(Un)expected Visitors 6: Compendium of Earth and Life Histories
By: Paul Rommel Elvira
Tags: Evolution, History, Organic Database, Human Genome, Earth

Compendium of Earth and Life Histories

“If you take the entire living biosphere, that’s the assemblage of 20 million species or so that constitute all the living creatures on the planet, and you have a genome for every species the total is still about one petabyte, that’s a million gigabytes… And somehow mother nature manages to create this incredible biosphere, to create this incredibly rich environment of animals and plants with this amazingly small amount of data.” - Freeman Dyson

If genes are a reflection of the environment of a cell or organism, then what do we make of an entire genome? An entire record of the environments where the cell or organism moves around and interacts with — that is what it is! Let us review: Pif gene indicates the availability of calcium ions in the marine environment of bivalves. Hemoglobin genes HBA or HBB signify the presence of oxygen in the air that the gene-bearer breathes. The gene for amylase, AMY1, hints at the presence of starchy plants in the vicinity of the organism. These are just three genes but if they are found in one organism, they would reveal a lot about that organism’s probable habitat. Imagine the different genes present in each bacterium, alga or fungus. The genomes of these organisms could provide snapshots of their environment. If one gene represents one photograph, then a single organism would generate an entire mosaic describing the organism’s habitat. Now, if we post on a continuous, circular wall all the mosaics that each earthling has produced, placing those from the same type of habitat or location together with the help of an algorithm, then we can create a rough representation of Earth using all of the genes that ever existed.

Of course, not all of the genes in an organism code for the physical or chemical attributes of the environment where it lives. There are genes that are involved in various other internal processes like reproduction and homeostasis. So, let us take a look at the organism with the smallest genome ever known — the bacterium Carsonella ruddii [1]. C. ruddii’s genome is so small it is only made up of only 160,000 base pairs. Compare that to the human genome which has 3 billion base pairs. This small size of the C. ruddii’s genome has led some scientists to say that it is not enough for survival since according to estimates, 400,000 base pairs is the minimum genome size for survival. But, guess what — this bacteria is alive. The interesting part is that C. ruddii has managed to reduce its genome to the bare essentials by designing around 90% of its genes to overlap with each other. Talk about efficiency! The downside, however, is that C. ruddii cannot survive on its own. Just like viruses, C. ruddii needs a host to provide it energy for its survival. Nonetheless, half of its genome is allocated for basic cellular processes such as handling and building amino acids into proteins — a function that is lacking among viruses. So what happened to C. ruddii? According to research, bacteria like C. ruddii can afford to shuttle its own genetic material over to its host given that it can survive just by feeding off of its host. Thus, these bacteria could have considered genes required for autonomous living as excess genetic baggage and thus expendable. In the case of C. ruddii, million years of evolution and gene transfer has led to an organism that gave away many of its genes and is therefore left with a very small genome that is unable to support survival outside a host.

The abovementioned findings mean that we can have 80,000 base pairs from the most basic bacteria and still be able to build genes for detecting and exploiting its environment. For bacteria, exploring the environment entails having sensors instead of eyes, ears, nose, hands and feet that we and other animals have. So how do bacteria “sense” their environment? Bacteria use two-component systems to detect light and chemical signals around them. The system is very basic or crude [2]. First, a bacterium employs a sensor kinase to detect signals from the outside world. Once a signal is detected, a process called phosphorylation is initiated, activating a response regulator that causes a gene to turn on or off, and viola! — the bacterium can now see its world.

Now, imagine more complex organisms: algae, protists, fungi, plants, worms, insects and higher animals. Their sensors have certainly become highly sophisticated through billions of years of evolution. If bacterial organic cameras started from being able to detect dark and bright, along the way the cameras of other species evolved into black and white analogue units until humans came along with high definition, Technicolor, digital cameras. That is just for the eyes. Animal ears evolved from very primitive airborne sound-detecting organs of our terrestrial vertebrate ancestors that lived 100 mya during the Triassic period [3]. So did the highly discriminating noses of dogs, boasting 300 million olfactory receptors that could be traced back to our common ancestors with fish-like chordates called lancelets that existed approximately 700 mya [4]. Our skin’s sensory cells and nervous system that we use to determine the presence, texture and temperature of things around us have its origin in the primitive nervous systems of Cnidarians such as corals, jellyfish, sea anemones and other aquatic animals [5]. In other words, the current set of genes that enable the functioning of our different sensory organs have a rich evolutionary history spanning millions to billions of years.

