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What’s a Hemimastigote Got to Do with Progressive Creationism?

By Anjeanette Roberts - February 21, 2019
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I love a good hiking story, and like all scientists I love the prospect of discovering something new. Really new. A recent “behind the paper” article posted on Ecology and Evolution (an online community from Nature Research) unpacks a tale with both elements. In spring of 2016, on a hike through Nova Scotia, Yana Eglit stopped to collect a soil sample that harbored not just one but two rare organisms from a seldom-encountered group of predatory protists (single-celled eukaryotes) known as hemimastigotes.1 Discovery and analyses of these tiny creatures has been instructive and it bears directly on evolution/creation discussions.

Searching for Common Ground

As part of my work for RTB, I occasionally venture onto science-faith and apologetics online discussion sites. One site, called Peaceful Science, seeks to bring scientists from all faith persuasions into discussions about various origins models, including RTB’s progressive (old-earth) creationism model and evolutionary mainstream models. Needless to say, we don’t interpret some scientific data the same way, especially when it concerns origins. Discussions can be challenging!

One complicating factor is that it is often difficult to understand someone’s model from their vantage point when it seems incongruent with one’s own worldview model. Consider evolution, which says all life, extinct and extant, has developed through neutral and adaptive mutations and eons of common descent (with or without God’s preprogramming or tweaking the system along the way). And then consider the progressive creation model, which says God created distinct “kinds”—introducing them, in due course, over long epochs of creation. Now, add 280 years of observations by scientists and naturalists who have classified organisms into various taxa according to the Linnaeus system of naming and classification (i.e., taxonomy). How does one begin to talk coherently across these two origin models? Where do we find grounds for clear communication?

What Is a “Kind”?

Introduced by Swedish scientist Carl Linnaeus in 1735, scientists still use the Linnaeus system of classification but they have introduced several additional categories or taxa (e.g., subphyla, supra kingdoms, suborders, etc.). Many organisms undergo frequent reclassification as new data emerges. Since Linnaeus’s system is based on observed morphologies, behaviors, and ecological space, classifications entail subjective elements according to observers and which characteristics they prioritize. Naturalists often disagree about variants and specific species identifications. So, classification of organisms is a bit arbitrary as to when something falls within one taxon or a closely related taxon.

In my engagements with evolutionary proponents on Peaceful Science, some have insisted that I define created kinds and first principles in order to support a progressive (old-earth) creationist model for life on Earth. I’ve responded that created kinds cannot be defined a priori but must be determined through observations and comparisons. And due to the somewhat arbitrary nature of various taxa, “kinds” may not be definable across taxa. For example, some created “kinds” might fall at the level of phyla and others at the level of class. Perhaps other “kinds” would even fall at the level of species or subspecies (e.g., Homo sapiens sapiens).

Within an evolutionary model, the modern synthesis of Darwinian evolution adds consideration of genetics (inheritance of DNA), population modeling, and now comparative genomics to the determination of descent with modification. Distinctions arising from these considerations have resulted in additional non-Linnaean classifications. Clade (from Ancient Greek, meaning “branch”) is one such classification that describes distinct groups that share common ancestry. Clade may provide a current accepted designation that could come close to a created kind—a realization that materialized in my online discussions with evolutionary proponents.

My assertions that kinds must be determined observationally (through extensive comparative genomics and, when possible, through experimental validation) have been criticized for lack of predictive value. Critics insist that evolutionary theory predicts nested hierarchies (levels of relatedness) and that phylogenomic analyses show just such relationships among various organisms. According to evo-devo predictions, each new organism should fit into the scheme that roughly—depending on which organisms and which genes or gene sets are being compared—depicts the historical relatedness of Earth’s organisms. And they claim that phylogenomic analyses have proven that evolution is correct (and therefore all YEC and OEC claims are falsified) and that all life fits this scheme (of nested hierarchies) and therefore shares common ancestry and descent.

I remain highly skeptical that any molecular data supports evolutionary speculations that presumably account for development of novelties and ever-increasing complexities. I also think evolutionary speculations and just-so stories fall short of realistically accounting for extreme orchestration of highly complex, finely tuned biological systems—whether intracellular, intra-organismal, or ecological in nature.

