equation out to linear order in the potential function.
Fig 10.2b page 406: time axis labels should be 0.5, 1.5.
Fig. 10.14: The figure shows two local maxima as we traverse the dashed line, not one.
Fig 12.17 caption refers to Fig 12.6c but should instead refer to Fig 12.12c.
Remark: In this problem, you are asked to treat the electromagnetic field as a plane wave and the bead's response as a point electrostatic dipole. Neither of these approximations is accurate for visible light with beam width and particle diameter as given in the problem, so your answer will not be quantitatively precise. However, this approach to the problem does give the right order of magnitude for the force, and explains why any transverse force at all will arise.
Page 265 fig 7.8 caption: Behavior of counterionS.
Page 524 Fig 12.7 labels: subscript the ion names, not superscript.
Page 528, second line from the top: (Figure 12.5a on page 519)
Page 528, below eq 12.20, "page 514" should be "page 515".
On several occasions, Kirchhoff is misspelled "Kirchoff".