For systems biologists, life is optimally designed

Image: Human knee, by staff (2014). “Blausen Medical Medical Gallery 2014”. WikiJournal of Medicine 1 (2). DOI: 10.15347 / wjm / 2014.010. ISSN 2002-4436., CC BY 3.0 , via Wikimedia Commons.

In my last two articles (here, here), I described the ongoing revolution in systems biology where practitioners replaced evolutionary presuppositions with design-based assumptions such as the central role of teleology. Now, I will study how biologists have increasingly abandoned the belief that a misconception of life is pervasive. Instead, they generally assume that biological structures and systems are highly optimized.

Waiting for bad conception

The underlying logic of the Standard Evolutionary Model predicts that flawed design and non-functioning remains of organisms’ evolutionary past should litter the biosphere. The reason is well summarized in Wikipediathe article of “Argument of bad design”:

The “bad design” is consistent with the predictions of the scientific theory of evolution through natural selection. This predicts that the functionalities which have been developed for certain uses, are then reused or co-opted for different uses, or completely abandoned; and this suboptimal state is due to the inability of the hereditary mechanism to eliminate the particular vestiges of the evolutionary process.

In terms of the fitness landscape, natural selection will always grow ‘up the hill’, but a species cannot normally move from a lower peak to a higher peak without first crossing a valley.

Figure of Wikipedia of the fitness landscape. The landscape is a theoretical representation of how different organisms stack up against each other in terms of fitness. The x-axis (and often the y-axes) represent variation in traits (eg, height, fur color) and the z-axis represents fitness. Natural selection is expected to push fitness to its peak, but this peak is often not the highest.

The expectation of a bad design is not just a subjective conclusion based on intuition, but it has been rigorously demonstrated in computer models. Such a model created by Snoke, Cox and Petcher explained why evolutionary processes that allow increases in complexity must generate large amounts of unwanted DNA and non-functional elements. The details of their model are complex, but the underlying logic is simple.

For complex innovations to emerge, organisms must allow non-functional DNA to appear and persist in the population until a functional sequence appears. Such additions to the genome could occur through the duplication of a gene and then its repeated mutation. Unwanted DNA would inevitably accumulate to encompass a significant percentage of the genome. This requirement is why biologists once assumed that unwanted DNA made up up to 97 percent of the human genome.

Likewise, the origin of complex structures (eg, molecular machines) requires countless arrangements of trial and error of molecules or tissues until something beneficial emerges. Most of the tests would either be non-functional or ineffective. Therefore, only a minority of structures and biological systems should appear highly optimized.

Central argument against design

The most apparent difference in the predictions between intelligent design and nondirected evolution is the extent to which life displays suboptimal / nonfunctional design versus optimal design. Philosopher Philip Kitcher made this point in his book Living with Darwin: Evolution, Concept and Future of Faith. He used examples of what he believed to be awkward and incompetent designs as the main argument for rejecting smart design:

If you were a talented engineer designing a whale from scratch, you probably wouldn’t think of outfitting it with a rudimentary basin. … If you designed a human body, you could surely improve the knee. And if you were to design the genomes of organisms, you certainly wouldn’t fill them with garbage.

In the same vein, the biologist Nathan Lents argued in his book Human errors: a panorama of our glitches, from useless bones to broken genes that the “clumsy” design seen throughout the human body demonstrates that we are not the product of an intelligent designer but of an undirected evolutionary process:

The third category includes human faults which are due only to the limits of evolution. All species are stuck with the bodies they have, and they can only progress through the smallest changes, which happen randomly and rarely. We have inherited structures that are horribly inefficient but cannot be changed.

This is why our throats carry both food and air through the same tiny space, and why our ankles have seven unnecessary bones dangling. Correcting either of these mediocre conceptions would require far more than one-to-one mutations could ever accomplish. To suppose that these living things were created separately is to regard the creative agent as fanciful, clumsy, a mediocre engineer, an unintelligent designer.

p. xi-xii

Change point of view

Yet most of the supposedly poor design examples cited by Kitcher, Lents, and other skeptics have been canceled (here, here, here, here). The others generally represent degradations of formerly optimal designs or appeal to the error of imperfection of the gaps.

Alleged examples of poor design usually represent opinions resulting from the limited understanding of wheelchair reviews in the technical literature and their lack of engineering training. For example, in direct contradiction to the assertions of Kitcher and Lents, engineers routinely reuse design patterns in new ways, just as seen with the whale’s pelvis. And medical professionals and engineers have demonstrated how the human knee and ankle are optimally and exquisitely designed (here, here, here, here). Engineers even drew inspiration from these structures to design artificial limbs (here, here).

In addition, most of the human genome is now known to be functional thanks to the ENCODE project. The devastating ramifications of this revelation for the theory of evolution have not gone entirely unnoticed. Biochemist Dan Graur put the following bluntly:

If the human genome is indeed devoid of unwanted DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome. If, on the other hand, organisms are designed, then all of the DNA, or as much as possible, should have some function. If ENCODE is right, then the evolution is wrong.

“Underlying optimization principles”

Equally important, systems biologists now recognize that the optimal design hypothesis leads to the most productive research. For example, Nikolaos Tsiantis, Eva Balsa-Canto and Julio R. Banga have developed a model for studying biological systems based on the identification of “underlying principles of optimality”. And in their 2018 Bioinformatics article, they interviewed leading researchers who also demonstrated the predictive power of the optimality hypothesis:

Sutherland (2005) argues that these optimality principles allow biology to move from a simple explanation of models or mechanisms to the ability to make predictions from first principles. Bialek (2017) insists that optimality assumptions should not be adopted for aesthetic reasons, but as an approach that can be directly tested by quantitative experiments. Mathematical optimization could therefore be considered as a fundamental research tool in bioinformatics and in the biology of computational systems.

Other researchers have even shown that biological systems such as DNA replication and translation, embryological development and sensory processes operate with efficiencies close to the limits of what is physically possible. Human engineering is nothing compared to such achievements.

The great preponderance of evidence corresponds to the design-based prediction of optimality. And this directly contradicts a central prediction of any unguided theory of evolution. Will this evidence convince critics like Kitcher and Lents to rethink their point of view? Probably not since their faith in scientific materialism is not based on empirical evidence but on their philosophical beliefs. Fortunately, many biologists have allowed the evidence to point them in the right direction despite social pressures to maintain the status quo. These scientists will lead biology through the next great scientific revolution that has just begun.

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