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Hachimoji DNA argues against evolution, despite recent claims

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The headlines were bold:

“Four new DNA letters double life’s alphabet” (Nature)1

“Scientists successfully double the DNA alphabet” (The Smithsonian)2

“DNA gets a new – and bigger – genetic alphabet” (The New York Times)3

“Synthetic doubling of life’s DNA alphabet suggests there’s nothing ‘magical’ about life on Earth” (The Genetic Literacy Project)4

Dr Steven Benner

A research group led by Dr Steven Benner at the Foundation for Applied Molecular Evolution (FAME)5 in Alachua, Florida has created four extra DNA letters. They recently published a paper on their work in the prestigious journal Science6 and, as we have already seen, it caused a flurry of ‘tweets’ and re-postings. By tweaking the structure of the already-existing four bases, adenine (A), cytosine (C), guanine (G) and thymine (T), they have expanded the DNA alphabet from four to eight letters. The two extra pairs of letters include ‘S’ and ‘B’, and ‘P’ and ‘Z’. The researchers have named the resulting eight-letter alphabet “hachimoji”, which is Japanese for “eight” and “letter”.

But Benner’s team merely tweaked the molecular structure of the four already-existing bases. P and B are purine analogs (similar to A and G), whereas S and Z are pyrimidine analogs (similar to C and T). The two new pairs of bases also pair with three hydrogen bonds, similar to the way C and G bond to each other when placed opposite each other on complementary strands of the DNA double helix (Figure 1).

Figure 1: Molecular structure of the eight so-called ‘hachimoji’ DNA bases6

These four new nucleotides are interesting, but they are not truly innovative. How about a pair of bases with four hydrogen bonds? Or a base with a steroid structure, like that of progesterone or testosterone? No, they are not pursuing radical new structures like these, because humans are better at copying and modifying existing things than they are at inventing brand new things from scratch. In the end, all of their work testifies to how much thought must go into the designing of any new ‘thing’. Despite the headlines, this argues against naturalistic evolution.

And some of the headlines are also a bit misleading. The incautious reader might be tempted to think that four new bases have been found in living organisms. This is not true. A slightly more cautious reader might conclude that scientists have built a working prototype where living cells actively create proteins using the modified DNA or can replicate the modified DNA as they grow and divide. This is also not true. However, great strides are being made toward these goals and we may, eventually, reach it.

Ideas like this have been floating around in science labs for a couple of decades already. There is really nothing to it other than the fact that scientists can apply a lot of intelligence to interesting challenges and problems. All they did was figure out that they could substitute chemicals other than A, T, C, or G into the DNA sequence. That is interesting, but they did not quantify how easy it would be to get the four alternative bases in nature, how they would (or even if they could) be integrated into cellular biochemistry, or whether or not there would be a net penalty to using those new letters over the four that are in use among all life on earth today.

The fact that some scientists in some lab somewhere synthesized a DNA alphabet with eight letters is fascinating, but what real bearing does it have on evolution? An eight-letter alphabet can code for genes, but it does not actually demonstrate evolution. The only thing we know is that we would have a more complicated DNA alphabet. But the big question remains unanswered: how this system arose in the first place. Even Benner himself cautioned in a press release that the eight-letter DNA alphabet is not “alien life”, and that without a steady supply of building blocks and proteins from a scientist, the new type of DNA would not be able to exist.7

For the sake of argument, let us just assume that an eight-letter DNA alphabet arose via evolution. In the current system, there are 64 (4x4x4) 3-letter codons. Assuming we still have 3-letter codons and a few stop codons, this would mean that we would need approximately 512 (8x8x8) tRNA molecules, each with their own 3-letter anti-codon and carrying one of the 20 amino acids used in all living cells. To carry that many tRNA genes, we would need to expand the genomes of living organisms, and most species have multiple copies of each tRNA gene. The human genome only has about 20,800 genes, including nearly 500 tRNA genes (2.4% of all genes). There are only 61 different tRNA genes, meaning each gene has an average of more than 8 copies. Our 8-letter DNA system would require the addition of about 4,000 tRNA genes (which would then make up 18% of all genes).

