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 » Cephalopods are weird.

Cephalopods are weird.

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1 Cephalopods are weird. on Fri Apr 14, 2017 5:19 pm

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Central Dogma Of Genetics May Not Apply To Cephalopods 1

Especially when one is speaking about the octopus or their cousins, the squid and the cuttlefish. You likely already know about their many physical capabilities and their high intelligence in comparison to other creatures. Now, scientists from MIT and Israeli universities have found that these species may also directly violate the central dogma of genetics. Rather than direct coding from DNA to RNA to then making proteins, they have the capability to edit their RNA and change the genes in the middle of being copied.
This sort of genetic plasticity is likely what allows them to adapt so well to new situations and, possibly, what gives them their smarts. But this process also has its downsides. By bucking the traditional trend of biology, they also leave behind their capability to evolve and mutate. Will this negatively impact them in the future, especially considering the world-altering effects of climate change and ocean acidification?

Delving into the depths of newly published science in the field of biotechnology,  The central dogma of molecular biology and genetics is pretty straightforward. You take DNA, then you transcribe the desired gene into RNA (usually mRNA) and, once outside of the nucleus, you translate that RNA using ribosomes into amino acids that then form proteins. Those proteins then do the actual function that their original genetic encoding directs. This process is usually rigid and cannot be reversed. DNA to RNA to proteins, simple as that. Except when it’s not. The Exceptions There have always been a few exceptions and they’re often terrifying. Like how retroviruses utilize a reverse transcription process to insert their own RNA into the genome of their host to make their host cell produce more of the invading virus. It is processes like these that make them so insidious to fight against. But there’s another exception.

It is a more innocuous and rare one, but also a more confusing one. While the central dogma is a good basis for the overall system, there are a lot of other mechanisms at play, especially after the point of transcription into RNA. It is possible for this RNA to be edited after the fact and change the resulting protein sequence. The main method of this RNA editing happens when the “A” nucleotides (adenosines making up adenine) are modified by ADAR enzymes, which stands for “adenosine deaminases acting on RNA”, into another form called inosine. During translation to make amino acids, inosine can be recognized instead as a “G” nucleotide (guanosines making up guanine), though it can also bind to other nucleotides too, making it extremely versatile. This change effectively alters the original genetic code without actually changing the genome that it was originally transcribed from. Some Cephalopods Buck The Trend This change is incredibly rare. Only 3% of human RNA messages have even a single base altered like this. And this number itself is only so high because, out of the 25 sites in total in the human genome that allow this reconfiguration, they are largely conserved genes, meaning they are highly coded for. All in all, such a change is not actually highly conserved and has disappeared from the rest of the human genome because of this. Researchers from MIT and Israel have recently published a study describing several species in the class Cephalopoda that wildly outstrip this pathetic chance, but only those species.

In fact, octopodes, squids, and cuttlefish appear to have a vast majority of their RNA messages changed like this. For practically every RNA message, at least one altered nucleotide event like this occurs, changing the resulting coded for message. As an example with squids, out of their 20,000 total genes, over 11,000 of them when transcribed lead to an RNA editing event. They also appear to be highly conserved and not allowed to be removed from the genome by natural repair and mutation mechanisms. What is the end result of this mechanism? The formation of proteins that are not actually coded for within the genome itself, but are nonetheless properly utilized and created by the organism when needed. Which means that there is a whole other layer of genetic instructions hidden away in these particular species that can’t be seen just from a full genetic sequencing. The Downsides But there is a trade-off and downside to be had. While this enables species like squids to be highly adaptable to their environment, such as being able to alter certain temperature coding genes at the RNA level when necessary, it also makes them very rigid. This is because the genes with these sites that invite RNA alteration cannot allow mutations to occur in the genes. Due to the complex RNA structures needed when coding for these sorts of genes, even a single mutation in them can stop the entire gene and resulting RNA from functioning.

This, in turn, would likely kill the organism, though it depends on the gene in question. So the genes must be conserved and extensively so. This means that their adaptability is entirely inherent, already existing in their genomes. But they cannot adapt beyond that. They cannot allow the rampant mutations that other species, including us, use to evolve and fit our changing environments on the fly. If octopodes, squids, or cuttlefish come up against something that their changing RNA structure isn’t fit to handle, they can’t adapt to it by changing their genome. Will It Work Out? Such a consequence results in them being very slow to evolve over time. Sure, their ability to apply so many kinds of RNA edits is likely one of the benefits that gives them their intelligence and so many of their flexible capabilities. But it also means that issues like climate change and ocean acidification may be topics they won’t be able to deal with, leading to a widespread die-off of the species as a whole. Though, on the other hand, maybe not. Perhaps their RNA editing abilities are robust enough even to handle those concerns. They certainly appear to be some of the closest organisms to humans when it comes to mental and developmental complexity. Only time will tell in that regard.

Massive RNA Editing and the Octopus

Evolution has been utterly demolished

Click the video to see an octopus mimic algae. Octopuses have an amazing ability to sense and mimic the coloration, shape, and texture of their surroundings. They literally “blend in” as the video illustrates. Note how the audience appropriately responds at the end of the video. You can read more about this amazing ability here. The idea that such mimicry evolved is unlikely. The problem is that evolution’s random mutations are not up to the task. Too many of them are required. And no, natural selection doesn’t make it happen. Selection cannot coax, cajole, persuade or otherwise sweet talk mutations into happening. Selection is simply a label for what happens afterwards: in a word, harmful mutations are eliminated. Indeed, evolution co-founder Alfred Wallace thought the term “natural selection” should be dropped altogether, because it really doesn’t do anything and so is misleading. According to evolutionary theory, selection can have no forward influence on mutations. It cannot cause helpful mutations to occur—no teleology. But helpful mutations are what is needed, and in spades. The octopuses amazing mimicry needs both to sense the surrounding environment, and then to perform its amazing blending ability. Sensing without blending is useless. And blending without sensing is useless. You need both, and that is beyond the reach of random mutations. It isn’t going to happen. In fact, this same problem applies to both sensing and to blending, taken individually. This is because a large number of mutations are required to construct either one. And to add insult to injury, research at the molecular level is just making things worse.

