Monday, April 11, 2016

Evolution Breakthrough? Or...

The headline is breathtaking: Fast evolution is discovered!
Primate evolution in the fast lane

The pace of evolution is typically measured in millions of years, as random, individual mutations accumulate over generations, but researchers at Cornell and Bar-Ilan Universities have uncovered a new mechanism for mutation in primates that is rapid, coordinated, and aggressive. The discovery raises questions about the accuracy of using the more typical mutation process as an estimate to date when two species diverged, as well as the extent to which this and related enzymes played a role in primate evolution.
Wow!! What is it then??
Alon Keinan, associate professor of Biological Statistics and Computational Biology at Cornell, and Erez Levanon, co-senior author and an associate professor with the Mina and Everard Goodman Faculty of Life Sciences at Bar-Ilan University in Israel, describe the novel, and rare, process triggered by a member of the APOBEC family of virus-fighting enzymes in the journal Genome Research. As primates evolved--including chimpanzees, Neanderthals, and modern humans--the number of types of viruses tailored for targeting primates multiplied. APOBECs in our cells mount a vigorous defense, bombarding the viral genome with clusters of mutations to render them unable to continue an infection. However, having such a mutation-based defense is risky for cells, since "friendly fire" could wreak havoc on our genome as well. Indeed, the enzymes have been shown to cause mutations in the tumor cells of breast and other cancers.
So the "friendly fire" which attacks the single strand DNA of a virus with mutations which render it inoperable... will cause beneficial mutations, producing primates?
The discovery is particularly significant because the enzyme has a tendency to alter regions of the genome that code for proteins as well as the areas responsible for their regulation. It's a vestige of their primary function in viral defense: Many viruses are composed of single stranded DNA or RNA, and DNA being actively used as a template for proteins is temporarily single stranded and unwound from the double helix. To the enzyme, they look the same.

The researchers looked for the signature of past mutations in humans and our closest hominid relatives, focusing on one of the enzymes in the APOBEC family, APOBEC3, since it has expanded into several subtypes during primate evolution, each with unique mutational signatures.

They knew that the enzyme recognizes a specific motif in the DNA and it targets only one of the DNA bases for mutation. Another telltale sign: multiple mutations occurring close together. Using conservative criteria, they identified thousands of such instances unique to primate genomes and, as negative control, did not identify any in other vertebrates such as mice that lack many of the APOBEC3 genes.

"What is appealing is that it's an accelerated evolutionary mechanism that could generate a large change in a gene in a single generation," said Levanon. "It's like playing the lottery--it could not have an impact, or it could have a major one."

"These events potentially mutate dozens of DNA bases in a small region less than the size of a gene. It is reasonable to think that most of these mega-mutations will be deleterious and will disappear in evolutionary time, but we do see a large number that survived," added Keinan. "Importantly, those that survived are overrepresented in functionally important parts of the genome, which suggests that some of these mutations have been maintained by natural selection because they conferred an advantage."
So what, exactly, do we have here?

1. An enzyme which is part of the viral defense system can attack the Host DNA, leaving a mutated DNA behind.

2. This occurs only on single strand DNA, meaning that APOBEC3 attacked genetic DNA during reproduction, when it is split into single strand.

3.They looked at "mutations" (apparently a mutation is defined as "looking like the "signature" left by the attack enzyme, AND being different from mouse DNA"). They found lots of those, with the "mark" of that virus-killer enzyme.

Now, do they know that these are mutations, or are they merely defined as mutations because they are not the same as mouse DNA? It should be obvious that mouse construction is not the same as ape or human construction. So because evolution by mutation is presupposed as a First Principle, then it must be an evolutionary trait, rather than a mere difference between two similar but not identical things. Differences would not be called beneficial mutations without first presupposing that evolution is a First Principle.

Do they know that the "mutations" which are presumed to be carried over and propagated throughout a population are actually mutations, or could they just "look like" mutations, because mutations are what they were looking for?

If these actually were mutations and are really beneficial, as in creating something that mice don't have, then what is it? Or are they negative, deleterious mutations as in, say, removing the tail or body fur? Or more likely, are they even active at all, since random changes don't add information, they either subtract information or in rare cases are neutral. And even more likely yet, they have no idea whatsoever about what these "mutations" do, if anything, or even if they really are mutations.

What is the likelihood of APOBEC3 attacking a temporarily unwound host DNA in a sperm or egg cell, and coincidentally creating beneficial features which differentiate higher apes and humans from mice? The authors even admit that it's like winning the lottery (it's probably far, far less likely than that allusion), and they admit that most such "mutations" would be deleterious and selected for destruction rather than propagation throughout a population. And that is especially the case if APOBEC3 mutates "dozens of DNA bases in a small region less than the size of a gene". That many "mutations" would be exponentially unlikely to produce valid and valuable information - especially while maintaining prior functionality. In fact, if there are "dozens of changes" from the mouse genome, and they are functional, then the actual overwhelming likelihood is that they were not mutations at all. Instruction books don't get better by making lots of random changes to the instruction set in the original book.

