Theory of Intelligent Design, the best explanation of Origins

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Theory of Intelligent Design, the best explanation of Origins » The catalog of life » squid recode their genetic make-up on-the-fly to adjust to their surroundings

squid recode their genetic make-up on-the-fly to adjust to their surroundings

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Organisms Changing the Products of Their Genes!

the central dogma of molecular biology:

DNA —-> RNA —–> Protein
In other words, DNA carries a set of “recipes” that tell your cells how to make the proteins they need to make. That recipe is copied by another molecule, RNA, and the copy is transported out of the nucleus of the cell to a ribosome, where the copy is then translated into a protein.As scientists learned more about the marvelous design of DNA, they found that the idea of one gene producing one protein was far too simplistic. In plants and animals (and many microscopic organisms as well), the genes are interrupted by stretches of DNA called introns. At first, geneticists lumped introns into the category of junk DNA, an evolution-inspired idea that couldn’t be more incorrect.  the introns are an integral part of a multi-layered data storage system that allows a single gene to code for up to tens of thousands of different proteins through a process called alternative splicing.

One Gene = One Protein? Not Even Close!

a gene is actually a recipe that the cell uses to make a particular protein. Since most of a cell’s DNA is in the nucleus, the “recipe” stored in that gene must leave the cell’s nucleus in order to be turned into a protein. To do that, the “recipe” is copied by a molecule called messenger RNA (mRNA). The mRNA then takes the copied “recipe” out of the nucleus to the ribosome, which is where proteins are made.

In eukaryotic cells (the kinds of cells found in plants and animals), however, something very interesting happens before the mRNA leaves the nucleus. Some parts of the mRNA are cut away, and the remaining parts are then stitched back together. The parts of the mRNA that are cut away never leave the nucleus, so they are called introns (they stay IN the nucleus). The remaining parts that are stitched together are called exons (they EXit the nucleus). For a while, geneticists didn’t know the purpose of introns, so in typical evolutionary fashion, many decided that they had no purpose, and introns were lumped into the category of “junk DNA.” Of course, as we have learned more about genetics, we have learned that the evolution-inspired idea of “junk DNA” is, itself, junk, although some evolutionists still cling to it.

Nowadays, of course, we know the reason that introns exist. It is part of the design of the Creator, allowing DNA to store information in an incredibly efficient way. Each exon represents a “module” of useful information. If the cell stitches the exons together in one way, it makes one protein. If it stitches the exons together in another way, it makes a different protein. As a result, a single gene can actually produce many different proteins. The introns not only serve as a means by which the cell can identify the exons, they also regulate the amount of the various proteins that are being made.

The gene, which is called cSlo, is involved in hearing. The cochlea (the organ that does the actual hearing) in the chicken’s inner ear is lined with hair cells, each of which responds most strongly to specific frequency of sound. One end of the cochlea contains hair cells that respond best to low-frequency sounds, and the other end holds the hair cells that respond best to high-frequency sounds. In between, the hair cells vary smoothly so as to respond best to the sound frequencies in between. Part of why each hair cell has its own “best frequency” to detect is a result of how electrically-charged particles are transported into and out of the cell. The proteins produced by the cSlo gene aid in that process.

Well, recent studies show that the cSlo gene uses alternative splicing to create 576 different proteins, each with a slightly different electrical response. As a result, when researchers studied the hair cells on one end of the cochlea, they found one of the proteins. When they looked at the hair cells on the other end, they found another protein. In between, they found 574 other proteins, each of which was ideal for producing a strong response to a specific sound frequency!1

In other words, the exons and introns of the cSlo gene have been set up so that each hair cell can use alternative splicing to produce a protein that is perfect for the frequencies to which it is supposed to respond most strongly! The design is so detailed that each hair cell can choose from among 576 different proteins in order to get a good response. All of this is the result of a single gene!

DNA is already amazing, but to think that a single gene can produce 38,000+ different proteins is truly awe-inspiring. However, the biology professor pointed out something that I hadn’t even thought about: the implications that these results have on the process of comparing the genomes of two different species.

For example, I have written several times about the difficulty involved in comparing the human genome to the chimp genome. Depending on the study, geneticists have found that the chimp genome is 72-95% similar to the human genome

we only know the human genome to an accuracy of 6% and the chimpanzee genome to an accuracy of 9.5%, it is not clear how anyone can really say how similar the two genomes are. However, given what we now know about alternative splicing, it’s not clear that it matters how similar the two genomes are to one another

Let’s just say for the sake of argument that the human genome is 95% similar to the chimpanzee genome. I seriously doubt it is, but I think that’s the highest level of similarity possible, given what we know about the two genomes right now. If many genes can produce hundreds or thousands of different proteins, then in the end, even 95% similar genomes can produce radically different sets of proteins, which would result in radically different species. Thus, given the amazing design that we see in DNA, it’s not clear that comparing genomes is the best way to judge the similarities of two different organisms.

Essentially, the introns divide a gene into several “modules of information.” The cell can chop up the RNA copy and splice those modules together in different ways. Each different way the modules are spliced produces a different protein. Once alternative splicing was figured out, the idea of one gene producing one protein was discarded. One gene can, in fact, produce lots and lots of different proteins. However, even in alternative splicing, the information contained in the DNA is preserved. Each individual module of information codes for a specific part of a protein, and if you look at that specific part of the protein, it is made exactly the way that module of information says it should be made.