Evolution is supposed to be caused by random mutations in the genome. Mutations in segments of the DNA where genes reside may change the gene product, such as a protein. But organisms have a way of creating such genetic changes on the fly, and it is called RNA editing. After a gene is transcribed, the RNA copy can be edited, for example by altering a single nucleotide. This RNA editing, or recoding, is done by a protein machine.

RNA editing is typically not very common. But in recent years, high levels of recoding have been found in the octopus, and new research is adding to the story. In the octopus and allied species, the majority of RNA transcripts are found to have an edited nucleotide and, importantly, they are often conserved across the species.

In other words, whereas in most species that have been studied there is relatively little RNA editing, in the octopus and its closest neighboring species there is extensive RNA editing and the recoding sites are often conserved across these neighboring species. Also the DNA flanking sequences, on either side of the recoding sites, tend to be conserved across these neighboring species.

This evidence demolishes evolution. Here are seven reasons why.

First, why would these few species suddenly have such an escalation of RNA editing? Evolution has no explanation why this mechanism would suddenly take on such importance in this small group of species. As one evolutionist admitted, “Most organisms have very few functional [editing] sites in coding regions. This is why we find it so unusual and surprising that in squid, octopus, and cuttlefish, we see exactly the opposite.”

Second, the flanking sequences are difficult to evolve. These consist of hundreds of nucleotides, and once transcribed they need to form RNA secondary structures which the RNA editing protein recognizes. These sequences can be highly specific. In some cases even a single nucleotide substitution can abolish RNA editing. In other words, evolution’s random mutations must somehow luckily find these specific sequences. Without the right secondary structure, RNA editing is greatly slowed. But at the start of the search evolution is most likely nowhere close to having a sequence that will form the right secondary structure. And it would be unlikely for a random mutation to make the difference. In other words, multiple mutations are required before even a hint of success is obtained. And of course this all must occur while not disrupting any preexisting messages the sequence carries. This is highly unlikely. And yet this must occur not just once, but twice, on both sides of the recoding site. And furthermore, this must occur not just twice but, err, hundreds of thousands of times, at the many different recoding sites. It’s not going to happen.

Third, these long conserved flanking sequences, hundreds of nucleotides long on either side of the recoding sites, imply evolution loses the ability to evolve.

Fourth, according to evolutionary theory the fact that these recoding sites are conserved across different species means that they are adaptive. In other words, they improve fitness. This massive RNA editing is a feature, not a bug. But given that there are many thousands of these recoding sites, evolution faces a combinatorial explosion. Not only is there an astronomical number of different combinations of RNA editing actions, but for any given gene there is the question of which RNA transcripts to recode? Unless a very simple solution is found, this combinatorial explosion is way beyond the meager resources of evolution’s random mutations.

Fifth, undoubtedly RNA editing is used to respond to changing conditions. Recoding has been shown, for example, to affect potassium channel function. But if RNA editing is a mechanism for response to changing conditions, then there must be signaling instructions that tell the RNA editing protein when and where to perform its editing. But the origin of that signaling system would require a great many mutations. Again, that likely would be beyond evolution’s resources.

Sixth, this massive RNA editing capability will not function properly without its many components in place. You need the recoding site, the flanking sequences, the RNA editing protein, and the signaling system. It will do no good to have the proper DNA sequences without the editing protein, or both of those without the signaling system, or the signaling system without the flanking sequences. In other words, there are multiple, interdependent components which all need to be in place for this RNA editing capability to function.

Seventh, it is silly to think evolution could find the right recoding sites. The problem is that, even if this RNA editing capability could evolve and all the different interdependent components could fall into place, it would not likely pick the right recoding site. Simply put, each evolutionary experiment would require a monumental effort and time span before the needed feedback could be obtained about whether or not the recoding site was a good one. Evolution would need to evolve the recoding site and the flanking sequences before natural selection could act. Undoubtedly most recoding sites would not help. They might be neutral, or they might be harmful. But they would not help to construct the adaptive RNA editing capability we find in the octopus. Therefore this evolution search problem is astronomically difficult. It needs to search through a large number of mostly useless candidate recoding sites, and each try would require an eternity. But it gets worse, for it is likely that any single recoding site isn’t going to accomplish much all by itself. There are many thousands of these recoding sites, and undoubtedly multiple recoding sites are needed to work together. So even if evolution could somehow accomplish the search for a single recoding site, which is astronomically difficult, it likely would not improve fitness by itself.

One look at the video above and anyone can see evolution is not a good theory. This is just common sense. Not surprisingly, the science confirms this common sense. In fact, the science doubles down, many times over.

There simply is no excuse for continuing to thinking evolution created the species. There are just too many contradictions, too many absurdities, too many ridiculous examples showing evolution to be a complete failure.

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods 2

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function.

1. http://ascienceenthusiast.com/central-dogma-cephalopods/
2. http://www.cell.com/cell/fulltext/S0092-8674(17)30344-6

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