Tag: evolution

I find it remarkable that despite this apparent order of magnitude, (or more), change in the complexity of the DNA code, (now codes), even the genetic scientists who made the discovery are failing to grasp its obvious implications with regards to conventional Neo-Darwinian selectionism:

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code is similar for all organisms and is stored in one of the two DNA strands as non-overlapping, linear sequence of nitrogenous bases Adenine (A), Guanine (G), Cytosine (C) and Thymine (T). These four letters are the ‘alphabet’ of the genetic code and are used to write code words. The code consists of three-letter words (also called triplets or codons). There are a total of 64 codons.

Now, researchers have found that the codons, which they refer to as duons, can be used for gene control. The team says that about 15 percent of codons could act as duons and that these bilingual genetic codes have shaped protein evolution.

At this point, one is beginning to wonder if the scientists are so focused on the evolutionary trees that even a copyright notice would somehow escape their attention. Copyright (c) 6000 BC God. All rights reserved. “Well, obviously that is a codal pattern that evolved early in a common ancestor and merely happens to look like alphabetical characters, from which the various divergent mutations didn’t happen to provide any selection advantages.”

Here is the point that so many die-hard evolutionists can’t seem to grasp. Let me try to walk them through the logic of my skepticism with a simple analogy.

Charlie has a car. Charlie is speaking to you in Minneapolis. Charlie says he left Chicago seven hours ago and drove to Minneapolis on a single tank of gas. However, in the car, you discover two receipts, both dated today, from gas stations in Colorado Springs and Sioux Falls.

Now, if you can understand how this indicates that Charlie’s story is false, you should be able to understand how adding an additional order of magnitude of complexity to the DNA programming process completely rules out the time-scale of the conventional Neo-Darwinian selectionist model. There were already real problems with the model, hence the development of hypothesized excuses such as Punctuated Equilibrium.

But by adding the time needed for another level of mutation on top of what was already required by the previous single-code model, I don’t see how it is possible to seriously insist that the conventional natural selection model can hold up in light of this discovery. Now, perhaps I’m missing something, but it seems to me that either the DNA mutation process has to take place considerably faster than has been observed over the past 50 years or a new model will be required.

My guess is that the initial explanatory defense will be that the mutations are more frequent, but more significant using the two-code process, but this is a defense unlikely to do more than buy a little time, as it will soon be possible to observe whether such mutations are actually taking place or not. Remember, the main reason that TENS has been able to survive so long is that its long timescales required resisted observation. If the timescales are shorter and the mutations selected more frequent, then we can observe and falsify them.

And, of course, even if the new, faster model turns out to be correct, this opens up a whole new can of worms that Jonathan Haidt correctly identifies as the likely consequences of a faster evolutionary model:

A wall has long protected respectable evolutionary inquiry from accusations of aiding and abetting racism. That wall is the belief that genetic change happens at such a glacial pace that there simply was not time, in the 50,000 years since humans spread out from Africa, for selection pressures to have altered the genome in anything but the most trivial way (e.g., changes in skin color and nose shape were adaptive responses to cold climates). Evolutionary psychology has therefore focused on the Pleistocene era – the period from about 1.8 million years ago to the dawn of agriculture — during which our common humanity was forged for the hunter-gatherer lifestyle. But the writing is on the wall.

It should be interesting to see how those who are true believers in both a) the religion of TENS and b) the myth of human equality react to this scientific claim from Penn State that Africans are less evolved than Europeans:

Light skin in Europeans stems from a gene mutation from a single person who lived 10,000 years ago. This is according to a new U.S. study that claims the colour is due to an ancient ancestor who lived somewhere between the Middle East and the Indian subcontinent. Scientists made the discovery after identifying a key gene that contributes to lighter skin colour in Europeans.

In earlier research, Keith Cheng from Penn State College of Medicine reported that one amino acid difference in the gene SLC24A5 is a key contributor to the skin colour difference between Europeans and West Africans. ‘The mutation in SLC24A5 changes just one building block in the protein, and contributes about a third of the visually striking differences in skin tone between peoples of African and European ancestry,’ he said.

We already know that the three major continental groups are not even equally human on the genetic level, with Africans being the only pure homo sapiens sapiens. This new claim indicates that Africans are lower in the evolutionary order, not that the skin color gene can be described as a speciation event. Regardless, one wonders why those who stubbornly, and ignorantly, continue to insist on human equality despite these undeniable genetic differences which are much more than skin deep are not yet tarred by the label “science denier”.

