Category Archives: machines

When is a Flaw not a Flaw?

As you know, I have often pointed to the proteins as an incredible design material, raising the question as to just how much the blind watchmaker is dependent and indebted to protein biochemistry.  A recent study highlights yet another way in which protein biochemistry may be an essential prerequisite for the evolution of complex life.

First, you can read the summary of this research by Ariel Fernández and Michael Lynch here.  Then, come back and I will help you detect the teleological echo of this work.

Continue reading

Design over time

In the last blog entry, I suggested that man-made machines lie further to left on the distance from equilibrium continuum than life’s machines.  But what if we considered man-made machines as a function of time?

Continue reading

Machines at the Edge

Below is figure 1 from the Macklem paper I just promoted in the previous entry:

Continue reading

Metaphors and perception

Over at the BioLogos blog, Michael Ruse offers a short summary of his new book, Science and Spirituality: Making Room for Faith in the Age of Science.  Go read it and come back for a few observations below the fold.

Continue reading


Found a nice animation of the SRP in action:

A Clever Connection

When reading through the works of those who study the SRP pathway, it becomes clear that these scientists have tremendous respect for the subject of their research.  There are no complaints about the system being jury-rigged, a hodgepodge, or messy.  On the contrary, as we have come to better understand how this system works, the researchers are under the impression that it is a very sophisticated system.  It has been independently described as an “elegant pathway,” [24] an “elegant mechanism,” [25] and “a very elegant solution” [26].  We can likewise get a feel for the way scientists greatly respect the sophistication of this system by considering some excerpts from their studies.  One team of researchers notes that “structural studies suggest that the relative position of the N and GTPase domains change during the targeting cycle in response to external cues and serves as an important indicator of the status of the protein”  [13].  They also observe ”it appears that two half-reactions (binding of the signal peptide and assembly or activation of the translocon) must be monitored independently and then brought together before a translocation event can be initiated.”  Another team notes, “targeting involves a series of ordered steps in which cargo binding and release must occur at the proper stages.  Each of the conformational changes in the GTPase domains of the SRP and SR described above provides a potential point at which such control can be exerted, thereby coordinating the loading and unloading of cargoes” [27].  A team of reviewers comments that an “intrinsic advantage of cotranslational protein targeting is that the coupling of translation and translocation should prevent misfolding of the nascent chain in the cytoplasm” [9].  And yet another set of SRP researchers comment on the way the M domain interacts with the NG domain after binding of the signal sequence, observing that this “would elegantly link signal sequence binding to the M domain with GTP binding to the G protein” [10].  The same researchers also describe the central role of the particle protein (SRP54):  “SRP function relies on the tightly controlled communication of SRP54 with the external regulators (e.g., the ribosome, the SR, and the translocon) and on internal communication between the domains of SRP54.”   Since “the efficiency and fidelity of the targeting process are crucial for maintaining the remarkable organization that is essential for life” [16], it is not surprising that such an elegant and logical system would have been put into place to carry out the task.

Continue reading

The Analogy Continues to Hold Up

The articles in this special issue of Molecular BioSystems focus on this fascinating area of multi-protein complex chemistry, biochemistry and molecular biology. They reveal that the Alberts paradigm of thinking of these complexes as highly interactive, tightly regulated biochemical machines has held up well over the years and guided many of the important studies that have elucidated their mechanism of action.


Rise of the machines: Bruce Alberts and the biochemistry of multi-protein complexes.  Mol. BioSyst., 2008, 4, 1043–1045