The genes that make our eyes, ears, nose and skin work have been changing through the years, all the while being improved, overhauled and polished by the different organisms that had or still have them. Through sequence analysis, we can determine which genes are the oldest and which ones are newer. We can also pinpoint the last common ancestor that had the earliest form of these genes. A phylogenetic tree or an evolutionary tree can show the evolutionary relationships among different organisms based on these genes.

The evolutionary history of life is also the history of Earth itself because of the association between genes and the environments as just discussed. Therefore, if an advanced extraterrestrial observer gets ahold of an evolutionary tree, that being could likely generate a picture or an idea about how Earth looked like in the past or how it has been changing as time passes by. So, the alien scientist only needs the information about our genetic material and everything about genetic materials to deduce what Earth looked like or looks like, from afar (millions or billions of lightyears away).

The most fascinating part is, even without a phylogenetic tree on hand, an alien scientist can still discover facts about Earth based on one highly-evolved, modern extant species — say for example, humans. The human genome can tell a lot not just about our species and our relationship with other organisms on Earth. Our genome can also serve as a standalone historical record of our planet. How did this happen? The clues are in the different genetic or evolutionary processes already described on the previous pages of this book.

One of these clues is horizontal gene transfer. As has been mentioned, bacteria and viruses regularly facilitate HGT between them and with their respective hosts. We may recall that HGT has been implicated in the production of orphan genes. HGT has also been suggested as one of the probable mechanisms behind the acceleration of evolution rates among early prokaryotes (discussed in Part Three, Chapter 1).

Now, it appears that HGT is a significant contributor not only to the evolution of microorganisms but also of many animal species. In humans alone, 128 genes from foreign species’ genes have been identified. Many of these introduced genes were involved in metabolism and originated from bacteria and protists according to University of Cambridge’s Alastair Crisp. Crisp’s study added to the 17 already-reported genes integrated to the human genome by way of HGT. Aside from genes involved in metabolism, Crisp also found genes playing roles in immune responses, antimicrobial defense, antioxidant functions and protein modification. In addition to bacteria and protists, other groups like viruses and fungi have also been reported to contribute to the human genome through HGT that occurred along a time-span starting from the appearance of the common ancestor of Chordata up to the emergence of the common ancestor of primates [6].

Humans have not been spared from HGT. For instance, the human immune system’s origin has been associated with a horizontal gene transfer insertion event around 400 mya. However, HGT as a hallmark of the human genome has been refuted by some scientists. Steven Salzberg of Johns Hopkins University has claimed that the extraordinary conclusions made by Crisp and colleagues provided no extraordinary supporting evidence. Salzberg re-analyzed the various genes implicated in HGT into the human genome and arrived at a conclusion that not a single gene has been transferred in this manner. According to Salzberg, more mundane mechanisms are more likely to be behind the phenomenon observed by Crisp, noting that inheritance of genes by vertical descent has been established as the explanation for the presence of the vast majority of genes in the human genome [7]. It remains to be seen whether Crisp’s assertions can be confirmed by more recent research and with the availability of newer tools and additional DNA sequence information. Nonetheless, HGT in metazoans is a probability given the prevalence of this process among viruses and bacteria. Are metazoans a special group of organisms such that they are exempted from HGT? It is quite difficult to think of any reason to support this.

We already know that virus genes are present in the human genome. As mentioned in the previous chapters, viral DNA makes up 8% of our genome. Ancient viruses were able to introduce their DNA into the genome of our ancestors around 100 mya and one of the evidences of these events is the presence of a protein called HEMO in the human fetus and placenta. A research group from Gustave Roussy Institute in France led by Thierry Heidmann has reported that the mysterious protein is expressed in pregnant women for no apparent reason [8]. What makes HEMO unusual is that it is produced by the fetus and in the placenta, not by the mother. Even more unusual is the source of the gene that encodes for this protein — a virus that infected the mammalian ancestors of humans. Heidmann suggested that HEMO proteins are some kind of signal for the mother from the fetus which tells the mother’s immune system not to attack the fetus.

