Here’s a conundrum for evolutionists: similar design principles and strategies are found across kingdoms. Plants and animals use similar proteins as switches to activate the immune response when invaded by pathogens. The story is told in Science Magazine. The editors call it “Shared logic in diverse immune systems.”

The innate immune systems of both plants and animals depend on the ability to recognize pathogen-derived molecules and stimulate a defense response. Jones et al. review how that common function is achieved in such diverse kingdoms by similar molecules. The recognition system is built for hair-trigger sensitivity and constructed in a modular manner. Understanding such features could be useful in building new pathways through synthetic biology, whether for broadening disease defenses or constructing new signal-response circuits. [Emphasis added.]

The authors, Jones, Vance, and Dangl, use standard Darwinian terms throughout — common ancestor, natural selection, co-evolution, etc. Yet they can’t help but notice how similar the “strategy” is in “evolutionarily ancient” lineages. Since the mechanisms are largely “conserved” between plants and animals, they chalk it up to the usual evasive, circular explanation: convergent evolution.

Multicellular eukaryotes coevolve with microbial pathogens, which exert strong selective pressure on the immune systems of their hosts. Plants and animals use intracellular proteins of the nucleotide-binding domain, leucine-rich repeat (NLR) superfamily to detect many types of microbial pathogens. The NLR domain architecture likely evolved independently and convergently in each kingdom, and the molecular mechanisms of pathogen detection by plant and animal NLRs have long been considered to be distinct. However, microbial recognition mechanisms overlap, and it is now possible to discern important key trans-kingdom principles of NLR-dependent immune function. Here, we attempt to articulate these principles.

Their basic “principle” goes like this: if something works, it must have evolved.

We propose that the NLR architecture has evolved for pathogen-sensing in diverse organisms because of its utility as a tightly folded “hair trigger” device into which a virtually limitless number of microbial detection platforms can be integrated.

How clever of separate kingdoms of organisms to have figured that out independently! The authors just know that these things evolved, because like Phillip Johnson once said, “If science is to have any explanation for biological complexity at all it has to make do with what is left when the unacceptable has been excluded” (Darwin on Trial, 1991, p. 28). We see the awkward explanatory tinkering in the number of times the authors use the word “likely” associated with “evolved”:

• “The NLR domain architecture likely evolved independently and convergently in each kingdom….”

• “…Drosophila DARK and nematode CED4, and likely evolved from a class of prokaryotic ATPases…”

• “Thus, plant and animal NLRs likely evolved from distinct ancestral NBD lineages…”

• “This suggests that paralogs of genuine targets of virulence proteins may have evolved to resemble that target…”

• “NLRs likely derived from a common ancestor….”

• “Animal NLRs, in contrast, carry a distinct NBD subtype … that also likely derived from a distinct prokaryotic ancestral domain.”

Argument by assertion is easy once all competition has been eliminated from the field. But they do wonder about it.

Nevertheless, despite remarkable diversity in upstream and downstream signaling events, we are forced to contemplate what is so fundamentally advantageous about the NLR architecture that could explain why it arose convergently in plants and animals to play a role in pathogen detection and defense activation.

It’s true that there are differences in the numbers of NLR proteins and their downstream activations, but both kingdoms seem to use four similar strategies, at least three of which are common to both plants and animals. And there may be even more commonality:

The full spectrum of mechanisms in each kingdom suggests that there is scope for more conceptual similarities than previously suspected. Given this diversity, we propose that one advantage of the NLR architecture may simply be its ability to function as a robust on-off switch in diverse signaling contexts.

Figure 2 shows an “NLR-o-gram” between human genes and those of the lab plant Arabidopsis. The similarities are striking despite the vast time for evolution after diversification from a one-celled organism, which undoubtedly lacked all the coordinated parts of the system.

Maybe NLRs can drift easily from organism to organism. That does not appear to be the case.

Functional transfer of plant NLRs across species barriers has proven largely impossible. This restricted taxonomic functionality is poorly understood….

That’s not the only thing that is poorly understood. The complexity of NLR mechanisms shuts the door to the excuse that they are simple and easy to evolve:

Despite breakthroughs in our molecular understanding of NLR activation, many important questions remain. Biochemical mechanisms of NLR activation remain obscure. Events downstream of plant NLR activation and outputs such as transcription of defense genes, changes in cell permeability, localized cell death, and systemic signaling remain opaque. We do not know whether activated plant NLRs oligomerize or, if they do, how this is achieved, given the diversity of subcellular sites of activation observed for various NLRs. It is not clear whether and how the different N-terminal domains of plant NLRs signal. We have increasing knowledge regarding how animal NLRs assemble and signal, although knowledge gaps remain.

Sizing up the situation, we find a complex system involving hair-trigger switches made of proteins. These NLR proteins interact with many other components of the cell. In each species, they are different enough to preclude transfer across species, yet they share common functions and employ similar strategies.

Does this not sound a little like auto parts? When you go to the parts store, you buy a muffler or spark plugs or an air filter that fits your vehicle. The guy behind the desk looks up your make and model, and finds the model number that’s right for you. There are obvious similarities in function, but you don’t put an air filter from your lawn mower into a pickup truck.

You might see some “evolution” of air filters between different model years of the same truck, but we all know every part is intelligently matched to its vehicle, because the parts all have to work together.

Since the evolutionists are baffled by their explanation, we would like to liberate them from the straitjacket Darwin has put them in. Instead of looking at the immune response as another mysterious example of “convergent evolution,” why not consider intelligent design of the “principles” and “strategy” used by different kinds of organisms? And when there do appear to be some ancestral commonalities between species, genera and families, why not consider possible design principles inherent in the system — some pre-programmed robustness — to allow for modifications as conditions change?

We’re just trying to help, since you are admittedly “forced to contemplate” the advantages of the “architecture” you’ve investigated. Thinking design might also facilitate reaching the goal stated at the top: “constructing new signal-response circuits.” Constructing circuits is usually best approached by intelligent design.

Photo: Arabidopsis (rockcress), by Brona [GFDL or CC-BY-SA-3.0], from Wikimedia Commons.