What I find amusing is that the scientists have already leaped in with some strained explanations to cram natural selection into the process when it is very clear from modern human behavior that the rapidity of the growth of the mutation would much more likely have stemmed from sexual selection. There need not be any environmental advantage to lighter skin for it to be preferred. Of course, that would also be a hate fact, as it would be scientific evidence that whites are more attractive than blacks. That being said, a fact is a fact.

However, that’s not the intriguing stuff. Here’s a much more interesting thought. The 10,000 year time frame is not all that far off from Bishop Usher’s famous 6,000 year estimation for the Age of the Earth. But most forget that the bishop’s estimate was based on Adam, not the Earth. So, what if it can eventually be determined that the single genetic mutation was actually an artificial one? That would certainly set the cat among the equality pigeons.

As usual, I appear to be well in advance of the scientists. Isn’t it simply astonishing that a non-scientist can so readily and reliably predict the inaccuracy and unreliability of the current scientific consensus? How is that even theoretically possible? How can ignorance trump credentials and actual science education? And yet….

In a paper in the journal Nature, scientists reported Wednesday that they had retrieved ancient human DNA from a fossil dating back about 400,000 years, shattering the previous record of 100,000 years.

The fossil, a thigh bone found in Spain, had previously seemed to many experts to belong to a forerunner of Neanderthals. But its DNA tells a very different story. It most closely resembles DNA from an enigmatic lineage of humans known as Denisovans. Until now, Denisovans were known only from DNA retrieved from 80,000-year-old remains in Siberia, 4,000 miles east of where the new DNA was found.

The mismatch between the anatomical and genetic evidence surprised the scientists, who are now rethinking human evolution over the past few hundred thousand years. It is possible, for example, that there are many extinct human populations that scientists have yet to discover. They might have interbred, swapping DNA. Scientists hope that further studies of extremely ancient human DNA will clarify the mystery.

There isn’t a mystery here. The TENS true believers keep thinking that genetics will color in the lines of their rudimentary evolution-based models, but instead, the science keeps breaking their lines. All of the conceptual models are wrong. Pretty much all of the carefully calculated timelines are wrong. Evolution by natural selection is a red herring of a theory that was developed at a time when the scientific tools were crude and largely unscientific. So, it should be absolutely no surprise that the improved data being provided by advancements in genetic science is repeatedly overturning the conclusions that were previously reached.

Mendel didn’t expose the physical gene, of course (that would come a
century later), but the conceptual gene. And this conceptual gene,
revealed in the tables and calculations of this math-friendly monk,
seemed an agent of mathematical neatness. Mendel’s thousands of
crossings showed that the traits he studied — smooth skin versus
wrinkled, for instance, or purple flower versus white — appeared or
disappeared in consistent ratios dictated by clear mathematical
formulas. Inheritance appeared to work like algebra. Anything so
math-friendly had to be driven by discrete integers.
It was beautiful work. Yet when Mendel first published his findings in 1866, just seven years after Charles Darwin’s On the Origin of Species,
no one noticed. Starting in 1900, however, biologists rediscovering his
work began to see that these units of heredity he’d discovered — dubbed
genes in 1909 — filled a crucial gap in Darwin’s theory of evolution. This recognition was the Holy Shit! moment that launched genetics’ Holy Shit! century. It seemed to explain everything. And it saved Darwin.

Darwin had legitimised evolution by proposing for it a viable
mechanism — natural selection, in which organisms with the most
favourable traits survive and multiply at higher rates than do others.
But he could not explain what created or altered traits. Mendel could. Genes created traits, and both would spread through a
population if a gene created a trait that survived selection….

These days, Dawkins makes the news so often for buffoonery that some might wonder how he ever became so celebrated. The Selfish Gene
is how. To read this book is to be amazed, entertained, transported.
For instance, when Dawkins describes how life might have begun — how a
randomly generated strand of chemicals pulled from the ether could
happen to become a ‘replicator’, a little machine that starts to build
other strands like itself, and then generates organisms to carry it — he
creates one of the most thrilling stretches of explanatory writing ever
penned. It’s breathtaking.

