train wreck
To improve a sophisticated machine, fire at it with a rifle, blindfolded. Is that the way to improve the machine? Darwinians have no other tool than rifling through random mutations in hopes of adding new functional information to the genomes of living things, making slow progress up Mount Improbable. But natural selection can only select what random mutations give. Having sworn off intelligent causes, Darwinians must rely on random mutations to get from the first molecular replicator to the human brain. A new study gives them bad news and worse news.

Bad and Worse

Evolutionists know that mutations can be deleterious, but many mutations are expected to be neutral, and a few might be beneficial. A simplistic view of neo-Darwinism focuses on one gene or protein at a time. The rare beneficial mutation might help a particular gene or protein improve its function, and therefore increase the organism's fitness. A more realistic view of mutations needs to consider possible unintended consequences: the "collateral damage" that can result from an otherwise beneficial mutation.

That's what a group of ten biomolecular engineers, primarily from Johns Hopkins University, set out to investigate. Led by Jacob D. Mehlhoff, the team published results of their study on "Collateral fitness effects of mutations." Their paper in PNAS begins with an affirmation of Darwin dogma: "Mutations provide the source of genetic variability upon which evolution acts." From there, it's all downhill for Darwin.
Deleterious protein mutations are commonly thought of in terms of how they compromise the protein's ability to perform its physiological function. However, mutations might also be deleterious if they cause negative effects on one of the countless other cellular processes. The frequency and magnitude of such collateral fitness effects are unknown. Our systematic study of mutations in a bacterial protein finds widespread collateral fitness effects that were associated with protein aggregation, improper protein processing, incomplete protein transport across membranes, incorrect disulfide-bond formation, induction of stress-response pathways, and unexpected changes in cell properties. [Emphasis added.]
The six collateral fitness effects they found were all bad. In fact, one can look in vain for any evidence of a raw beneficial mutation that did not cause collateral damage. There is no mention of innovation. There is no mention of novel function. There is no mention of new information. In all of the 230 mentions of "fitness" in the paper, there is not one clear-cut example of an improvement in fitness — the kind of progress that a Darwinian must hope for to believe in universal molecules-to-man evolution.

The team focused on a version of beta lactamase in E. coli as a prototype for understanding the collateral effects of mutations.
The distribution of fitness effects of mutation plays a central role in constraining protein evolution. The underlying mechanisms by which mutations lead to fitness effects are typically attributed to changes in protein specific activity or abundance. Here, we reveal the importance of a mutation's collateral fitness effects, which we define as effects that do not derive from changes in the protein's ability to perform its physiological function. We comprehensively measured the collateral fitness effects of missense mutations in the Escherichia coli TEM-1 β-lactamase antibiotic resistance gene using growth competition experiments in the absence of antibiotic. At least 42% of missense mutations in TEM-1 were deleterious, indicating that for some proteins collateral fitness effects occur as frequently as effects on protein activity and abundance.
That's part of the bad news; a "missense mutation" in a protein not only damages the protein, it just as often causes collateral damage somewhere else. Design advocates understand this; in car engines, a broken part of an engine is likely to lead to other collateral damage, such as overheating or loss of steering control. Why would anyone think that a complex cell will perform better when a part goes "missense" — meaning its sequence no longer allows it to fold and function?

Why Are Darwinians Surprised?
The surprising prevalence of deleterious collateral fitness effects suggests they may play a role in constraining protein evolution, particularly for highly expressed proteins, for proteins under intermittent selection for their physiological function, and for proteins whose contribution to fitness is buffered against deleterious effects on protein activity and protein abundance.
The phrase "may play a role in constraining protein evolution" is jargon for, "collateral damage stops protein evolution in its tracks." Stepping on the brakes is a constraint, all right. How is a hopeful Darwinian going to get a brain for E. coli by slamming on the brakes every time a cosmic ray hits a gene?

Notice that the collateral damage "particularly" affects the very proteins that the hopeful Darwinian needs to evolve the most: (1) the ones that are highly expressed, (2) the ones that are under selection for their function, and (3) the ones with armor ("buffered against deleterious effects on protein activity and protein abundance"). These are the very proteins that are particularly constrained by the collateral fitness effects of mutations.

