Horizontal Gene Transfer

Gene sharing among organisms of different species has been a prominent topic of discussion among the scientific community for the last few decades. Numerous ideas have been proposed: some with empirical basis, others with a more speculative bent. One such idea that was popularized and expanded by this discussion was that of horizontal gene transfer.  Like much else in the discussion, there are empirical aspects and speculative aspects. Separating fact from speculation is necessary to understand genetics from a creation worldview.

Horizontal gene transfer, otherwise called lateral gene transfer, was discovered in 1928 as the result of a detailed set of experiments conducted by Frederick Griffith on bacteria that cause pneumonia.[1] Bacteria that were not virulent (disease-causing) could be made virulent by mixing them with long-dead virulent bacteria. The DNA in the dead bacteria was being taken in by the inert (disease-free) bacteria and added to their genomes, causing the formerly inert bacteria to become virulent.  Since DNA neither had been demonstrated as the molecule of heredity nor had its structure elucidated, Griffith did not grasp the mechanism that conferred the virulence on the inert bacteria. His discovery would gain importance once DNA and genetics became a major part of science. Since his discovery, other mechanisms of horizontal gene transfer have been discovered. Horizontal gene transfer is any transfer of genetic material between organisms that does not involve the vertical transmission to offspring. It is termed horizontal because the two organisms are on the same level of a hypothetical family tree, whereas vertical transfer involves going to a different level of the tree, parent to offspring.

The most well-known mechanism of horizontal gene transfer is performed by bacteria. Bacterial genomes, unlike those of most other organisms, are contained in special circular units rather than chromosomes. They also have special structures called plasmids, which contain genetic material. These plasmids, when replicated, can be passed in whole or part to other bacteria by means of a process called conjugative transfer.[2] The two bacteria involved in the transfer need to be adjacent to one another. One of the bacteria will form a small tube, through which is passed either the entire plasmid copy or certain pieces of it.  This method of gene transfer allows bacteria populations to rapidly adapt to changing environmental conditions.

While horizontal gene transfer has been known in bacteria for a while and is strongly supported by evidence, finding horizontal gene transfer in plants is a more recent development.  There are several types of proposed horizontal gene transfer involving plants.  The one with the most discussion is from plants to bacteria. However, claiming this has experimental support is misleading as it implies that plant genes were taken into bacteria. That is not what happened. Instead, genetically modified plants, infused with a bacterial gene which conferred resistance to streptomycin, were used. Unsurprisingly, the bacteria were able to pick up the streptomycin-resistant gene from the plant.[3] However, no genes from the plant were expressed in the bacterial genome.

A second study that demonstrated horizontal gene transfer involved chloroplast DNA. In this study, different members of the tobacco genus that do not normally reproduce together were grafted together. Grafting is the process in which a branch from one plant is attached to a different plant. In this experiment, the normal cultivated tobacco’s chloroplasts were modified to include a gene for streptomycin resistance and a fluorescent protein. These modified chloroplasts were found in the grafted stems, demonstrating they had been transferred.[4]

The remaining horizontal gene transfers involving plants are based almost exclusively on phylogenetic studies.  Recently plant-to-plant horizontal gene transfer has become much more popular as an explanation for genetic similarity in plant mitochondrial DNA. A recent study, in particular, relied heavily on phylogenetics. The two methods they used to infer past horizontal gene transfer both relied on phylogenetics. The first method was the building of a phylogenetic tree, which, obviously, required phylogenetics. The second method was less obvious about it.  “This method identifies HGTs (hits) from distantly related organisms compared to closely related taxonomic lineages.”[5] There is a hidden assumption in the article. The authors speak of the two plants involved as being distantly related. Relationships in the evolutionary paradigm are determined by a phylogenetic study. Thus the authors are reliant only on phylogenetic trees for both their direct and indirect evidence.  They demonstrate relationships by using phylogenies, then use the phylogeny data to prove the plants are undergoing horizontal gene transfer with distant relatives, which they determined by phylogeny.  They have reasoned themselves in a complete circle.

Proposed movement of nuclear DNA as the above authors suggest is relatively rare but does happen. A paper as far back as 2005 was the first to propose this. This paper suggested a transposon had been passed between millet and rice at some point in the past. The transposon itself was only 89% similar between the two but the researchers justified their result by saying “Our conclusion that a MULE was horizontally transferred between the Setaria and rice lineages leans heavily on evidence that these lineages diverged roughly 50 million years ago.”[6] The researchers go on to note that it was phylogenies that told them that the Setaria millets and rice split that long ago.

The problem with placing such a heavy reliance upon phylogenetics is that if the phylogenetics are wrong, the HGT-in-plants model loses all foundation and will collapse under its own weight.  Unfortunately for the scientists promoting the model, phylogenetics, otherwise known as cladistics, is a circular failure.  Phylogenetics starts with one basic assumption, namely that evolution is true.[7] One author, despite insisting molecules to man evolution is factual, wrote this of phylogenetics: “Therefore, the a priori assumption of descent with modification fails to provide independent ontological support for systematics. If ‘the background knowledge the bearing of descent with modification’ underlying cladistics is not testable by independent means, it would seem to be more a metaphysical First Principle like vitalism or orthogenesis than a component of a Popperian hypo-thetico-deductive approach.”[8] Another evolutionist went even further. “I do not think that claims made by cladists themselves can always be taken at face value.”[9] Despite evolutionists themselves openly doubting the veracity of cladistics, it continues to be used as proof that things happened in the past.