And regarding our current topic, I’m also skeptical that phylogenomic analyses actually show that all life is related by common descent. What the data indicates is that phylogenomics can show a variety of possible but uncertain inferred relationships.2 But as far as nested hierarchies go, there’s a bit of a challenge because a progressive creation model would also expect nested hierarchies within clades or created kinds. However, a progressive creation model would also predict that there are independent hierarchies (unrelated organisms), each stemming from an organism created by fiat and filled out through secondary cause-and-effect reproduction. These original created organisms would not be static but dynamic, able to adapt to changing environments and diversify over long epochs of time and would entail many familiar mechanisms such as epigenetic changes and gene flow.

A Prediction That Could Distinguish Origins Models

A dogma within molecular biology and genetics holds that descent with modification is traceable at the genetic level. Genetic sequences can be changed through progressive accrual of neutral and beneficial mutations and even, perhaps, of detrimental mutations that are not severely damaging. Inheritance, gene flow, and sexual recombination allow for greater changes in genetic sequences, as do gene duplications, rearrangements, and lateral or horizontal gene transfer (HGT) from other organisms (albeit arguably HGT is extremely rare in higher organisms). These types of genetic changes can be tricky to account for in phylogenomic analyses. And even in progressive creation models, these changes within clades would occur as frequently as they would in evolutionary models. Further complications to data interpretation would occur when, for providential reasons, common (shared) archetypes (at molecular levels) occur in various created kinds. These processes and design features could present an insurmountable hurdle for phylogenomic analyses. Computational biologists would need to maintain flexibility in allowing the previous types of genetic changes into analyses without creating false signals of descent arising from common molecular archetypes occurring across independent hierarchies.

So a question arises: Is there a prediction that stems from a progressive creation model’s assertion of independent hierarchies (even if containing nested hierarchies within)? One might imagine that as scientists continue to sequence more and more environmental samples or newly discovered organisms, some organisms will emerge that do not fit nested hierarchies already in place. Newly discovered (and sequenced) organisms should fit into the ever-bushier plethora of nested hierarchies depicting evolution’s common descent from the last universal common ancestor in the evolutionary model. In contrast, if true, progressive creationism would predict that independent hierarchies may be discovered.

Hemimastigotes Fit This Predictive Aspect of Progressive Creationism

Not possible in previous encounters with hemimastigotes, Eglit and her colleagues were able to isolate single cells and sequence transcriptomes (RNA sequences) from the two captured hemimastigotes: Hemimastiix and Spironema.3 Previous observations had placed hemimastigotes in a phylum of eukaryotes designated as Hemimastigophora.4 The Hemimastigophora were thought to be similar to Euglenophyta (euglenids) or perhaps alveolates or Rhizaria (Sar), apusomonads or ancyromonads (Amorphea+) based on shared morphological features.5

After isolating and characterizing the newly collected hemimastigotes but prior to sequencing their intracellular RNAs (transcriptomes), Eglit and colleagues made some bets on which supergroup their newly sequenced organisms would fall into. Following extensive bioinformatic clean-up, phylogenomic trees comparing the new sequences to existing eukaryotic sequences revealed that no one won the bet.6 Hemimastigotes did not fall within any previously characterized major group of eukaryotes. They represented a supergroup, now designated as a new supra-kingdom, of their own.7

This current hemimastigote study does not compare genomes; it compares concatenated gene sets from existing eukaryotic sequences and extensively culled transcriptome sequences. Nevertheless, it provides enough data to indicate that a new supergroup of organisms exists that are “always distantly related”8 to other known eukaryotes. Certainly, this finding can be fit into an evolutionary interpretation of the data. However, researchers do so with statistically based inferences, a degree of subjectivity, a degree of uncertainty, and speculation, as indicated by the authors, methods, and supporting phylogenomic analyses.9 Evolutionary interpretations are always possible. However, the data in this study suggests that an independent hierarchy of organisms has been discovered and is now partially described. It also highlights some possible molecular archetypes such as Golgi and cytoskeletal proteins and additional proteins involved in membrane trafficking.

Regardless of whether evolution or progressive creationism is true, this study shows that some model features may be predicted, but others are not predictable and must simply be discovered. This is the nature of reality and is a first principle for progressive creationism.

Why So Many Similarities if Evolution Isn’t True?