Dawkins assembles genetics’ dry materials and abstract maths into a
rich but orderly landscape through which he guides you with grace,
charm, urbanity, and humour. He replicates in prose the process he
describes. He gives agency to chemical chains, logic to confounding
behaviour. He takes an impossibly complex idea and makes it almost
impossible to misunderstand. He reveals the gene as not just the centre
of the cell but the centre of all life, agency, and behaviour. By the
time you’ve finished his book, or well before that, Dawkins has made of
the tiny gene — this replicator, this strip of chemicals little more
than an abstraction — a huge, relentlessly turning gearwheel of steel,
its teeth driving smaller cogs to make all of life happen. It’s a
gorgeous argument. Along with its beauty and other advantageous traits,
it is amenable to maths and, at its core, wonderfully simple.

Unfortunately, say Wray, West-Eberhard and others, it’s wrong.

The best part of all this is that Dawkins clearly knows it’s wrong too. Not that he’s going to admit it, though, not yet.

I phoned Richard Dawkins to see what he thought of all this. Did
genes follow rather than lead? I asked him specifically about whether
processes such as gene accommodation might lead instead. Then he did
something so slick and wonderful I didn’t quite realise what he’d done
till after we hung up: he dismissed genetic accommodation… by
accommodating it. Specifically, he said that genetic accommodation
doesn’t really change anything, because since the gene ends up locking
in the change and carrying it forward, it all comes back to the gene
anyway.

‘This doesn’t modify the gene-centric model at all,’ he said. ‘The
gene-centric model is all about the gene being the unit in the hierarchy
of life that is selected. That remains the gene.’

‘He’s backfilling,’ said West-Eberhard. ‘He and others have long been
arguing for the primacy of an individual gene that creates a trait that
either survives or doesn’t.’

They backtest and they backfill. That’s due to the crumbling state of TENS. They’re still clinging to natural selection, of course. But the TENS model is in crisis and it will collapse soon enough. It is even beginning to look as if we may get to see it happen in our lifetimes. Gene expression is more compatible with Intelligent Design than with TENS. We are not evolved, we are created. DNA is our C++ equivalent, and the womb is our compiler. Compile it differently, get different results. This is not New Age mumbo jumbo, but a scientific hypothesis that will be testable once we understand it well enough to become proficient in programming it ourselves.

And the utter implausibility of evolution by natural selection, among other things:

Humans today are a puffed-up and overconfident species. We know everything, we believe, or shortly will. We have a sense of near-omniscience equaled only by that of teen-agers. For do we not have have smart phones and Mars landers and PET scans, and do we not all speak wisely of DNA? We are, if not gods, at least godlings on the way up. If you don’t believe this, just ask us.

It was not always so. A thousand years ago, mankind cast a small shadow on the earth and lived in a dark and mysterious world. Little was known, about anything. Gods of countless sorts walked the earth. Spirits inhabited sacred groves. Lightning, the moon, the stars were…what? We had no idea. This brought humility.

We now believe that that nothing is or can be beyond our powers. A contemplative skeptic might advert to a few remaining details: We don´t know where we came from, why we are here, where “here” is, where we are going, or what we ought to do. These are minor questions. We only think about them when we wake up at three a.m. and remember that we are not permanent. We are kidding ourselves.

When people become accustomed to things that make no sense, they begin to seem to. Though we no longer notice it as we peck at tablet computers and listen to droning lowbrow shows about the conquest of nature, we still live in a weird and inexplicable universe, an apparently unending emptiness speckled with sparks of hydrogen fire. It is wicked mysterious. More things in heaven and earth, indeed.

We are not as wise as we think. I reiterate Fred´s Principle: The smartest of a large number of hamsters is still a hamster.

It’s a long one. Read the whole thing. It encapsulates why Darwinism, even in its neo-synthesized form, is caught up in crisis and is being increasingly rejected as unconvincing pseudo-science by the secular and the religious alike.

While I am an evolutionary skeptic rather than an Intelligent Design advocate, (by which I mean that I am skeptical that the Theorum of Evolution by Natural Selection as per the current Neo-Darwinian Synthesis is the correct factual explanation for the way in which one species is transformed into another), one thing that has always struck me as strange about the attempts of evolutionists to criticize the advocates of Intelligent Design as an alternative is that their criticisms were consistently irrelevant.