But it is not just the size of the genome that would cause problems. DNA repair also suddenly becomes a major obstacle. Currently, there are multiple DNA repair systems in living cells, with each type of repair system designed to work on a different type of problem (e.g. double-strand-breaks, single-strand breaks, cytosine deamination, etc.). There is already an existing problem with our DNA repair systems: they are imperfect, and this leads to mutation accumulation over time. In an 8-base system, the DNA repair systems would need to be much more complex, and thus the possibility of a mismatch or other kind of mutation would be much higher. This would lead to accelerated mutational meltdown. And the more complex DNA-repair mechanisms would require many more proteins to deal with DNA repairs after mutation. This would require an even further expansion of the genome. Thus, practically speaking, a DNA alphabet with 8–12 letters would be extremely detrimental to the organism.

Instead, the already-existing four letters of the DNA alphabet, A, C, G and T, were optimally designed by God to code for 20 amino acids, which already code for an exponentially large number of possible proteins to begin with. With 20 amino acids, we can theoretically manufacture 20100 possible proteins 100 amino acids long (and those are pretty short for a biological protein). Scientists estimate that there are only 1080 atoms in the universe. This means that there are more possible proteins than the number of atoms in the universe. So, we already have enough variety with a smaller alphabet.

Despite these difficulties, evolutionists speculate that a larger DNA alphabet could have arisen on other planets, making more diverse life forms possible. But ‘larger’ only makes life more complicated and thus the evolution of those life forms becomes that much more improbable.

They also downplay the origin of the information stored on DNA:

“The ability to store information is not very interesting for evolution,” says Benner. “You have to be able to transfer that information into a molecule that does something.”1

But here is the main author of the paper ignoring the giant chicken-and-egg problem staring him in the face. Not only do you need nucleotides to come about through naturalistic means, and not only do you need them to spontaneously polymerize, but the DNA molecule is useless without a predetermined set of instructions coded upon it. As Dr John Sanford says in Evolution’s Achilles’ Heels:

“Life isn’t based upon biochemicals. You can have all the biochemicals you want. It’s not going to give you life. You can have all the amino acids you want. You can have all the proteins you want. You can add RNA to the ‘soup’. You can add DNA to the ‘soup’. You can even add membranes to the ‘soup’. But, for one, they will never assemble into a coherent, correctly assembled cell. And even if they could, you still wouldn’t be anywhere near creating life, because you have not introduced into those molecules … information.”

The drive toward creating artificial life is fascinating, but it raises additional questions. Is it ethical? If so, can we do it? And what will it take?

But, as we study it more, it only becomes even more clear that 1) life is complicated, 2) life is improbable, and 3) a lot of intelligence is required to create something (life) that is so contrary to nature (random chemicals).

Published: 12 March 2019

References and notes

  1. Warren, M., Four new DNA letters double life’s alphabet, Nature 566(436), 2019 | doi: 10.1038/d41586-019-00650-8. Return to text.
  2. Thulin, L., Scientists successfully double the DNA alphabet smithsonianmag.com/smart-news/scientists-just-doubled-number-letters-dna-alphabet-180971552/, 25 February 2019. Return to text.
  3. Zimmer, C., DNA gets a new – and bigger – genetic alphabet, nytimes.com/2019/02/21/science/dna-hachimoji-genetic-alphabet.html, 21 February 2019. Return to text.
  4. Anonymous, Synthetic doubling of life’s DNA alphabet suggests there’s nothing ‘magical’ about life on Earth, geneticliteracyproject.org/2019/02/26/synthetic-doubling-of-lifes-dna-alphabet-suggests-theres-nothing-magical-about-life-on-earth/, undated. Return to text.
  5. The Foundation for Applied Molecular Evolution is also associated with the for-profit Firebird Biomolecular Sciences. While they have been in operation for a number of years, little information about them is available on their respective websites. There is nothing wrong, per se, with a for-profit company publishing scientific papers, but let the reader understand that they do have a commercial interest in the publication and promotion of their results. All of this attention was ‘good for business’. Return to text.
  6. Hoshika, S. et al., Hachimoji DNA and RNA: a genetic system with eight building blocks, Science 363(6429):884–887, 2019 | doi:10.1126/science.aat0971. Return to text.
  7. Foundation for Applied Molecular Evolution. (2019, February, 21). A Synthetic DNA Built from Eight Building Blocks [Press Release]. Retrieved from ffame.org/downloads/Hachimoji_PressRelease_FfAME_20190221.pdf. Return to text.