Some organisms can edit their RNA to make a final protein that is actually different from what the modules of information in the gene actually specify!

Its DNA specifies a series of proteins that work best in warmer waters. Using those proteins, the octopus wouldn’t survive well in cold waters. To fix this problem, the octopus copies the gene using RNA, does alternative splicing where necessary, and then edits the result to make the proteins work better in cold water! This process is called RNA editing. How does the octopus “know” to do RNA editing? As far as I can tell, we have no idea. We only know that it does.

But how common is this? Well, a study I read recently gives us some clues about that. First, the study says that all eumetazoans (a group that contains most animals) express the chemicals necessary to do RNA editing. Thus, it is at least possible that the vast majority of animals have the ability to change the products of their genes. It then gives references to several studies that have seen small amounts of RNA editing in certain mammals, like mice. However, it then references another study that shows Drosophila (commonly called “fruit flies”) edit up to 3% of all the RNA they produce!

The focus of the article, however, was an analysis of Doryteuthis pealeii, a species of squid. They concentrated on the proteins related to the squid’s nervous system, and they found that, remarkably, 60% of them are made with RNA editing.1 In other words, the majority of nervous system proteins that this squid makes are not faithful to the original information stored in the DNA. Somehow, the squid isn’t “satisfied” with what the DNA tells it to do, so it gets out the “red pen,” makes a few edits, and produces a different protein! Why does it change so many of its proteins? The authors have two thoughts:

An equally intriguing question is why squid edit to this extent? The process clearly creates tremendous protein diversity, and this may in part explain the behavioral sophistication of these complex invertebrates…The large number of sites in squid suggests that editing is well positioned to respond to environmental variation. Most model organisms studied so far are mammals which are homeotherms. Future studies of more diverse species are needed to reveal the extent to which cold-blooded organisms might utilize extensive editing to respond to temperature changes and other environmental variables.

Of course, while this is really incredible, it isn’t surprising to a creationist. After all, we know that the Creator built His organisms with many means by which they can adapt, so it make sense that He would build an editing system that would allow organisms to vary the products of their genes so as to quickly respond to environmental changes.

Of course, how the octopuses do RNA editing and how they know how much of it to do is pretty much unknown. However, it is clear that RNA editing is yet another way the Creator has designed His creation to adapt to change. I expect as scientists study this more closely, they will find that it is fairly common throughout creation.

The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

Squid Recodes Its Own RNA

How the Genome "Decides" Where to Splice

The Spliceosome: A Dynamic Ribonucleoprotein Machine

Squid recode their genetic make-up on-the-fly to adjust to their surroundings

Make Like a Squid and Transform

The principle of adaptation — the gradual modification of a species' structures and features — is one of the pillars of evolution. While there exists ample evidence to support the slow, ongoing process that alters the genetic makeup of a species, scientists could only suspect that there were also organisms capable of transforming themselves ad hoc to adjust to changing conditions.

Now a new study published in eLife by Dr. Eli Eisenberg of Tel Aviv University's Department of Physics and Sagol School of Neuroscience, in collaboration with Dr. Joshua J. Rosenthal of the University of Puerto Rico, showcases the first example of an animal editing its own genetic makeup on-the-fly to modify most of its proteins, enabling adjustments to its immediate surroundings. The research, conducted in part by TAU graduate student Shahar Alon, explored RNA editing in the Doryteuthis pealieii squid.

"We have demonstrated that RNA editing is a major player in genetic information processing rather than an exception to the rule," said Dr. Eisenberg. "By showing that the squid's RNA-editing dramatically reshaped its entire proteome — the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time — we proved that an organism’s self-editing of mRNA is a critical evolutionary and adaptive force." This demonstration, he said, may have implications for human diseases as well.

Using the genetic red pencil

RNA is a copy of the genetic code that is translated into protein. But the RNA "transcript" can be edited before being translated into protein, paving the way for different versions of proteins. Abnormal RNA editing in humans has been observed in patients with neurological diseases. The changing physiological appearance of squid and octopuses over their lifetime and across different habitats has suggested extensive recoding might occur in these species. However, this could never be confirmed, as their genomes (and those of most species) have never been sequenced.

For the purpose of the new study, the researchers extracted both DNA and RNA from squid. Harnessing DNA sequencing and computational analyses at TAU, the team compared the RNA and DNA sequences to observe differences. The sequences in which the RNA and DNA did not match up were identified as "edited."

"It was astonishing to find that 60 percent of the squid RNA transcripts were edited. The fruit fly, for the sake of comparison, is thought to edit only 3% of its makeup," said Dr. Eisenberg. "Why do squid edit to such an extent? One theory is that they have an extremely complex nervous system, exhibiting behavioral sophistication unusual for invertebrates. They may also utilize this mechanism to respond to changing temperatures and other environmental parameters."

"Misfolding" the proteins

The researchers hope to use this approach to identify recoding sites in other organisms whose genomes have not been sequenced.

"We would like to understand better how prevalent this phenomenon is in the animal world. How is it regulated? How is it exploited to confer adaptability?" said Dr. Eisenberg. "There may be implications for us as well. Human diseases are often the result of 'misfolded' proteins, which often become toxic. Therefore the question of treating the misfolded proteins, likely to be generated by such an extensive recoding as exhibited in the squid cells, is very important for future therapeutic approaches. Does the squid have some mechanism we can learn from?"

The researchers recently received an Israel-U.S. Binational Science Foundation grant to explore the subject of genetic editing in octopuses.

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