Microscopic Superheroes Challenge Inferences in Science

Microscopic Superheroes Challenge Inferences in Science

Faster than a speeding bullet! More powerful than a locomotive! Able to leap tall buildings in a single bound! . . . It’s a bird! It’s a plane! It’s . . . Mighty Moss Piglet!

The Super Ts

Actually, it’s just a tardigrade, and they aren’t really fast. Their name actually means “slow stepper.” And they’re not really superheroes, but maybe they should be. They can withstand extreme environments, including temperature ranges from near absolute zero to 300°F (well over the boiling point of water), high levels of radiation (hundreds of times the lethal dose for humans), the vacuum of space, pressures up to six times greater than the deepest ocean trench, and extremely low levels of life’s elixir—water! These creatures transform via cryptobiosis, a physiological state where metabolic processes seemingly cease. This poorly understood transformation allows cryptobiotic tardigrades to withstand extreme desiccation and extreme cold (even for decades) before being reanimated! It’s not exactly resurrection from the dead, but it’s a good case for elevating this microscopic organism to superhero-like status.

Due to their appearance and habitats, tardigrades have acquired the nicknames “water bears” and “moss piglets.” First discovered in 1773, these micro-animals are rather cosmopolitan, showing up in a variety of Earth habitats. Their translucent, segmented bodies facilitate microscopic visualization of simple neurological and muscular structures. In the past 18 months, these eight-legged, microscopic wonders of survival have been drawn into a debate about the extent of horizontal gene transfer in the evolution of its highly unique phyla of animals, Tardigrada, containing more than 1,000 different species.

In 2015, researchers reported a tardigrade, Hypsibius dujardini, draft genome indicating signs of extensive horizontal gene transfer.1 The report indicated that 17.5 percent of the 38,145 predicted genes in the 212.3 megabase (Mb) genome of the tardigrade depended upon transfer of foreign genes, primarily (>90 percent) of bacterial origin. However, subsequent sequencing by a second research group indicated <0.5 percent of genes in the 135 Mb tardigrade genome were acquired through functional horizontal gene transfer (around 0.2 percent bacterial and another 0.2 percent foreign genes from nonmetazoan eukaryotes).2 That’s a huge difference! These two studies highlight some very significant challenges that science faces in the modern genomic era and the era of an extended evolutionary synthesis.

Extended Evolutionary Synthesis 

The extended evolutionary synthesis (EES) addresses, among other things, an obvious inadequacy of gradual, unguided mutations under natural selection (neo-Darwinism) as a sufficient mechanistic explanation for the complexity and diversity of life on Earth. Therefore, adherents to an EES share common critiques of Darwinian and neo-Darwinian evolutionary claims to those raised by progressive creationists and other critics of Darwinian evolution.

EES appeals to various other naturalistic explanations and molecular mechanisms for the acquisition and accrual of large amounts of genetic information and material over relatively short transition times. These mechanisms include genome duplication, transposition/translocation, horizontal (or lateral) gene transfer, and endosymbiosis.3 The exact contributions and combinations of these mechanisms in accounting for a naturalistic explanation of life’s complexity, diversity, and history are unknown and have been referred to as the muddy middle layer of mechanism. EES and many theistic evolutionists believe the muddy middle layer will be clarified over time through progressive scientific studies and discoveries.

As scientists, we dare not fail to acknowledge that mechanisms like horizontal gene transfer (HGT), genome duplication (whole or partial), and transposition contribute significantly to biological functions and adaptive mechanisms. As I’ve said elsewhere, I actually think molecular mechanisms such as these point to brilliant, insightful engineering that will assure the survival and thriving of species in response to ever-changing, challenging environments. (See “Demystifying Evolution and the Species Problem” and “Do Devils Evolve?” for related articles.)

However, I believe that a naturalistic appeal to these varieties of mechanisms as those responsible for the evolutionary history and complexity of life will make it ever more difficult to draw meaningful scientific conclusions that are practical for application from the data. The first publication of the tardigrade draft genome highlights this hazard.

Misinterpreting the Data—HGT, Convergence, or Contamination?

Horizontal, or lateral, gene transfer refers to the real or presumed transfer of genetic material from one organism to another. In single-celled organisms, HGT occurs via human intervention in the laboratory or in nature by the uptake of genetic material from the environment. Both cases where this occurs are known as transfection. HGT also occurs through vector-mediated transfers by viruses (transduction), or by direct transfer from one organism to another (conjugation). Successful transfer of genetic information affects all subsequent progeny in unicellular organisms. However, in multicellular organisms, HGT is typically vector-mediated (via viruses) or, presumably, through direct environmental uptake of bacteria or single-celled organisms (parasites or symbionts). In multicellular organisms, HGT only affects subsequent generations and progeny if the transfer occurs in the germ line.

