Evolution Worked Magic in Plants

Some evolutionary papers are filled with verbs like arose, emerged, and originated.  Do these convey scientific understanding, or are they veils concealing ignorance?  Is it like saying “abracadabra” to say something “arose” by evolution?  A recent paper about sophisticated metabolic enzymes in plants is a case in point.

In a paper by Weng, Philippe and Noel in Science (29 June 2012: Vol. 336 no. 6089 pp. 1667-1670; DOI: 10.1126/science.1217411), the magic starts right in the title: “The Rise of Chemodiversity in Plants.” It rose to a crescendo throughout the overture to evolution’s uncanny power to bring things forth out of nothing.¹  In the following excerpts, the magic words, hedging words and personifications are highlighted in bold:

• The Emergence of Metabolism
• New metabolic branches continuously arose throughout land-plant evolution….
• Since its origin as a fundamental property of the cell, metabolism is generally regarded as having evolved toward increasing order and catalytic efficiency….
• Primary metabolism likely arose from promiscuous primeval metabolic reactions and evolved toward greater catalytic precision and efficiency. Specialized metabolism likely emerged from primary metabolism.
• Even deleterious changes appearing in one paralog may be tolerated and not eliminated by selection, when the other paralog contributes to fitness. In such cases, the evolution of advantageous activities can now be favored in new environments.
• ….increased catalytic promiscuity likely molded the evolution of specialized enzymes.
• Once a duplication-derived progenitor emerged, mutations may have loosened the energetic interdependencies….
• For instance, the evolution of rosmarinic acid biosynthesis in Lamiaceae herbs arose from gene duplication of a BAHD acyltransferase.
• The emergence of rosmarinic acid synthase (RAS) in Lamiaceae likely followed substrate permissiveness of its evolutionary progenitor HCT, a more conserved enzyme ubiquitous in land plants.
• By exploiting the broader substrate recognition of ancestral DFR, I. gesnerioides evolved a red flower color….
• After a gene-duplication event, one gene copy likely was selected for increased activity toward this substrate, resulting in the emergence of a new metabolic step….
• Recurring Patterns of Metabolic Evolution
• The phenotypic outcome of an evolving plant-specialized metabolic system relies on the recruitment of multifunctional enzymes…
• In addition to the recruitment of individual enzymes into emerging pathways, enzymes with expanded substrate recognition that act consecutively in a particular pathway can reappear, operating on disparate metabolites.

Surely the authors attempted to explain how things “emerged,” didn’t they?  Indeed, they did in a couple of places.  But the magic words are there again:

In contrast to primary metabolism, in which selection constrained mutations to maintain the most stable and functional enzyme forms, we hypothesize that specialized metabolic enzymes may have emerged through early gene duplication, followed by mutations that broadened substrate selection and flattened activation barriers of their catalyzed reactions. The resulting mechanistic elasticity allowed single enzymes to catalyze multiple reactions and biosynthesize multiple products (Fig. 1A). This scenario is consistent with directed evolution focused on enzyme promiscuity and the biochemical characterization of mutant libraries derived from phylogenetic relationships in several plant-specialized metabolic enzyme families….

A little later, they stated:

Supporting this view, a number of current specialized metabolic enzymes exhibit, on average, a greater ability to accept a broader range of substrates and to employ multiple energetically similar reaction mechanisms than related primary metabolic enzymes. Moreover, these enzymes seem to traverse functional space more easily than their structurally related cousins in primary metabolism to evolve new and often several metabolic products while retaining a modicum of their original function…. Diminished catalytic efficiency of multifunctional metabolic enzymes probably coincided with greater substrate permissiveness and the occurrence of several mechanistic routes to multiple products with little cost to the fitness of the host population. As long as the enzyme that must produce multiple products by virtue of its chemical mechanism yields at least one conferring a fitness advantage, the enzyme can be retained, barring issues of by-product toxicity. An enzyme does not have to evolve to perfection or absolute product specificity; it merely has to produce enough of the desired compound for the gene to be maintained in the population. As populations experience fluctuating abiotic and biotic ecological changes, one of the minor metabolites may also assume an advantageous function, thus resulting in fixation of the multifunctional paralog.

It’s not clear, however, that suggestive terms like “mechanistic elasticity,” “enzyme promiscuity,” or “substrate permissiveness” provide visible light or black light.  They may be merely giving the illusion of making emergence glow without aiding understanding of how unguided processes produced highly complex, functional molecules that human researchers have a hard time duplicating.  A critical reader might wonder why these scientists are helping themselves to “barring issues of by-product toxicity,” for instance.  Poison kills.  Can they sweep this problem away by arbitrarily barring it?  And without defining functional space, which by all accounts is an extremely tiny subset of a vast sequence space (most of which is functionless or toxic), they seem to be taking liberties to say that mutated molecules will traverse functional space in a finite time.  “Mechanistic routes” are, by definition, mindless and without purposeful aim.  Manufacture of these metabolite molecules, furthermore, requires coded information in the genome, and molecular machines to assemble them.

