An anonymous user on Reddit recently wrote a post claiming to be a PhD molecular biologist involved in top secret research on recovered bodies of an Exo-Biospheric-Organism (EBO). The description of the EBO's genetics are so detailed and novel that it seemed worth a review. Here is the genetics section of the post with some comments from my research on the plausibility of the story:

Genetics:

First, I'd like to discuss their genetics. Their genetics are like ours, based on DNA. This fact was very puzzling for me when I first learned about it. We imagine that beings from an alternate biosphere would have genetics based on a completely foreign biochemical system and surprisingly, this is not the case. Several conclusions can be drawn from this surprising revelation. The one that immediately comes to mind is that our biosphere and theirs share a common ancestry. They're eukaryotes, which means their cells have nuclei containing genetic material. Which suggests that their biosphere would have been separated from ours sometime after the appearance of this type of organism. The term Exo-Biospheric-Organism is actually a misnomer, but as it's a historical term, it's still used. Their genetics are not only based on the same genetic system, but they’re also even compatible with our own cellular machinery. This means that you can take a human gene and insert it into an EBO cell, and that gene will be translated into protein, and this of course works in reverse with a human gene inserted into an EBO cell. There are important differences in post-translational modifications that will make the final protein non-functional, but I'll discuss these later. Their genome consists of 16 circular chromosomes.

A quick genetics refresher: DNA is the molecule of life. It's made of two strands in the shape of a double helix, where each strain is a chain of bases that are always paired with another on the other strand (base pairs or bp). You can think of the base pairs as one digit of the genetic code, and a sequence of base pairs can define a gene which encodes how to create a protein.

It's certainly possible for EBOs to have the same genetic system as ours, but it would mean we have a common ancestry. If DNA evolved through random mutations, we wouldn't expect organisms that evolved in alien environments to develop the same genetic system.

Organisms on Earth do have a varying number of chromosomes, from as low as 8 in fruit flies to as high as 15,600 in a microorganism called oxytricha trifallax. Circular chromosomes exist but are only seen in microorganisms on Earth (usually prokaryotes and rarely some eukaryotes like yeast, but not any animals).

You're probably familiar with the concept of intergenic region or "junk DNA". These are basically DNA sequences that don't code for proteins. These are evolutionary residues, transposons, inactivated genes and so on. To give you an idea, in humans, intergenic regions represent approximately 99% of our genome. I'm aware that these sequences aren't completely useless, they can be used as histone anchors, as buffers to protect coding DNA from radiation or even as alternative open reading frames, but that's rather peripheral.

What's particularly striking about the EBO genome is the uniformity of these intergenic regions. We see the same sequences repeated everywhere, and the distance in bp between the genes is virtually the same throughout their genome. The result is a minimalist, highly condensed genome. In fact, it's much smaller than ours. Moreover, the quantity of protein-coding genes is even significantly lower than ours, probably due to genetic refinement but also to biological processes that are absent in EBO. The uniformity of these sequences is a major indication of the artificiality of these beings. There is no complex organism on earth that has such elegance in its sequences. There is no evolutionary pressure that can lead to this kind of characteristic other than genetic engineering.

The term "junk DNA" is used to describe segments of the genome that don't code for proteins, as the author suggests. Some uniformity in sequences can evolve naturally, for example there is Huntington's Disease which is a category of "trinucleotide repeat disorders" where groups of 3 nucleotides repeat. However, a fixed number of base pairs between *each* gene would be so ordered that we could not assume it evolved that way through random mutation.

Speaking of genetic engineering, following sequencing of their genomes, we noticed a troubling and universal characteristic in the 5' of the regulatory sequence of each gene which we call the Tri-Palindromic Region. The TPR are 134bp sequences containing, as its name suggests, 3 palindromes. In genetics, a palindrome is a DNA sequence that when read in the same direction, gives the same sequence on both DNA strands. They serve both as a flag and as a binding site for proteins. The three palindromes in the TPR are distinct from one another and have been poetically named "5'P TPR", "M TPR" and "3' TPR". The TPR is composed (in 5' - 3' order) of 5'P TPR, 12bp spacer, Chromosomal address, 12bp spacer, M TPR, 12bp spacer, Gene address, 12pb spacer and 3' TPR. The chromosomal address is composed of 4 bp and is identical in each TPR of the same chromosome, but distinct between each of the 16 chromosomes of the genome. The Gene address is a 64bp sequence that is unique for each gene in the whole genome. It's therefore understandable that the TPR serves as a unique address not only for numerically identifying a gene, but also for identifying its chromosomal location. For those with only a basic knowledge of genetics, this is completely unheard of. No living thing in our biosphere has this kind of precise address in its genome. Once again, the presence of TPR cannot be explained by evolutionary pressure but only by genetic engineering on a genomic scale.