In the first publication of the tardigrade draft genome, researchers were quick to interpret data within the genomic sequences as that of bacterial and non-metazoan eukaryotic foreign DNA acquired by HGT. This interpretation of the data fits nicely into a neo-Darwinian or EES understanding of universal common descent where more complex organisms must co-opt genetic material necessary for survival from other simpler organisms, since accruing point mutations over time is not sufficient or efficient enough to ensure survival. Appealing to HGT to account for tardigrade genomic sequences allowed the researchers to further speculate that the tardigrades’ abilities to survive extreme environments were achieved by co-opting bacterial systems that allow bacterial extremophiles to thrive under similarly harsh conditions. The researchers’ commitment and desire to show an evolutionary relevance led them to some poor and hasty conclusions. This is so often true in vast troves of the scientific literature today, since such speculation is much simpler than the hard work of designing well-controlled functional experiments that prove rather than just infer significant function.

In the second genome publication, the researchers were much more meticulous in their work and sequencing, and seemingly much more committed to getting at the truth than advancing a particular interpretive paradigm. Carefully evaluating sequence scaffolds and controlling assembly parameters, they found that only ~0.5 percent, not 17.5 percent, of the genome may be associated with HGT from bacteria and non-metazoan eukaryotes. Of course, the 0.5 percent may be of functional significance, acquired through HGT, and relevant to understanding the tardigrade organism, but all of that has yet to be analyzed and is far from being proven.

When are evolutionary stories telling us nothing substantive? Forcing a universal common descent model onto the interpretation of the data in order to account for the presence of specific genomic components in various organisms is bad and hasty science. We have no idea if the ~0.5 percent of the genome is truly indicative of HGT, convergence, or even residual contamination in the DNA sequences. Only good research will address these questions.

Joining the Questioners

Does the evolutionary paradigm facilitate scientific advancement and contribute to a reliable, growing foundation of knowledge? Or is a blind assumption of universal common ancestry clouding the waters by promoting inference-only scientific conclusions? If we want to gain true knowledge and understanding that can be harnessed for practical applications and advancements, researchers must do the hard work—looking for genes and regulatory mechanisms and proving associated functions—rather than just inferring function or lack of function based on evolutionary rhetoric. Inference is not evidence—it is just inference.

Inference may be right and it may be wrong. And hasty, inference-laden assumptions, received with uncritical open arms, embracing any evolutionary conclusion will continue to swamp the scientific literature with premature claims that cloud access to true scientific knowledge. A commitment to progressive creationism actually forces the scientist to do the hard work of linking form and function for each organism of interest before publishing. Progressive creationism is a paradigm that will push us to scientific conclusions of greater integrity and reliability.

Tardigrade Superheroes

Perhaps these tardigrade superheroes will help deliver us from speculative science driven by ever more creative evolutionary narratives. The first two reports of tardigrade’s genomic analyses have certainly highlighted a major hazard in scientific literature—showing that researchers too quickly assume too much about draft genome sequences. When others build on these assumptions, the literature becomes a fog of self-supporting assertions, often built on very little data and mountains of speculation.

Certain critiques raised by the EES toward neo-Darwinian evolution are extremely helpful in opening up scientific inquiry. But perhaps these critiques do not take us far enough toward freeing scientific inquiry from the endless inferences built on naturalistic assumptions and commitments to universal common ancestry. Unswerving commitment to a universal common ancestry paradigm plus the mechanisms of EES may lead to greater mayhem and confusion in the absence of real, functional, and mechanistic data. Dogmatic evolutionary theory may one day destroy scientific access to reality.

We should always ask ourselves, what’s best for getting at the underlying truth? As we discover more and more scientifically, I am convinced it will point more and more to the complexity of God’s brilliant, insightful designs. God’s revelation in nature will become more and more apparent as he desires for more people to see him, seek him, and find him in redemptive reconciliation.

  1. Thomas Boothby et al., “Evidence for Extensive Horizontal Gene Transfer from the Draft Genome of a Tardigrade,” Proceedings of the National Academy of Sciences, USA 112 (December 2015): 15976–81, doi:10.1073/pnas.1510461112.
  2. Georgios Koutsovoulos et al., “No Evidence for Extensive Horizontal Gene Transfer in the Genome of the Tardigrade Hypsibius dujardini,” Proceedings of the National Academy of Sciences, USA 113 (May 2016): 5053–58, doi:10.1073/pnas.1600338113.
  3. Perry Marshall, Evolution 2.0: Breaking the Deadlock between Darwin and Design (Dallas: BenBella Books, 2015).