Other scientists offer more disturbing explanations. One such claim is that viral proteins are expressed in fetuses to help keep stem cells from losing their pluripotency or the cells’ ability to turn into any tissue in the human body. As stem cells divide, they lose their pluripotency since they have to commit to becoming one of the potential cell types. Once they have managed to become a particular cell type, these cells usually turn off any viral genes they carry. By preventing stem cells from losing their pluripotency, viruses were able to coax the embryos to make more copies of the viruses and distribute these foreign invaders into the various parts of the human body. Viruses, however, could target eggs and sperm cells in particular because doing so increases the chances that the viruses are passed down as well to the next generation.

One of the viruses that has been regularly inherited in a small percentage of the human population is the human herpesvirus 6 or HHV-6. HHV-6 is the only human DNA herpesvirus that is capable of inserting its own genes into the human genome, allowing the virus to be routinely inherited by its host. According to a study by Alex Greninger and Louis Flamand from the Laval University in Quebec, the integration of the HHV-6’s DNA into the human genome could have been accidental given the presence of repetitive DNA sequences in the virus genome just like what is observed in human chromosomes [9]. The research group has found that several of the HHV-6 genes were being actively expressed in a few human individuals, albeit with a low and sporadic expression. Nonetheless, the expression of selected genes was identified to be occurring in the brain, esophagus, adrenal gland and testes of some human hosts. The researchers also found that the HHV-6 genes inherited in the human genome help the body mount a stronger immune response against new invading viral proteins.

Another clue supporting the observation that the human genome can be used as a reference for genomes in other organisms is the existence of genes in some species of fish with human counterparts. This is only natural because humans and fish share a common ancestor that lived approximately 450 mya. The fact that humans and fish possess many similar genes is really not surprising since this is exactly how evolution works. However, what is remarkable is that most of these genes did not change dramatically since and are still performing the same roles in vertebrate anatomy and physiological development. Equally interesting is that there are still new genes in the human genomes being discovered through the analysis of fish genomes.

Take for example the case of pufferfish Fugu rubripes. An international team of researchers have reported the existence of 961 novel human genes matching those in the Fugu genome [10]. The human genome is approximately eight times larger than the Fugu genome although this discrepancy is attributed to the abundance of repetitive DNA in the former. However, 75% of the 31,000 genes in Fugu have been found to have equivalents in humans. It appears that the pufferfish has contributed a lot of its genome to ours! This also shows how much anatomical and physiological characteristics we humans share with other vertebrates. So, Neil Shubin was indeed spot-on when he said that we have an inner fish in our body. Shubin has shown in his book Your Inner Fish that our hands and heads somehow take after the fins and heads of ancient fish. It is really hard to deny the evidences when it comes to our evolutionary origin.

If our hands and head organization came from fish, then the chamber of our hearts can be traced back to turtles, lizards and other reptiles. That is according to researchers from the Gladstone Institute of Cardiovascular Disease in San Francisco, California. Benoit Bruneau’s team has revealed the common genetic factor involved in the development of reptilian hearts. Their study has shown that the gene Tbx5 holds the key to how evolution led to four-chambered hearts and warm-bloodedness. Bruneau has claimed that reptiles served as the link between the three-chambered hearts of amphibians and the four-chambered hearts of mammals, including ours. By studying mutations in the Tbx5 gene, his team has found the protein it codes for is a transcription factor that, when disrupted, causes defects in the development of the ventricular septum or the wall of muscle between sections of a ventricle [11]. Knowing this, we can therefore say that we are partly reptilian deep within our hearts.

These are just some of the examples how humans share genes and morphological characteristics with other organisms on Earth, implying the common environments that all earthlings experienced during the billions of years of evolution of life. We can find more of such genes, organelles and organs that are present in humans but were actually from ancestral life forms, often with different original functions.

