Hachimoji DNA argues against evolution, despite recent claims

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Published: 12 March 2019 (GMT+10)

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

Steven-Benner
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).

Hachimoji-DNA
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).

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.

Readers’ comments

Neil O.
Did 'FAME' operate entirely by 'naturalistic' means i.e.did it begin with "a singularity"? Or was it "done in collaboration with research teams at Firebird Biomolecular Sciences LLC (Alachua, FL), Indiana University School of Medicine (Indianapolis), the University of Texas (Austin), and the University of Chicago."? Sounds like a LOT of intelligence brought to bear... But, it IS a catchy title, "hachimoji" and 'FAME' will no doubt attract a research FORTUNE...
Matthew Cserhati
Exactly, in order to create or expand the DNA code we need a lot of intelligent input. Random chance would not be able to create anything like this. Note that the FAME researchers simply tweaked the existing four bases by rearranging a few atoms here and there. This furthermore goes to show that not only is DNA intelligently designed we as humans merely copy what God had created, similar to how human engineers copied sonar from bats.
Bill P.
This world has already managed to turn upside down those things which The Lord God (Creator of heaven and earth and everything in it) has ordained from the beginning. Marriage between a man and a woman, being fruitful in having children, creating both male and female, etc etc, where now these things are twisted by this world into lies that go against "The Truth" of God's Word.
What's left now for them to turn upside down (against God's Word) but creation itself. So called wise men who are spending time and money trying to prove they have the power and wisdom to create life. I don't believe they will ever be able to do this BUT, I will say that if they could the next thing they will claim to the world is that they are gods.
Soon The Living God is going to say enough is enough and this world will learn the hard way Who Truly is God.
Matthew Cserhati
Indeed it is a worrisome trend that man is trying to play the role of the Creator. This is exactly what we get when we replace the authority of God's Word with our own ideas. But as we can see, the experiment really shows that the only thing we can do is to take already existing material (the original four bases) and tweak them around a little. We ourselves are incapable of creating something new. Similar experiments have been done by other researchers with similar results (namely that they only modified some existing molecular system).
John C.
No, unlike progesterone and testosterone, these 'new bases' are not 'natural'. Do they not even see that they have INTELLIGENTLY DESIGNED these useless additions? Even one of the headlines calls them 'synthetic' (man-made)! If human intelligence could operate to produce an EXTENDED genome, what is so 'supernatural' about an All-knowing Designer producing the ORIGINAL? They have just shot themselves in the proverbial foot.
Matthew Cserhati
Exactly, if it takes intelligence for such a small step, imagine how much Intelligence it would have taken for the original.
Greg F.
Thank you all again for your timely, relevant, and scientifically accurate articles! It is very helpful as we discuss current events with our friends and neighbors. The fruit of CMI is indespensible.
Dan M.
The naturalistic view of life's origins is counter-intuitive at best. It really is impossible because it takes a designer to figure out all the complexity of the system and how it is going to work together and then program it to produce meaningful data to make it work. It's like assuming by natural means a 747 aircraft could be produced without the aerospace engineers, the factory machinery and the skilled technicians to do the work. It's all got to be there or nothing will result. Besides if evolution could do it, what's the big deal with the headlines? They didn't accomplish anything very difficult indeed if unguided, indifferent, careless nature did it first purely by chance. Did they just stumble on this variation of the DNA code or did they design it with intelligence? Their paradigm is irrational and seriously flawed! They can't see the forest for the trees. They can deny the truth all you want but the truth is an unmovable rock! John 14:6, Matthew 16:18.
Lester V.
They added 8 new "letters" to the DNA "alphabet". So what! If we added some new letters to the English alphabet, such as by adopting some letters from the Cyrillic/Russian alphabet, it wouldn't do anything except confuse the current users of English. The new letters have to be understood by the "readers", and that takes a sophisticated decoding system that simply doesn't spring into existence with the introduction of the new letters. Knowing the chemical makeup and arrangement of the DNA letters doesn't explain the origin of the information they carry any more than analyzing the paper and ink used to print an encyclopedia explains the origin of the knowledge it presents. These "experts" strain at a gnat and swallow a camel.
Matthew Cserhati
Correct, even for adding a single letter into the DNA code would involve extra proteins to regulate transcription and make it error-free. With more letters in the alphabet the greater the possibility that an error is made when copying the DNA, which leads to a wider range of possible mutations.
Mark Z.
“and that without a steady supply of building blocks and proteins from a scientist,” What are we talking about here? The mutilation of cattle for material? The fetus? The modern trend of death will pave the way to even more of the same
Matthew Cserhati
What the researchers who created the hachimoji DNA mean by this is that it needs a steady supply of special building blocks synthesized only in the laboratory. If this special hachimoji DNA were to escape the lab into the wild, it wouldn't be able to replicate any longer because of the lack of building blocks it needs.
Cameron J.
This reminds me of a passage in Werner Gitt's book "No Excuse" in the section "An optimised code?" He looks at whether or not we can deduce that the quaternary code currently used in living things is the best of all possible coding systems given the following criteria found in living systems:
1. Material space
2. Repair mechanisms
3. Redundancy
4. Informational content vs. Word length
(I'm going from memory here so I may be forgetting some things)
He only looked at the protein coding regions of DNA for this research, but he concluded that the current arrangement makes the best compromise between these competing factors. An 8 letter genetic base, he found (as has been said here) will compromise the size of the molecule making it unnecessarily bulky and it will increase the risk of errors entering into the system. In any case if 8 letters would produce a better genome surely evolution would have hit upon this system considering the number of other miraculous wonders it has hit during the history of life....right? Also how can Steven Benner say that the ability of DNA to store information is not very useful for evolution, what does he mean by that?
Matthew Cserhati
You are correct, if evolution was true, then we would expect life to have evolved a variety of different codes. The fact that the code is universal implies that it had a single, intelligent Designer. What Brenner means by information storage is that the information in the genes has to be translated to proteins which actually play a role in the functioning of the cell.
Philippus S.
What a surprise it is going to be for those who do not recognize the Majestic Creation by an Ineffable God, who sent His own Son to bring peace between man and Himself, and still loves those who sit in his lap and do not recognize His total Greatness while they all use His Creation to disprove Him. I thank and praise Him for allowing them the chance to repent and open their eyes and see His loving-kindness while they slap Him in the Face. Thank you Drs. Matthew Cserhati and Robert Carter, and if one day you will be in Perth Western Australia and I want to discuss the very thing you call DNA with you, as I think there is some uniqueness in the DNA of the people of Israel, and please note I say Israel not Jews, but describe them as Israel once they accepted the Gospel of Jesus Christ. God did not Create this world out of a laboratory or synthesized materials, He used the real stuff, and I know because I have been playing with molecular engineering creating synthesized colors. 1Cor. 1:21-24: For after that in the wisdom of God the world by wisdom knew not God, it pleased God by the foolishness of preaching to save them that believe. For the Jews require a sign, and the Greeks seek after wisdom: But we preach Christ crucified, unto the Jews a stumbling block, and unto the Greeks foolishness; But unto them which are called, both Jews and Greeks, Christ the power of God, and the wisdom of God. 
North N.
What in the world does this do anyway? It seems as if these new letters have little function compared to what God has already made. Man needs to stop it with the artificial intelligence and all this weird stuff, it is causing many problems to the world, and not only that, but I find it A LOT messed up to mess with God's Creation by tampering with it. This is nothing new, I saw videos on scientists using artificial intelligence to control flies by messing with their brains in order to control them with remote control. I am surprised scientist have not reconsidered their world view who do stuff like that, I find it just sick. Anyways, adding on to what I said earlier, are there any new functions with these new letters, and what purpose will they serve for scientists yet again playing God?
Nathan G.
Since science is based upon experimentation, why doesn't Dr. Benner use his new, intelligently-designed nucleotides to replace all of the A,C,G and T in an m-RNA chain with their brand-new counterparts? Has he also created a uracile U analog, since thymine is replaced by uracil (a demethylated thymine molecule) in RNA molecules?