I hear this question from time to time. My response is that it really should be no surprise that life shares common design at molecular levels, not because evolution is necessarily true or because God was limited in imagination or by designated physical laws of this creation, but because God’s providence provides for our stewardship of creation as vice-regents bearing his image and entrusted with creation’s care. Because all life shares common building blocks and similar biological processes, we can study a variety of organisms and gain knowledge that allows us to discover true biological (metabolic and physiological) features about ourselves and other organisms where direct study would be ethically prohibitive or physically unfeasible. All discoveries demonstrate how God in his goodness has designed and populated a world for our delight, discovery, and good stewardship.

Endnotes
  1. Yana Eglit, “Microbes Underfoot Yield a New Lineage of Eukaryotes,” Ecology and Evolution (website), Nature Research, November 14, 2018, https://natureecoevocommunity.nature.com/users/180640-yana-eglit/posts/41039-microbes-underfoot-yield-a-new-major-lineage.
  2. Ding He et al., “An Alternative Root for the Eukaryote Tree of Life,” Current Biology 24, no. 4, (February 17, 2014): 465–70, doi:10.1016/j.cub.2014.01.036; Laura A. Katz et al., “Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life,” System Biology 61, no. 4 (July 1, 2012): 653–60, doi:10.1093/sysbio/sys026; Romain Derelle and B. Franz Lang, “Rooting the Eukaryotic Tree with Mitochondrial and Bacterial Proteins,” Molecular Biology and Evolution 29, no. 4 (April 1, 2012): 1277–89, doi:10.1093/molbev/msr295. Also see figure 1 in Fabien Burki, “The Eukaryotic Tree of Life from a Global Phylogenomic Perspective,” Cold Spring Harbor Perspectives in Biology 6, no. 5 (May2014): a016147, doi:10.1101/cshperspect.a016147.
  3. Gordon Lax et al., “Hemimastigophora Is a Novel Supra-Kingdom-Level Lineage of Eukaryotes,” Nature 564, no. 7736, (December 2018): 410-14, doi:10.1038/s41586-018-0708-8; Wilhelm Foissner, Hubert Blatterer, and Ilse Foissner, “The Hemimastigophora (Hemimastix amphikineta nov. gen., nov. spec.), a New Protistan Phylum from Gondwanian Soils,” European Journal of Protistology 23, no. 4 (October 1988): 361-83, doi:10.1016/S0932-4739(88)80027-0. See also notes 1 and 5.
  4. Lax et al., “Hemimastigophora Is a Novel Supra-Kingdom-Level Lineage of Eukaryotes”; W. Foissner, Blatterer, and I. Foissner, “The Hemimastigophora.”
  5. Lax et al., “Hemimastigophora Is a Novel Supra-Kingdom-Level Lineage of Eukaryotes”; W. Foissner, Blatterer, and I. Foissner, “The Hemimastigophora”; Ilse Foissner and Wilhelm Foissner, “Revision of the Family Spironemidae Doflein (Protista, Hemimastigophora), with Description of Two New Species, Spironema terricola N. Sp. and Stereonema geiseri N., G., N. Sp.,” Journal of Eukaryotic Microbiology 40, no. 4 (July 1993): 422–38, doi:10.1111/j.1550-7408.1993.tb04936.x. The authors note: “The main differences between the three genera and five species recognized are contractility, length of kineties, body size, shape of cell and nucleus, and particulars of the cortex and extrusomes. The phylogenetic relationships of the Hemimastigophora are still uncertain. However, the diagonal symmetry of the cortical plates and the pronounced euglenoid movement of Spironema spp. suggest a common ancestor with euglenids.”
  6. Eglit, “Microbes Underfoot Yield a New Lineage of Eukaryotes.”
  7. Lax et al., “Hemimastigophora Is a Novel Supra-Kingdom-Level Lineage of Eukaryotes.”
  8. Lax et al., “Hemimastigophora Is a Novel Supra-Kingdom-Level Lineage of Eukaryotes”; W. Foissner, Blatterer, and I. Foissner, “The Hemimastigophora.”
  9. Lax et al., “Hemimastigophora Is a Novel Supra-Kingdom-Level Lineage of Eukaryotes”; W. Foissner, Blatterer, and I. Foissner, “The Hemimastigophora.”

Category
  • Genomics
  • Common Design vs. Common Descent
  • Creation vs. Evolution
Tags
  • phylogenomics
  • Linnaeus
  • kinds
  • hemimastigotes
  • first principles
  • Blogs

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