Another example are our cells’ mitochondria which have been hypothesized to have descended from non-sulfur bacteria, incorporated into the prokaryotic or eukaryotic cytoplasm after surviving endocytosis. However, recent genomic studies are challenging these previously widely-acknowledged assumptions [12]. Nevertheless, no matter how tortuous the path that mitochondria took to reach us, the fact remains that this organelle is nothing but an important addition to human cells. We humans also have with us remnants of reptilian brain in the form of the basal ganglia. This primal brain has been known to control the self-preservation behavior of humans such as those related to eating, fighting, fleeing and reproducing [13]. In addition to the reptilian brain, we also have the paleomammalian (limbic system) brain and the neomammalian brain to complete the Triune Brain model developed by Paul D. Maclean [14]. For those not familiar with this information might find it highly interesting that our brain has a very intriguing history, too. The human lungs can likewise be traced back to our primitive ancestors. It has been reported that lungs did not really evolve from fish swim bladders, as Charles Darwin had suggested. Darwin recognized the homology between the two organs and suggested in his On the Origin of Species that the lungs of respiratory vertebrates could have been derived from a more primitive bladder. However, the lungs of humans and other land vertebrates are now being considered to have evolved from the primitive lung of a common ancestor — prehistoric Polypterus — we share with swim bladder-bearing fish [15].

If we continue with the enumeration of the genes, organelles and organs that we share with or co-opted from our ancestors, we would be confronted with the undeniable fact that humans have virtually no original body part to speak of. This is to be expected because this is exactly how evolution works. It would not be surprising to find almost all of the genes in our genome to have duplicates in several other species. We can make new ones in the form of de novo genes and other mechanisms but the fate of these genes is a bit uncertain and their number is likely insignificant.

In other words, we humans are nothing but a living record of duplicated — albeit improved — genes of our ancestors. This is good news for the alien scientists because if they are able to obtain a single human specimen, they would be able to reverse engineer our body, study its modular parts, tease out all the relevant genes and generate a picture about the evolution of life and extrapolate this with Earth’s geologic history.

Even if the human space explorers decide not to divulge the location of our home planet upon realizing that the alien civilization is not a friendly one (or even if the aliens found the whole human exploration crew deceased), these extraterrestrial sleuths would still be able to find Earth based on the evidences the human body would offer.

The first clue that could point to where the human explorers came from would be through the analysis of our circadian rhythm genes such as BMAL1, NR1D1, BHLHE40, et cetera. These are just a few of the major canonical clock genes that have been found to have circadian rhythmicity in their expression in peripheral human tissues and brains [16]. These can hypothetically lead alien scientists to the occurrence of day and night in the home planet of the human explorers. More importantly, they would likely find out about the existence of the 24-hour cycle of the human circadian rhythm.

They now have information about the amount of time that Earth takes to rotate with respect to the Sun. Next the alien scientists would probably have an idea about seasons and that these correspond to a planet’s axial tilt or — possibly — revolution around its star (for planets with pronounced elliptical orbits). If they look close enough, then they would find seasonal genes in the human genome. Researchers from the Queensland Brain Institute have reported that expression of some genes involved in immune function have a 12-month seasonal cycle. The genes the research team found to have seasonality are those regulating blood cell count levels that involve red blood cells, neutrophils, monocytes and platelets [17]. This information could potentially provide alien scientists a rough estimate of the tilt of Earth’s axis with respect to the Sun. In other planets with extreme orbits, seasonal genes could help aliens estimate the duration of a planet’s orbit around its star.

So, they now have two important clues about Earth: that it rotates on its own axis and orbits a star (as expected) and that these take 24 hours and 12 months to complete, respectively. The alien scientists then would only need to search their databases for planets that rotate for 24 hours on their own axis and revolve around their stars for 12 months.

If the above information are not enough, they could narrow down their search further based on the probable size and mass of Earth. And how do they determine this? By looking at the density of bones of the human skeleton, researchers have found that we can stand gravity that is three to four times that of Earth [18]. This means that a bigger and denser planet could spell trouble for our bones, although it is also difficult to estimate the density of planets from afar. Nevertheless, alien scientists would probably be able to do the calculations and come up with a narrow range that covers Earth’s radius which is 3,963 miles. Using these three educated guesses, the alien scientists would be able to obtain a few candidate planets for further cross-referencing or validation.

Having seeded Earth with the starting materials of life and/or accelerants of evolution, the alien scientists would likely have basic data about our planet and also know where to find us. If an entirely different advanced civilization happened to make contact with the human explorers or came upon their bodies, then their search for Earth would likely be less straightforward.