The various proposals of ID never struck me as markedly less falsifiable than those of TENS, considering how many tenets of TENS have been historically falsified and subsequently “revised”, to be polite. But not until I read Thomas Kuhn’s The Structure of Scientific Revolutions was I able to articulate what was bothering me about the common evolutionist criticisms of ID, which tend to revolve around ID not being a science because it is untestable and does not involve research, experimentation, and observation.

For example, the Union of Concerned Scientists explains why Intelligent Design is not science and attempts to refute what it describes as ID’s primary claims:

There is scientific controversy over evolution: There is no debate about evolution among the vast majority of scientists, and no credible alternative scientific theory exists. Debates within the community are about specific mechanisms within evolution, not whether evolution occurred.

Structures found in nature are too complex to have evolved step-by-step through natural selection [the concept of “irreducible complexity”]:  Natural selection does not require that all structures have the same function or even need to be functional at each step in the development of an organism.

Intelligent design is a scientific theory: A scientific theory is supported by extensive research and repeated experimentation and observation in the natural world. Unlike a true scientific theory, the existence of an “intelligent” agent can not be tested, nor is it falsifiable.

Intelligent design is based on the scientific method: Intelligent design might base its ideas on observations in the natural world, but it does not test them in the natural world, or attempt to develop mechanisms (such as natural selection) to explain their observations.

Setting aside the very arguable point of whether one can reasonably consider TENS a science under these parameters, when one reads how Kuhn describes the way in which one scientific paradigm gives way to another, it should be more than obvious that even if ID is complete and hopelessly incorrect, such criticisms are wholly misplaced and betray a basic failure to understand the philosophical foundations upon which all science rests.

In XII. The Resolution of Revolutions, Kuhn writes:

“Any new interpretation of nature, whether a discovery or a theory, emerges first in the mind of one or a few individuals. It is they who first learn to see science and the world differently, and their ability to make the transition is facilitated by two circumstances that are not common to most other members of their profession. Invariably their attention has been intensely concentrated upon the crisis-provoking problems; usually, in addition, they are men so young or so new to the crisis-ridden field that practice has committed them less deeply than most of their contemporaries to the world view and rules determined by the old paradigm. How are they able, what must they do, to convert the entire profession or the relevant professional subgroup to their way of seeing science and the world? What causes the group to abandon one tradition of normal research in favor of another?

“To see the urgency of those questions, remember that they are the only reconstructions the historian can supply for the philosopher’s inquiry about the testing, verification, or falsification of established scientific theories. In so far as he is engaged in normal science, the research worker is a solver of puzzles, not a tester of paradigms. Though he may, during the search for a particular puzzle’s solution, try out a number of alternative approaches, rejecting those that fail to yield the desired result, he is not testing the paradigm when he does so. Instead he is like the chess player who, with a problem stated and the board physically or mentally before him, tries out various alternative moves in the search for a solution. These trial attempts, whether by the chess player or by the scientist, are trials only of themselves, not of the rules of the game. They are possible only so long as the paradigm itself is taken for granted. Therefore, paradigm-testing occurs only after persistent failure to solve a noteworthy puzzle has given rise to crisis. And even then it occurs only after the sense of crisis has evoked an alternate candidate for paradigm. In the sciences the testing situation never consists, aspuzzle-solving does, simply in the comparison of a single paradigm with nature. Instead, testing occurs as part of the competition between two rival paradigms for the allegiance of the scientific community.”

As puzzle solvers wholly engrossed in the existing paradigm, biologists and evolutionists are the very last people that we should expect to either have a reasonable perspective on the limits of their consensus paradigm or to be able to appreciate the potential superiority of the new one.

Intelligent design represents a potential new paradigm, not a better way of solving the existing puzzles under the current paradigm. To expect it to do so is irrational. And while it may be true that biologists are not yet cognizant of the second crisis of Darwin, the fact is that TENS is observably awful at the sort of puzzle-solving that most more reputable sciences reliably deliver.  As per Kuhn, if ID ever begins to show a superior ability to solve the puzzles that TENS can’t, then and only then should we expect to see its advocates begin to abandon the old paradigm in favor of the new one.

None of this should be taken as a statement that I am an advocate of Intelligent Design. I am not; I have not considered the matter in any significant detail and I see little reason to do so unless and until it can solve some of the problems that TENS cannot. But anyone with even a reasonable amount of intellectual honesty should resist the urge to dismiss a proposed new paradigm for reasons that cannot possibly be considered relevant to the matter.