A faithful Darwinian might take refuge in exaptation theory: the idea that some idle sequences of amino acids are silently waiting in the wings for their chance in the limelight. Maybe a duplicated gene or divided gene could take advantage of neo-functionalization or sub-functionalization. Maybe a pseudogene could come back to life (but see our article on pseudogenes). It's no good. The moment the bench player gets up to bat and becomes "highly expressed" or under selection, it also gets in the line of fire for collateral fitness effects when the next mutation comes along.

To keep spirits high, maybe stating more Darwin dogma can help.
Fitness is one of the most important concepts in evolutionary biology. Despite its importance, fitness can be difficult to measure because it is a combination of many traits that interact in complex ways. Accordingly, researchers generally estimate fitness using fitness components — traits like fecundity and survivorship that are thought to be the result of the most important traits affecting fitness. Although these estimates have been very useful for evolutionary research, they tell us little about the underlying mechanisms of these fitness components.
Translated, this says, "We're clueless about one of the most important concepts in evolutionary biology." That's odd. Wasn't Darwin's great achievement the discovery of a "mechanism" for evolution? And now, 169 years later, they can't even measure it? Think about this a moment; if "fitness" (whatever that is) is measured by fecundity, does that mean that pandas and rhinos are unfit? If fitness is measured, on the other hand, by "survivorship," how is that not circular? The fit survived because they are fit. The survivors are fit because they survived. Measurements based on fecundity and survivorship may indeed be "very useful for evolutionary research," but "they tell us little about the underlying mechanisms" of evolution.

No Good News Here

It's hard to find any good news in this paper for doctrinaire Darwinians. All the fitness (whatever that is) goes downward. In the Discussion, the authors say,
Our results caution against using measures of protein properties as a proxy for biological fitness or employing a nonnative context in DMS [deep mutational scanning] experiments, as the former risks underestimating the fraction of mutations that are deleterious in their native context and the latter risks reporting on nonbiologically relevant collateral fitness effects.
Then they list, for the third time, the six kinds of collateral damage they actually witnessed when they tinkered with the sequence of one protein in one bacterium.

There's another important conclusion in this paper. A molecular biologist cannot just study an isolated protein in a dish to see if it folds or not, or has any function at all. He or she must study it in the context of the cell or organism in which it is embedded in real life. All damage is bad:
In terms of a mutation's impact on protein evolution, the cause of the deleterious effects is irrelevant. Collateral fitness costs arise from the mutation's impact on some cellular process(es) that in turn causes a fitness decrease. These costs will constrain protein evolution, provided they are not offset by beneficial primary fitness effects or mitigated by a second, compensatory mutation that alleviates the effect or lowers expression level.
This holds out one last hope: compensation. But do they describe any real-world examples of damage "offset by beneficial primary fitness effects"? Do they describe any damage compensated by another mutation? Guess. Answer: no. They just hope that in some other mythical environment that damage will work out better. Maybe in some molecular Eden, the gene will come under positive selection, and human brains will be one step closer. Or maybe it will just stop having the bad effect (i.e., go neutral). Keep the faith.
However, it is the fitness across all environments an organism experiences that will govern the gene's evolution. When the gene comes back under selection, such silenced alleles will be rapidly purged because they are not functional. Environment-dependent regulation of gene expression could alleviate this issue; thus, collateral fitness effects might provide an evolutionary advantage for the evolution of gene expression regulation.
Evolutionists keep hoping for the mythical "evolutionary advantage" that can make brains from bacteria, but real-world observations continue to disappoint.

Nature Fights Mutations

The bad news is that beneficial mutations are rare. The worse news is that they are usually accompanied by collateral damage. The authors know that "protein sequence evolution is under selective constraint both to maintain function and to avoid collateral negative effects." Advocates of intelligent design do not expect random mutations to do any good. Instead, they perceive evidence of foresight that prepared cells and organisms for the inevitable harm of mutations, and gave them the tools to repair the damage.