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About That Genetic Code
A Smoke Screen
A common response from evolutionists, when presented with evidence such as this, is that we still don�t understand biology very well. This argument from ignorance goes all the way back to Darwin. He used it in Chapter 6 of Origins to discard the problem of evolving the electric organs in fish, such as the electric eel (which isn�t actually an eel). The Sage from Kent agreed that it is �impossible to conceive by what steps these wondrous organs� evolved, but that was OK, because �we do not even know of what use they are.�
Setting aside the fact that Darwin�s argument from ignorance was a non-scientific fallacy, it also was a set up for failure. For now, a century and half later, we do know �what use they are.� And it has just gotten worse for evolution.
Darwin�s argument has been demolished, once again demonstrating that arguments from ignorance, aside from being terrible arguments, are not good science.
The truth is, when evolutionists today claim that the many problems with their chance theory are due to a lack of knowledge, they are throwing up a smoke screen.
Religion drives science, and it matters.
Here is Why Steven Novella is Wrong About That Harvard Experiment
Going Nowhere Fast
First off, Novella deserves some credit for acknowledging at least some limitations in the experiment�s results:
Of course, this one piece of evidence does not �prove� something as complex and far ranging as the evolution of life on Earth.
Novella also deserves credit for acknowledging that evolutionary change that requires a few mutations, rather than merely one, is a big problem. Novella has solutions which he believes resolve this problem (as we shall see below), but at least he acknowledges what too often is conveniently ignored.
What Novella does not acknowledge, however, is that bacteria adaptation research, over several decades now, has clearly shown non evolutionary change. For instance, bacterial adaptation has often been found to be rapid, and sensitive to the environmental challenge. In other words, when we look at the details, we do not find the evolutionary model of random variation slowly bringing about change, but rather environmentally directed or influenced variation.
That is not evolution.
And indeed, the Harvard experiment demonstrated, again, very rapid adaptation. In just 10 days the bacteria adapted to high doses of lethal antibiotic. As one of the researchers commented, �This is a stunning demonstration of how quickly microbes evolve.�
True, it is �stunning,� but �evolve� is not the correct term.
The microbes adapted.
The ability of organisms to adapt rapidly falls under the category of epigenetics, a term that encompasses a range of sophisticated mechanisms which promote adaptation which is sensitive to the environment. Given our knowledge of bacterial epigenetics, and how fast the bacteria responded in the Harvard experiment, it certainly is reasonable to think that epigenetics, of some sort, may have been at work.
Such epigenetic change is not a new facet of evolution, it contradicts evolution. Not only would such complex adaptation mechanisms be difficult to evolve via random mutations, they wouldn�t provide fitness improvement, and so would not be selected for, even if they did somehow arise from mutations.
Epigenetic mechanisms respond to future, unforeseen conditions. Their very existence contradicts evolution. So the Harvard experiment, rather than demonstrating evolution in action, is probably yet another example of epigenetic-based adaptation. If so, it would contradict evolution.
Another problem, that Michael Behe has pointed out, is that it appears that most of the mutations that occurred in the experiment served to shutdown genes. In other words, the mutations broke things, they did not build things. This is another way to see that this does not fit the evolutionary model. It�s devolution, not evolution. Novella begs to differ, and says Behe has made a big mistake:
Behe is wrong because there is no such thing as �devolution.� Evolution is simply heritable change, any change, and that change can create more complexity or more simplicity. Further, altering a protein does not �degrade� it � that notion is based on the false premise that there is a �correct� sequence of amino acids in any particular protein. Evolution just makes proteins different. Proteins perform �better� or �worse� only in so much that they contribute to the survival and reproduction of the individual. If it is better for the survival of the organism for an enzyme to be slower, then the slower enzyme is better for that organism.
First, Novella ignores the fact that many of the mutations introduced stop codons, and so did not merely slow an enzyme but rather shut it down altogether.
Secondly, it is not Behe here who is making the mistake, it is Novella. He says �Evolution is simply heritable change ��
But this is an equivocation.
On the one hand, evolutionists want to say that shutting down or slowing a gene is �evolution,� but on the other hand, evolutionists say that a fish turning into a giraffe is �evolution.�
Unfortunately evolutionists routinely make this equivocation. This is because they don�t think of it as an equivocation. In their adherence and promotion of the theory, the distinction is lost on them. All change just smears together in one big long process called evolution. You can see other examples of this here and here.
So the comments, press releases, and articles send a misleading message. Readers are told that the researchers have seen �evolution in action.� The message is clear: This is evolution, the evolution. But it isn�t. There is nothing in these findings that show us how a fish turns into a giraffe.