In the “Future Directions” section at the end, the authors’ Darwinian proclivities emerged amidst of flock of stage doves:

Although a few studies have interrogated the minimum set of mutations that dictate the emergence of specific functions in divergent plant-specialized metabolic enzymes,, no particular study has addressed all viable mutational paths in these metabolic systems. This limits our ability to postulate evolutionary scenarios consistent with the stepwise assembly of mechanistically divergent metabolic pathways within the framework of Darwinian evolution² and to quantify the incremental emergence of new activities with each mutational step. Could specialized metabolic enzymes and their pathways evolve along a wider set of evolutionary trajectories than their cousins in primary metabolism?

To make sure the audience appreciated the difficulty of their magic act, they wrote in conclusion:

The remarkable chemodiversity in plants and its underlying metabolic diversity are reached via exploration of sequence space restrained by enzyme catalysis, protein stability, emerging and extant metabolic pathways, and, ultimately, organismal fitness. The ability to bridge the fields of evolutionary biology, chemistry, biophysics, and mechanistic enzymology to cooperatively tackle the complexity of specialized metabolism will provide a more informed understanding of the amazing tapestry of plant-specialized metabolites that are so essential to the sessile lifestyle of plants.

This implies that their understanding, if any, was less informed than it should be.

By contrast, another paper in the same issue of Science had little to say about evolution, but a lot about revolution.  In “Mining the Biodiversity of Plants: A Revolution in the Making” (Science, 29 June 2012: Vol. 336 no. 6089 pp. 1658-1661, DOI: 10.1126/science.1217410), four scientists from Brock University were excited about the potential health benefits for humans of “mining” the diversity of plant metabolites for medical applications:

Approximately two-thirds of new drugs in the past 25 years have originated from the discovery of particular secondary metabolites derived from natural biodiversity. This success has been attributed to the structural complexity of molecules found in living organisms, which have an average of 6.2 chiral centers per molecule as compared to an average of 0.4 chiral centers found in combinatorial libraries. Such chemically complex molecules are very difficult and costly to produce efficiently by chemical synthesis….

…but plants do it so well for us, the message continued, we can and should exploit their design prowess for our benefit.  These authors didn’t use the word “originated” in a magical sense.  The new drugs “originated” not by unguided processes, but by intentional search and discovery, a form of intelligent design.

1. The authors’ job was not to describe degradation or variations of existing functional molecules, but to explain how new cellular machines (proteins and metabolites) that provide new, useful functions arrived: i.e., how plants that did not have these functional molecules got them.  Darwinians need to start from the bottom up; creationists start from the top down.  Creationists do not discount natural variations, but question the ability of an unguided, aimless, purposeless process like neo-Darwinism to “innovate” new complex functions possessing more genetic information than before.  Every scientist knows, furthermore, that entropy cannot be ignored.

2. In a similar vein, they stated, “Positing that protein functional promiscuity serves as the starting point for functional innovation through natural selection….”

Caught in the act!    The authors of the first paper just admitted, in print, that they have limited their thinking to postulating “evolutionary scenarios consistent with the stepwise assembly … within the framework of Darwinian evolution.”    How to we translate that into plain English, class?  Storytelling!  What’s a scenario?  A play.  What’s a framework?  A stage.  What’s the plot?  Darwinian evolution only.  And what is the acronym for “Darwin Only, Darwin Only”?  D.O.D.O.  We just watched a comedy!  It’s tragic.

It’s tragic, and it’s magic.  These authors did little more than wave their hands and shout “Abracadabra!”  Behind black curtains, they pulled Darwin rabbits out of Darwin black hats under Darwin black light, and then had the gall to tell you the rabbit “emerged, arose, originated, occurred.”  The fast-talking magicians distracted you with a steady stream of impressive phrases like “substrate permissiveness,” “mechanistic elasticity” and “evolutionary trajectory”.  They even tossed in a little sexual titillation, talking about “enzyme promiscuity.”  SUCH WORDS CONVEY NO UNDERSTANDING.  They are the tools of snake oil salesmen and charlatans, used only to distract and impress you while they steal your watch.

Think of CEH as your backstage guide to show you how the Darwin magic tricks are done.  They tried to steal your watch, but you watched them steal.  You were ready.  You were alert.  When you know the secret, and you train your mind not to be distracted by the irrelevant jargon, the act looks more like what it is: an act.  Sorry to spoil the show, but you need to know.  Now teach someone else.  Better yet, bring them to daily CEH deprogramming sessions.