Sunday, 12 March 2023

Molecular biology and the edge of Darwinism.

Darwinism's metaphysics?

Octopuses troll Darwinism,?

Massive RNA Editing and the octopus.

Cornelius G Hunter

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.

So it shouldn’t be too surprising that all of this leaves evolutionists a bit shell-shocked. They can manage little more than the usual Aristotelian teleology. As one headline explained, “ ‘Smart’ cephalopods trade off genome evolution for prolific RNA editing.” Trade off genome evolution for prolific RNA editing? That is teleological. Likewise, an evolutionist explained, “Mutation is usually thought of as the currency of natural selection, and these animals are suppressing that to maintain recoding flexibility at the RNA level.” Again, more teleology. The infinitive form tells all.

The research paper explains that these species “invented” the massive recoding. Invented? The paper also turns these species into intelligent agents:

..... Why would the coleoids choose to alter genetic information within RNA rather than hardwire the change in DNA?

Choose to?

This is absurd.

Evolution has been demolished by science. We are far, far beyond any kind of controversy. While evolutionists want to claim they do legitimate science, the empirical evidence has long since left the station. Evolution has been utterly demolished.

Yet more on Darwinism as secular superstitition

New evolution book reviewed by Hans Madueme.

Cornelius G Hunter

If you want to understand evolutionary thought just read the literature. Charles Darwin accurately characterized his 1859 book on evolution as “one long argument.” That argument was based on several popular religious beliefs leading to faulty science. For example, throughout the volume Darwin’s ideas rely on a popular religious doctrine called utilitarianism, and in Chapter Six Darwin explicitly states that his theory would absolutely fail without it.

Ever since Darwin, little has changed. One after the other, evolutionists have attempted to explain and prove Darwin’s idea. And one after the other, they have simply confirmed that evolutionary thought is not a scientific theory in the normal sense but rather is, at its core, a religious idea with little regard for the science. It really is nothing more than the ancient Epicureanism, inserted into modern science. Consider the latest entry, Adam and the Genome, a brand new Brazos Press title authored by Dennis Venema and Scot McKnight.

In the tradition of the evolution literature, the first part of the book presents a long list of arguments for why we should believe the biological world arose by evolution—a combination of chance and natural law. The second part of the book, as the title suggests, addresses the question of Adam and Eve. Simply put, the book argues that Scripture, read rightly, never did point to a historical Adam in the first place. This makes Scripture consistent with evolution’s call for humanity to begin as a relatively large population.

But this reading of Scripture is influenced by evolution. As McKnight explains, his approach accepts “the reality of genetic evidence supporting a theory of evolution”. [173] But, in fact, there is no such “reality.” The genetic evidence does not support evolution—quite the opposite.

Religious beliefs mandating evolution are what led to today’s theory of evolution, not empirical scientific findings. And now, new scientific observations (such as genetics) are interpreted according to evolution. The observations are theory-laden. Furthermore, with the broad acceptance of evolution, theologians such as McKnight are telling us we need to adjust our religious understandings in light of the “reality” of the scientific evidence.

This is what computer scientists refer to as Garbage-In, Garbage-Out (GIGO). It is little wonder McKnight and many others are calling for this “new” understanding of Scripture, for that “new” understanding is centuries old, and is what mandated evolution in the first place. What goes around comes around.

Unfortunately the myth that evolution is a scientific no-brainer, a given, a fact, and on par with gravity and the round Earth, is difficult to dispel. The powerful religious ideas mandating evolution have led to the myth that evolution is legitimate and compelling science.

For example, in his review of Adam and the Genome, Hans Madueme rightly explains that the history of science should give us pause regarding evolution. Too often scientists have had high confidence in ideas that later would be discarded. Madueme accurately detects such high confidence in evolutionary thought, as exemplified in Adam and the Genome.

Unfortunately Madueme also gives high marks to the science presented in the book. According to Madueme, it “unpacks the genomic evidence for evolution and common ancestry,” and even “skeptical readers will come away impressed at the deep explanatory power of evolutionary theory.” Impressed?

And what exactly is this “deep explanatory power of evolutionary theory” to which Madueme refers? Well, err, Madueme fails to mention any for he “skipped over most of the details.” But it is precisely in those details where the evidences and arguments fall apart. We have already seen that the book makes erroneous arguments that the fossil evidence and echolocation support evolution (here and here). In fact, as we saw, both these evidences and arguments, once stripped of the religion, far from supporting evolution, severely contradict the theory.

In my next post I will look at another one of the book’s arguments involving pseudogenes. What we will find, again, is not “deep explanatory power of evolutionary theory” but exactly the opposite.

meditations of aservantofJEHOVAH

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