Further yet, if this is an evolutionary process then why don't viruses sprout new features when they are attacked? In fact, why does such a process exist at all? What are the chances that an APOBEC family of "attack by mutation" enzymes came to exist... by virtue of some sort of mutation chain or cluster which was sequestered away until it became a complete and useful enzyme, stored in DNA somewhere? This question becomes acutely focused on evolution now that we know that all - ALL - the information in DNA is used, and even double coded; mutating any of it necessarily destroys functionality.

Well, the standard response to that issue (actually all issues) is "Deep Time", of course. Given enough depth of time, minerals overcome entropy to become living cells, and single cells mutate into all the phyla, which in turn mutate into hordes of creatures most of which die off while others increase in complexity until some of them become intelligent enough to create Creation Stories as "science", without the need for actual empirical evidence.

And why would the segment which has been accidentally mutated by "friendly fire" not be considered a loss of useful information? Would such mutations not be expected to pervert or destroy existing necessary functionality, every time such a mutation occurred? Or is the expectation that such mutations served two functions: to a) maintain prior functionality while b) simultaneously creating new, selectable advantageous features resulting in primates? The chances against that are staggeringly and vanishingly small, to the point of absolute absurdity.

Returning to the claims in this paper, what they actually know is that they found multiple cases of DNA segments, even within a gene, which resemble the effects which are caused by APOBEC3 viral killer mutations.

And here's what they do not actually know: these similarities are presumed but not known to be caused by APOBEC enzymes, and thus presumed but not known to be useful for rapid mutation resulting in beneficial characteristics, as the assumption is applied to the emergence of primates. This is presumed but not known to be the case, even thugh such mutations would generally be thought to be destructive of necessary information and therefore would necessarily be deleterious, due to eradicating information for making and/or expressing the proteins which were already being used prior to the supposed mutation.

Since they don't even know what the "mutations" do, if anything, much less how they actually got there, they are released from any boundary conditions on what they can speculate. And the true believers are not likely to question whether the speculation actually makes sense, especially in terms of overall probabilities and the absurdities determined by Reductio Ad Absurdum.

Overall, this paper fails to produce new, objective knowledge regarding actual evolution.


Phoenix said...


What are your thoughts on studies done on psychopaths which intends to prove that their condition is the result of genetics and environmental factors. These studies also demonstrate a different brain structure between psychopaths and "normal" folk. If correct, does this mean the source of our behavior is merely physical?

This study is often used by Atheists to support their views:

Stan said...

Interesting. I'll check it out.

Stan said...

OK. If anything, that article shows that genetic determinism for behavior is not the case. Even though the author's brain scan correlates with psychopathy scans, and his being an "asshole" and lacking empathy by his own admission, his behavior is civil. He tries to relate this civility to his exceptional upbringing. This appears to mean that even though there is a lacking of certain capacities in psychopaths, that it is possible to overcome that to a sufficient degree to become within the boundaries of civility.

As for the capacity for empathy, the author demonstrates that empathy must be faked, as he is doing out of competitiveness and possibly pure orneriness.

Psychopathy, and its further correlate, Atheism, are not proven to be brain issues except by "correlation = causation". However, if the correlation is 100%, then it would seem to be a falsifiable hypothesis. Mengele would have pursued that by creating it in humans in a twin test, but civilized people would engage empathy and declare it unethical, and thus unknowable from an objective knowledge standpoint.

I suspect that psychopathy can be found in people with non-damaged brains, too, but who knows for certain? So it is possible to say that non-empathetic Atheism correlates with non-empathetic psychopathy, but not much more than that, certainly not causation of one by the other. However, even resembling psychopathy is not a favorable human trait.

Talon said...

Whee! According to Neil deGrasse Tyson and Scientific American, Intelligent Design is now a valid scientific hypothesis, on a universe level. Tyson gives our universe a 50/50 chance of being created by simulation. Intelligent First Cause? It's science so long as it's Anything But God.

Steven Satak said...

This is just more grist for another series of 'Just So" stories. They never give up. Everything HAS to be seen through the warped lens of Evolution. Even if it STILL doesn't make sense, they never give up. They can speed things up all they want - what difference does that make when they have all the time in the world in the first place (Deep Time)?

The point is, evolution as put about by 'scientists' today is still impossible, and this is by their own standards of proof! Of course, those standards are waived in the case of Evolutionism, but that was something to be expected.

Phoenix said...


Every article I've seen on this topic seem to confirm that psychopathy is seen in abnormal brain structures. Like you say, it certainly does not imply causation. Correct me if I'm wrong: Observational studies can only infer correlation but experimental tests may imply causation. With that in mind, it seems all these studies done are observational because experimental tests could be deemed unethical as you've stated yourself.

However, even what it comes to studies which may infer causation I suspect an equivocation by its proponents. The definitions of cause is trigger/effect or origin/source. Usually the Materialists use the former meaning but may imply the latter. Theists usually mean the latter although will concede to the former.

For example: A gun's lever may trigger (cause) a bullet to fire. But we do not say the trigger is the origin (source of existence) of the bullet. This is how Materialists equivocate the meaning of cause, to state the former but imply the latter.
I hope you understand what I'm getting at.

Stan said...