The regulatory sequence of a gene is a sequence of base pairs (codes) that can increase or decrease the expression of the gene. "5'" or 5-prime describes the starting end of the DNA molecule and 3' or 3-prime is the other end, DNA is transcribed in this direction so in this context these numbers are indicating which end of the sequence we're talking about.

Palindromic DNA sequences do exist in organisms on Earth and have unique roles in genetic science. A common palindromic DNA sequence is the recognition site for the restriction enzyme EcoRI, which is "GAATTC". The bases of a DNA sequence always come in pairs, where G pairs with C and A with T, so if one strand of this sequence is "GAATTC" the other is "CTTAAG" (the second strand is a palindrome of the first).

Palindromic sequences are significant in molecular biology because they often serve as recognition sites for restriction enzymes, which are proteins that can cut DNA at specific sequences. The palindromic nature of these sequences allows the restriction enzymes to recognize and bind to them, facilitating the manipulation and analysis of DNA.

Here the author is describing a sequence of base pairs that appear before every gene, and they call it the TPR. The TPR can be further broken down into a pattern of sequences:

The author's claim is that each gene has a unique identifier (the chromosomal address and the gene address) sandwiched by 3 palindromic sequences which are commonly used as binding and cleavage sites in genetic engineering. With 4 base pairs you can represent 2^4 = 16 different chromosomes, and with 64 base pairs you can represent 1.84e19 different genes (humans have 20,000-30,000).

TPR opens the door to several possibilities. One of them suggests that EBO geneticists can insert or remove a gene from a cell in a way that is far more targeted and efficient than our technology allows. No proteins have been identified in the EBO genome that interacts with TPR. Rather, we believe that these proteins are exclusively targeted by external genetic engineering tools, probably used at the zygotic stage of embryonic development. The nature of these tools is unclear, but we definitely don't have anything like them. The probable absence of these proteins from the genome is a further indication of their artificiality. Given the high probability of artificiality of their genome and the apparent ease of modifying it with biomolecular tools, it's not out of the question that there could be polymorphism between individuals depending on their role and function. In other words, an individual could be genetically designed to have characteristics that give it an advantage in performing a given task, like soldier ants and worker ants in an anthill. Note that these previous statements are speculation. To my knowledge only one individual genome has been sequenced, I can't make a definitive statement on genetic variation between individuals.

The TPR coding schema described above could allow for EBO to be programmed while they're embryos to have specialized traits for whatever task they're needed for.

I've talked a lot about intergenic regions, now I'll briefly discuss intragenic sequences. Briefly, because there's not a lot less to say despite its obvious importance. Much like ours, their genes have silencers, enhancers, promoters, 5'UTRs, exons, introns, 3' UTRs etc. There are many genes analogous to ours, which is not surprising given the compatibility of our cellular machinery. What's disturbing is that some genes correspond directly, nucleotide by nucleotide, with known human genes or even some animal genes. For these genes, there doesn't seem to be any artificial refinement but rather a crude copying and pasting. Why they do it is nebulous and still subject to conjecture. There are also many genes which are not found in our biosphere whose role has not been identified. Finding the purpose of these novel genes is one of the aims of the program. I'd like to note before going any further that this heterogeneity of genes of known and unknown origin is an undeniable proof of the artificiality of EBOs.

The author here describes the non-junk part of the EBO gene sequence. In the terrestrial genome, we know there are sequences that perform specific functions like activating or inhibiting other genes (i.e. silencers and promoters) and it seems the EBO shares some of those sequences.

It's not entirely clear what the author means by "artificial refinement" vs "crude copying and pasting", but possibly they're suggesting the EBO genes that resemble human and animal genes do not have the well designed properties of the TRP genes above.

It is a bit perplexing that an intelligence could design an elegant, programmable genetic system but would then inject cruder sequences from us into it. If they've achieved mastery of genetics, what could they need from us that would justify such a hack job?

If this is some kind of creative fiction experiment, it's by far better researched than any science fiction I've read. The full post is worth a read, you can find it on Reddit. I still tend to lean towards this being a LARP, but it's an interesting thought experiment on genetics either way.