Another factor often overlooked when discussing plant phylogenies is the difficulties associated with plant taxonomies. Verne Grant, the premier expert on plant speciation and classification in the last century wrote, “The phylogeny of many or most groups of higher plants which have been studied carefully in the field and laboratory is seen to be reticulate rather than exclusively dichotomous and branching. The model of the phylogenetic tree cannot be carried over from zoology into botany without misrepresenting the relationships in many instances. In all major groups of higher plants we have to deal with phylogenetic networks rather than phylogenetic trees.”[10]  While Grant accepted the phylogenies as valid, he noticed they pointed to something completely different than the expected evolutionary tree of life: they pointed to an interconnected web, something not predicted by evolution.

Unfortunately, in all the numerous studies reviewed, there was no experimental basis for horizontal gene transfer of mtDNA in plants.  Phylogenetics provided the key thrust of each study. However, unlike the most recent study, most other studies proposed mtDNA rather than nuclear DNA or chloroplast DNA as the type of DNA being transferred.[11] In each case, phylogenetic trees are the primary evidence that horizontal gene transfer has taken place.[12],[13] Since phylogenetic studies are fraught with problems, these studies are suspect at best.

Equally troubling for the evolutionist is the fact that horizontal gene transfer has never been observed in mtDNA. In fact, in the study that demonstrated chloroplast DNA was transferred, the authors point out that there was no transfer of mtDNA.[14] While the researchers are quick to point out that their experiment was designed to find chloroplast DNA, not mtDNA, it is interesting that they looked for it and did not find it.

Horizontal gene transfer has been demonstrated to occur in the case of chloroplasts under specific circumstances in closely related plants of the same kind. However, all other incidences in plants are unconfirmed by any empirical evidence. That does not mean, however, that it does not happen.  It is possible that God designed plants with the ability to uptake mtDNA from their environment. Since plants do not move, it is much harder for them to adapt to their environment. Therefore, such a system may have been designed into them from the beginning. As yet, however, evidence demonstrating this occurs is absent.

Even if empirical evidence existed, horizontal gene transfer would not necessarily be a challenge to a creation worldview.  While nuclear DNA would appear to be a stretch, given the necessity of a mechanism to get it out of the nucleus and into another plant, mtDNA is more promising.  Since mtDNA is already outside the nucleus, it would be easier to move it from one plant to another. This would still require a specially designed mechanism, however, which has yet to be demonstrated. Whether horizontal gene transfer in plants exists in nature or not, Christians can be confident that the evidence points to the Creator and his design for his creation.

 

Do you know what’s going to happen when you die? Are you completely sure? If you aren’t, please read this or listen to this. You can know where you will spend eternity. If you have questions, please feel free to contact us, we’d love to talk to you.

 

[1] Frederick Griffith “The significance of pneumococcal types” Epidemiology & Infection 27, no. 2 (1928) Pages 113-159, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2167760/pdf/jhyg00267-0003.pdf

[2] Christopher M. Thomas and Kaare M. Nielsen “Mechanisms of, and Barriers to, Horizontal Gene Transfer Between Bacteria” Nature Reviews Microbiology 3 (2005) Pages 711-721, https://www.researchgate.net/profile/Christopher_Thomas3/publication/7623366_Thomas_CM_Nielsen_KM_Mechanisms_of_and_barriers_to_horizontal_gene_transfer_between_bacteria_Nat_Rev_Micro_3_711-721/links/0046352aafc4a1330d000000.pdf

 

[3] Alessandra Pontiroli et al. “Visual Evidence of Horizontal Gene Transfer between Plants and Bacteria in the Phytosphere of Transplastomic Tobacco,” Applied and Environmental Microbiology 75, no. 10 (2009) Pages 3314-3322, https://aem.asm.org/content/aem/75/10/3314.full.pdf

[4] Sandra Stegemann et al. “Horizontal transfer of chloroplast genomes between plant species,” Proceedings of the National Academy of Sciences 109, no.7 (2012) Pages 2434-2438. https://www.pnas.org/content/pnas/109/7/2434.full.pdf

[5] Zhenzhen Yang et al “Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants.” Nature Plants (2019) https://www.nature.com/articles/s41477-019-0458-0

[6] Xianmin Diao, Michael Freeling, and Damon Lisch, “Horizontal Transfer of a Plant Transposon,” PLOS B (2005) https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040005

[7] Arnold G. Kluge, “Total Evidence or Taxonomic Congruence: Cladistics or Consensus Classification,” Cladistics 14 (1998): 151–158, http://www.geocities.ws/cybermorphy/Kluge1998.pdf.

[8] Andrew V. Z. Brower, “Evolution Is Not a Necessary Assumption of Cladistics,” Cladistics 16 (2000): 143–154, https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1096-0031.2000.tb00351.x.

[9] David L. Hull “Cladistics Theory: Hypotheses That Blur and Grow” in Cladistics ed Thomas Duncan and Tod F. Stuessy. (New York: Columbia Univeristy Press, 1984.)

[10] Verne Grant Plant Speciation Columbia University Press; New York, 1981.

[11] Hyosig Wong and Susanne S. Renner. “Horizontal gene transfer from flowering plants to Gnetum,” Proceedings of the National Academy of Sciences 100, no.19 (2003) Pages 10824-10829. https://www.pnas.org/content/100/19/10824.full

[12] Aaron O. Richardson and Jeffrey D. Palmer “Horizontal gene transfer in plants,” Journal of Experimental Botany 58, no.1 (2007) Pages 1-9, https://academic.oup.com/jxb/article/58/1/1/515544

[13] Daniel L. Nickrent et al. “Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer,” BMC Evolutionary Biology 4 (2004) https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-4-40

[14] Stegemann et al, 2012.