Multiple mutations
As mentioned above, Novella also believes that evolution coming up with designs requiring multiple mutations is not a problem. Novella�s reasoning is that while this would be a problem if most mutations are harmful, they aren�t. Most mutations are neutral, so evolutionary drift can introduce the many needed mutations, and once the set of required mutations are in place, then you have the new design.
This is a profound misunderstanding of the problem evolution faces. You can�t evolve a protein, for example, with drift. That most mutations are neutral does not suddenly resolve the curse of dimensionality and resolve this astronomical search problem. There just is no free lunch.
Similarly, Novella makes yet another profound mistake involving what he calls �the lottery fallacy.�
The first is basically the lottery fallacy � considering the odds of John Smith winning the lottery by chance alone and concluding it could not have happened by chance. Rather, you should consider the odds that anyone would win the lottery. This is actually pretty good. Behe looks at life on Earth and asks � what are the odds that this specific pathway or protein or whatever evolved by chance alone. He is failing to consider that there may have been billions of possible solutions or pathways down which that creature�s ancestors could have evolved. Species that failed to adapt either migrated to an environment in which they could survive, or they went extinct. In other words, Behe should not be asking what the odds are that this bit of complexity evolved, but rather what are the odds that any complexity evolved. It is difficult to know the number of potential complexities that never evolved � that number may dwarf the odds of any one bit evolving. Right there Behe�s entire premise is demolished �
This is a terribly flawed argument for several reasons. First, life needs proteins. All life that we know of needs proteins.
Thousands of proteins.
Yet proteins are far beyond evolution�s reach. It is true, per Novella�s point, that there are a whole lot of ways to make a given protein. There are many, many different amino acid sequences that give you a globin. But �many, many� is like a grain of sand compared to the astronomical amino acid sequence search space.
There just is no free lunch.
But Novella goes further than this, and this brings us to the second flaw. Novella is not merely arguing there are many different ways to construct life as we know it. He is pointing out that there are, or at least there could be, a whole bunch of different ways to make life, in the first place.
If you take them all together, you could have a pretty big set of possibilities. Perhaps it is astronomical. So what we got in this world�the life forms we observe, are not point designs in an otherwise lifeless design space. Rather, the design space could be chocked full of life forms. And hence, the evolution of life becomes likely, and �Right there Behe�s entire premise is demolished.�
What Novella is arguing for here is unobservable. He is going far beyond science, into an imaginary philosophical world of maybe�s.
Not only is Novella clearly appealing to the unobservable, but even that doesn�t work. At least for any common sense approach. There is no question that the design space is full of useless blobs of chemicals that do nothing. A speculative claim? No, that is what this thing called science has made abundantly clear to us. Even the simple case of a single protein reveals this. Only a relatively few mutations to most proteins rob them of their function. Protein function is known to dramatically reduce as different amino acids are swapped in.
Of course this is all obvious to anyone who understands how things work. Sure, Novella may be right that there are other, unknown, solutions to life. But that isn�t suddenly going to resolve evolution�s astronomical search problem. That problem was never contingent on the life we observe being the only possible life forms possible
Novella calls himself a skeptic. In fact, he is exactly the opposite.
How the Peppered Moth Backfired
The Poster Child Became the Rebuttal
There are two main problems with peppered moths story. First, changing colors is hardly a pathway leading to the kinds of massive biological change evolution requires. It is not as though a change in the peppered moth coloration is any kind of evidence for how the moths evolved, or how any other species, for that matter, could have evolved.
In fact changing the color of a moth not only fails to show how species could evolve, it also fails to show how any biological design could evolve. The peppered moth case doesn�t show how metabolism, the central nervous system, bones, red blood cells, or any other biological wonder could have arisen by evolution�s random mutations coupled with natural selection.
The moths were already there. Their wings were already there. Different colors were already there. The changing of color in moth populations, while certainly a good thing for the moths, is hardly an example of evolution.
Second, research strongly suggests that the cause of the darkening, at the molecular level, is an enormous genetic insertion. In other words, rather than a nucleotide, in a gene, mutating to one of the other three nucleotides, as you learned in your high school biology class, instead what has been found is an insertion of a stretch of more than 20,000 nucleotides. That long inserted segment consists of a shorter segment (about 9,000 nucleotides) repeated about two and one-third times.
Also, the insertion point is not in a DNA coding sequence, but in an intervening region (intron), which have been considered to be �junk DNA� in the past.