References:

1. NASA (2017). Got calcium? NASA Goddard Space Flight Center Educator’s Corner. https://imagine.gsfc.nasa.gov/educators/calcium/got_calcium_litho.html

2. Nakabachi, A., Yamashita, A., Toh, H., Ishikawa, H., Dunbar, H.E., Moran, N.A., Hattori, M. (2006). The 160-Kilobase genome of the bacterial endosymbiont Carsonella. Science 314(5797): 267–267

3. Sebastian, R. Schmidl, F., Ekness, K., Sofjan, K. et al. (2019). Rewiring bacterial two-component systems by modular DNA-binding domain swapping. Nature Chemical Biology DOI: 10.1038/s41589–019–0286–6

4. Christensen, C. B., Lauridsen, H., Christensen-Dalsgaard, J. Pedersen, M. and P.T. Madsen (2015). Better than fish on land? Hearing across metamorphosis in salamanders. Proceedings of the Royal Society B: Biological Sciences 282(1802): 20141943

5. Niimura, Y. (2012). Olfactory receptor multigene family in vertebrates: from the viewpoint of evolutionary genomics. Current Genomics 13(2): 103–114.

6. Watanabe, H., Fujisawa, T. and T.W. Holstein (2009). Cnidarians and the evolutionary origin of the nervous system. Development, Growth & Differentiation 51: 167–183

7. Crisp, A., Boschetti, C., Perry, M., Tunnacliffe, A., and G. Micklem (2015). Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biology 16(1): 50

8. Salzberg, S. L. (2017). Horizontal gene transfer is not a hallmark of the human genome. Genome Biology 18(1), 85

9. Heidmann, O., Béguin, A., Paternina, J., Berthier, R., Deloger, M., Bawa, O. and T. Heidmann (2017). HEMO, an ancestral endogenous retroviral envelope protein shed in the blood of pregnant women and expressed in pluripotent stem cells and tumors. Proc Natl Acad Sci U S A. 114(32): E6642-E6651

10. Peddu, V., Dubuc, I., Gravel, A., Xie, H., Huang, M.-L., Tenenbaum, D., Jerome, K.R. et al. (2019). Inherited chromosomally integrated human herpesvirus 6 demonstrates tissue-specific RNA expression in vivo that correlates with an increased antibody immune response. Journal of Virology 94(1): e01418–19

11. Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.M. et al. (2002). Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297(5585): 1301–1310

12. Koshiba-Takeuchi, K., Mori, A. D., Kaynak, B. L., Cebra-Thomas, J., Sukonnik, T., Georges, R. O., Latham, S., Beck, L., Henkelman, R. M., Black, B. L., Olson, E. N., Wade, J., Takeuchi, J. K., Nemer, M., Gilbert, S. F. and B.G. Bruneau (2009). Reptilian heart development and the molecular basis of cardiac chamber evolution. Nature 461(7260): 95–98

13. Roger, A.J., Muñoz-Gómez, S.A., Kamikawa, R. (2017). The origin and diversification of mitochondria. Current Biology 27(21): R1177-R1192

14. Naumann, R. K., Ondracek, J. M., Reiter, S., Shein-Idelson, M., Tosches, M. A., Yamawaki, T. M., and G. Laurent (2015). The reptilian brain. Current Biology 25(8): R317–R321

15. Reiner, A. (1990). The triune brain in evolution. Role in paleocerebral functions. Paul D. MacLean. Plenum, New York, 1990. xxiv, 672 pp., illus. $75. Science 250(4978): 303–305

16. Tatsumi, N., Kobayashi, R., Yano, T., Noda, M., Fujimura, K., Okada, N. and M. Okabe. (2016). Molecular developmental mechanism in polypterid fish provides insight into the origin of vertebrate lungs. Scientific Reports 6: 30580

17. Li, J.Z., Bunney, B.G., Meng, F., Hagenauer, M.H., Walsh, D.M. et al. (2013). Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. Proceedings of the National Academy of Sciences 110 (24) 9950–9955

18. Goldinger, A., Shakhbazov, K., Henders, A. K., McRae, A. F., Montgomery, G. W., and J.E. Powell (2015). Seasonal effects on gene expression. PloS One 10(5): e0126995