Build the triplets necessary to code for insulin, which is an extremely tiny protein of only 51 amino acids. Then see if he can manufacture insulin in the lab using the same procedures that we use to make modern medicinal insulin. When he fails, because form begets function in biology, he will be forced to admit that the regulatory and repair mechanisms in the DNA for his four "new" letters cannot be neglected. (Nor can they be explained away by evolution, since Haldane's dilemma still holds true for onward, upward evolution, regardless of which nucleotides are involved.) Considering that about 97% of all DNA has control and regulatory functions and only about 3% is involved in actively coding for proteins, Dr. Benner has a big problem.

A point mutation that changes only one base letter in a triplet can cause a partial loss of protein function, merely because a similar (but not exact) amino acid replaces the correct one. A very different amino acid form can render the desired protein totally inactive. I would like to see a comparison of real insulin to the new, "Benner" insulin.


Even better, why doesn't he try to monkey around with the 20 amino acids and add an atom or two here and there? If Dr. Benner is correct, then neither the nucleotides nor the amino acids are very impressive or important, since dumb matter and energy allegedly created them. So changing the 20 amino acids should not be a big deal. Good luck with that one, doc.
Joshua S.
The only advantage to increasing the size of the genetic alphabet would have to be in decreasing the codon size from three bases to two, thereby decreasing the length of DNA necessary to encode proteins. After all 8^2 = 4^3 possibilities. In doing so, they also reduce the level of bonding between a hypothetical tRNA and codon. The big question for the researchers is whether the mRNA/tRNA interaction would still have the physio-chemical stability required for efficient decoding.
Joshua S.
There is evidence (cited below) which suggests removing the hydrogen bonds from one of the nucleotides in existing codons has a negative impact on translation of the codon, resulting in incomplete peptides and errors. The problem is most significant in eukaryotes which tend to use larger proteins. So, reducing the codon size from three nucleotides to two (which is the only conceivable advantage of a larger DNA alphabet in the context of evolution) would likely be a trade-off in reduced bonding affinity between a hypothetical tRNA/mRNA pair. Thus, the ability to form a more compact DNA language is not necessarily evidence that the one we have is a poor design which no intelligent Creator would make. There are other physical limitations to consider.
-Hoernes, T. P. and others. Translation of Non-Standard Codon Nucleotides Reveals Minimal Requirements for Codon-Anticodon Interactions. Nature Communications 2018, 9 (1). [link deleted per feedback rules]
-Hoernes, T. P. and others. Eukaryotic Translation Elongation Is Modulated by Single Natural Nucleotide Derivatives in the Coding Sequences of MRNAs. Genes 2019, 10 (2), 84. [link deleted per feedback rules]

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