This observed mutation (the insertion of a long sequence of DNA into an intron), is much more complicated than a single point mutation. First, there is no change in the gene�s protein product. The mutating of the protein sequence was the whole idea behind evolution: DNA mutations which lead to changes in a protein can lead to a phenotype change with fitness improvement, and there would be subject to natural selection.
That is not what we are seeing in the much celebrated peppered moth example. The DNA mutation is much more complicated (~20,000 nucleotides inserted), and the fact it was inserted into an intron suggests that additional molecular and cellular mechanisms are required for the coloration change to occur.
None of this fits evolutionary theory.
For example, evolutionary theory requires that the needed random DNA mutational change is reasonably likely to occur. Given the moth�s effective population size, the moth�s generation time period, and the complexity of the mutation, the needed mutation is not likely to occur. Evolution would have to be inserting segments of DNA with (i) different sequences, at (ii) different locations, within the moth genome. This is an enormous space of mutational possibilities to search through.
It doesn�t add up. Evolution does not have the resources in terms of time and effective population size to come anywhere close to searching this astronomical mutational space. It�s not going to happen.
A much more likely explanation, and one that has been found to be true in so many other cases of adaptation (in spite of evolutionary pushback), is that the peppered moth coloration change was directed. The environmental change and challenge somehow caused the peppered moth to modify its color. This suggests there are preprogrammed, directed adaptation mechanisms, already in place that are ready to respond to future, potential, environmental changes, which might never occur.
Far from an evidence for evolution, this is evidence against evolution.
So there are at least two major problems with what is celebrated as a key evidence for evolution in action. First, it comes nowhere close to the type of change evolution needs, and the details of the change demonstrate that it is not evolutionary to begin with.
Fake News From PBS on the DNA Code
Heighten Public (Mis)Understanding
Biologically and chemically, there is no reason why this particular genetic code, rather than any of millions or billions of others, should exist, scientists assert. Yet every species on Earth carries a genetic code that is, for all intents and purposes, identical and universal. The only scientific explanation for this situation is that the genetic code was the result of a single historic accident. That is, this code was the one carried by the single ancestor of life and all of its descendants, including us.
There was only one problem: that was fake news. The DNA, or genetic, code was and is, in fact, very special. This was known at the time of the PBS Evolution Project, and since then it has only gotten worse for the evolutionists.
It is the exact opposite of how the evolutionists informed their viewers. They could not have misrepresented the science any more than they did. Because when evolutionists seek to �heighten public understanding,� and �dispel common misunderstandings,� it doesn�t mean teaching science. It means promoting evolution, in spite of the science.
Religion drives science, and it matters.
The DNA Code and Evolution
My Dear Watson
1. The DNA code is universal. There are minor variations scattered about, but the same canonical code is found across the species.
2. The DNA code is special. The DNA is not just some random, off the shelf, code. It has unique properties, for example that make the translation process more robust to mutations. The code has been called �one in a million,� but it probably is even more special than that. For instance, one study found that the code optimizes �a combination of several different functions simultaneously.�
3. Some of the special properties of the DNA code only rarely confer benefit. Many of the code�s special properties deal with rare mutation events. If such properties could arise via random mutation in an individual organism, their benefit would not be common.
4. The DNA code�s fitness landscape has dependencies on the DNA coding sequences and so favors stasis. Changes in the DNA code may well wreak havoc as the DNA coding sequences are suddenly not interpreted correctly. So the fitness landscape, at any given location in the code design space, is not only rugged but often is a local minimum, thus freezing evolution at that code.
Observation #1 above, according to evolutionary theory, means that the code is the ultimate homology and must have been present in the last universal common ancestor (LUCA). There was essentially zero evolution of the code allowed over the course of billions of years.
This code stasis can be understood, from an evolutionary perspective, using Observation #4. Given the many dependencies on the DNA coding sequences, the code can be understood to be at a local minimum and so impossible to evolve.
Hence Francis Crick�s characterization, and subsequent promotion by later evolutionists, of the code as a �frozen accident.� Somehow the code arose, but was then strongly maintained and unevolvable.
But then there is Observation #2.
The code has been found not to be mundane, but special. This falsified the �frozen accident� characterization, as the code is clearly not an accident. It also caused a monumental problem. While evolutionists could understand Observation #1, the universality of the code, as a consequence of the code being at a fitness local minimum, Observation #2 tells us that the code would not have just luckily been constructed at its present design.