I'm not sure that I understand. Could you give an example of what Materialists would claim which is an equivocation?

Phoenix said...

For example, that stimulating certain regions of the brain may cause a specific reaction, such as stimulating the medial hypothalamus may cause rage. Since rage is always directed at a specific object, event or person, the subject might focus his rage at his boss for instance. Now Materialists will interpret the data as "the origin (cause) of the rage for his boss is merely a fuse in brain circuitry". Whereas the fuse in circuitry was in actual fact merely the trigger (cause) but not the origin (cause) which can be traced back to his boss forced him to work on Saturday resulting in him missing his daughter's soccer match.

I hope there's some semblance of sense in what I wrote.

Stan said...

Yes. Very good. I see what you mean. Let me see if I can rephrase it correctly.

By believing that all behaviors are results of electrochemical discharges in the neural components of the brain, and that those discharges are purely causally produced by prior states in the brain, such as specific electric charge values on certain neurons, THEN behaviors which are singular or aberrant are due ONLY to defects in the normal response path, and NOT due to rational or irrational responses to outside conditions.

I.e., rage = blown fuse, where the fuse is a material cause, which normally shunts rage somehow.

So yes, if the fuse itself is called the cause for behaviors, rather than identifying the origination of the actual primary causes which are released by the fuse, then the term "cause" is being equivocated. And it appears that there is a motivation for the equivocation: presupposition of Philosophical Materialism and pure Determinism.

I do suspect that there is such a thing as rage where the primary cause(s) are obscured or suppressed to the point where there might appear to be no primary cause. But messing around in the brain with an electric probe might be enough primary cause by itself. Statements of brain functions in terms of cause and effect are suspicious because there is no possibility of knowing what the states of all the pertinent neurons are, just prior to an event. Further, since there is no synchronizing clock in the brain, all neural functions are asynchronous and complete objective knowledge of an event would require complete knowledge of all the prior electrochemical events in all the pertinent neurons - clear back to an originating set of causes.

No brain technology does anything even close to producing the necessary knowledge to determine a single brain transaction which is involved in a single thought, much less how it is that a thought is originated, made a perception, corrected for rationality vs. non-valid beliefs, and articulated. That simple chain of mental functionality cannot be addressed with current (or proposed) technology, because the brain is simply too complex.

Materialists have to accept the belief that the (non-algorithmic and non-random) functionality and material complexity of the brain emerged for no particular reason, but was a selectable advantage because it works so well. That belief is not rational except under the irrational limitation of reality which Philosophical Materialism enforces in order to sustain Atheism.

Here's a possible falsification of material causation within the brain: Analysis of hypothetical situations which produce tactics and strategies for dealing with a range of non-existing future possible situations. This actually includes the beloved story-telling "sciences" which create non-physical hypotheses to cover extrapolated opinions regarding unseen and unseeable "material effects".

Phoenix said...

Materialists have to accept the belief that the (non-algorithmic and non-random) functionality and material complexity of the brain emerged for no particular reason, but was a selectable advantage because it works so well. That belief is not rational except under the irrational limitation of reality which Philosophical Materialism enforces in order to sustain Atheism

Interesting, because it seems that mere fact of the mind being non-algorithmic and non-random is also a falsification against Physicalist theories. Physicalists would of course state that making accurate predictions of mental activity is too complex and that such technology of how the brain creates subjective experience could also be created in the future. Is hoping for future possibilities really a testable prediction?

Another thought that sprang to mind yesterday is that dualists/theists are fond of using software and hardware analogies when referring to the mind/body relationship. However it seems this analogy fails quite soon for at least 3 reasons:
- Take the chicken and egg scenario for example. Which came first, the hardware or software? Obviously the hardware.
- Software cannot exist without the hardware.
- Software is developed by using hardware.

On the other hand if a Materialist were to use the software/hardware analogy to falsify dualist theories then that would fail too for an obvious reason, i.e., both hardware and software requires the ingenuity of an external mind for its creation.

Stan said...

It goes even deeper than that. First Life existed with both software (code) and hardware (DNA) already intact, correct, and surrounded by a support module which was both necessary and sufficient to function in rational conjunction with, and in support of, the hardware. The hardware (DNA) was coded both forward and backward. It came with mechanisms for translating, using RNA and RNA-ase plus other enzymes, and fabricating replacement proteins (necessary for growing after the cell splits). It also came with information not contained in the DNA, specifically the information to create internal feedback control systems for functions like metabolic balance, pH balance, but also the information to create the timing and function of the mitosis.

And another thing: if we all descended from a single primitive cell, there should be information for that cell in our DNA. Where in our DNA is the information for that cell? Evolutionists will claim that it all, every bit of it, mutated over time. That would be a lot of surprisingly beneficial and information bearing mutation. It would have to mean that very large chunks of beneficial code had all been changed simultaneously, and during the reproductive process. Any other scenario would result in immediate death of the child cells.

That problem goes in spades for the creation of all phyla in the Cambrian explosion. Large chunks of working, meaningful, beneficial code supplanted existing lesser code in DNA - suddenly, and simultaneously in separate events. In fact, DNA size probably increased considerably to accommodate the event.