evolution: finding useful proteins ; enormous odds (Introduction)

by David Turell , Sunday, July 05, 2020, 20:56 (1600 days ago) @ David Turell

An entry from an IDer:

https://evolutionnews.org/2020/07/mistakes-our-critics-make-protein-rarity/

"...our immunity system can manufacture at least a trillion unique antibodies, and at least one will typically bind to any invading germ. This achievement is possible since the probability is relatively high for a random search to locate an amino acid sequence that sticks to some molecule, so the required amount of new information is relatively small. For instance, only a few billion trials are needed to find an antibody that can bind to an antibiotic molecule and break it apart. The problem is that this task is much easier than randomly generating an entirely new amino acid sequence that folds into an enzyme’s three-dimensional structure and performs the required complex structural (conformational) changes. Highly specified dynamic structures are required to support an enzyme’s often very complex chemical activities.

"In contrast, antibodies are comprised of unchanging constant regions that already provide the needed structural support, so only generating functional variable regions is required. The difference between a random search finding an operative variable region and a random search stumbling upon a novel functional enzyme is comparable to the difference in difficulty of pushing a loaded wheelbarrow across a flat driveway and pushing it across a tightrope suspended across Niagara Falls.

***

"In the past, the general public lacked the technical knowledge to decipher the science underlying the evidence for protein rarity, so they were powerless to see past the critics’ smoke and mirrors (see here, here, and here). Fortunately, a straightforward analysis of the research by protein expert Dan Tawfik (see here, here, and here) not only confirms and generalizes Axe’s results, but is much more accessible to the public. Tawfik’s research on β-lactamase yielded results that almost perfectly confirm Axe’s rarity estimate. In addition, the former’s research and research on the HisA enzyme demonstrate that randomly altering less than 2 percent of the enzymes’ amino acids disables them over half of the time. And, altering 10 percent will disable them nearly 100 percent of the time. In contrast, altering 2 percent of a paragraph written in English is usually barely noticeable, and altering 10 percent still leaves a paragraph largely readable. Therefore, protein sequences are often far rarer than readable English sentences, so they are even more difficult to generate by chance."

Comment: There are two parts to this discussion. First our amazing immune system which is designed to add a specific addition to an existing functional base molecule. The system looks at the invader, isolates an attack point and creates an answering protein segment copied to destroy the invader. That system finds answers rather easily. What the discussion compares it to is findings a functional enzyme to do a precise job in a specific molecular process. Enzymes are enormous protein molecules with specific configurations. They must be designed to fit the need. That is not easy, which strongly suggests they must be designed by a designer as the odds of it happening by chance are vanishingly small.