If evolution somehow created a code to begin with, it would be at some random starting point. Evolution would have no a priori knowledge of the fitness landscape. There is a large number of possible codes, so it would be incredibly lucky for evolution�s starting point to be anywhere near the special, canonical code we observe today. There would be an enormous evolutionary distance to travel between an initial random starting point, and the code we observe.
And yet there is not even so much as a trace of such a monumental evolutionary process. This would be an incredible convergence. In biology, when we see convergence, we usually also see variety. The mammalian and cephalopod eyes are considered to be convergent, but they also have fundamental differences. And in other species, there are all kinds of different vision systems. The idea that the universal DNA code is the result of convergence would be very suspect. Why are there no other canonical codes found? Why are there not more variants of the code? To have that much evolutionary distance covered, and converge with that level of precision would very strange.
And of course, in addition to this strange absence of any evidence of such a monumental evolutionary process, there is the problem described above with evolving the code to begin with. The code�s fitness landscape is rugged and loaded with many local minima. Making much progress at all in evolving the code would be difficult.
But then there is Observation #3.
Not only do we not see traces of the required monumental process of evolving the code across a great distance, and not only would this process be almost immediately halted by the many local minima in the fitness landscape, but what fitness improvements could actually be realized would not likely be selected for because said improvements rarely actually confer there benefit.
While these problems obviously are daunting, we have so far taken yet another tremendous problem for granted: the creation of the initial code, as a starting point.
We have discussed above the many problems with evolving today�s canonical code from some starting point, all the while allowing for such a starting point simply to magically appear. But that, alone, is a big problem for evolution. The evolution of any code, even a simple code, from no code, is a tremendous problem.
Finally, a possible explanation for these several and significant problems to the evolution of the DNA code is the hypothesis that the code did not actually evolve so much as construct. Just as the right sequence of amino acids will inevitably fold into a functional protein, so too perhaps the DNA code simply is the consequence of biochemical interactions and reactions. In this sense the code would not evolve from random mutations, but rather would be inevitable. In that case, there would be no lengthy evolutionary pathway to traverse.
Now I don�t want to give the impression that this hypothesis is mature or fleshed out. It is extremely speculative.
But there is another, more significant, problem with this hypothesis: It is not evolution.
If true this hypothesis would confirm design. In other words, a chemically determined pathway, which as such is written into the very fabric of matter and nature�s laws, would not only be profound but teleological. The DNA code would be built into biochemistry.
And given Observation #2, it is a very special, unique, detailed, code that would be built into biochemistry. It would not merely be a mundane code that happened to be enabled or determined by biochemistry, but essentially an optimized code.
Long live Aristotle.
The problem is there simply is no free lunch. Evolutionists can try to avoid the science, but there it is.
Michael Skinner on Epigenetics: Stage Three Alert
Over the Top Lies
1. Reject and persecute
2. Delegitimize and minimize
3. Rename and incorporate
Skinner�s position represents the move, which has been taking place in recent years, into Stage 3 (for example, see here).
Skinner�s Aeon article provides an excellent rundown of findings, both old and new, that confirm and elucidate what evolutionists have aggressively and violently opposed for a century: that epigenetics is not only real, but significant in causing long-term biological change. Natural selection plays no role in this process.
From 18th century observations of plants adapting to hotter temperatures, to Conrad Waddington fruit fly experiments in the 1950s (for more tidbits see here), to more recent observations of a range of species, Skinner provides an accessible summary and makes the inescapable conclusion:
Much as Lamarck suggested, changes in the environment literally alter our biology. And even in the absence of continued exposure, the altered biology, expressed as traits or in the form of disease, is transmitted from one generation to the next.
Much as Lamarck suggested? That is an astonishing admission given how evolutionists have, in the past century, vilified Lamarck and anyone who would dare associate with his ideas. And to this day such resistance continues, but it is waning. Hence evolutionists such as Skinner can broach the truth.
Skinner also comes clean on the problem that evolution�s basic source of biological variation, DNA mutations, is insufficient:
the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed. Scientists, well-aware of the issue, have proposed a variety of genetic mechanisms to compensate: genetic drift, in which small groups of individuals undergo dramatic genetic change; or epistasis, in which one set of genes suppress another, to name just two. Yet even with such mechanisms in play, genetic mutation rates for complex organisms such as humans are dramatically lower than the frequency of change for a host of traits, from adjustments in metabolism to resistance to disease.
Mutations are too slow for evolution? Again, this is an astonishing admission. The last time mathematicians reported this inconvenient truth they were told by evolutionists that it didn�t matter because, after all, we all know that evolution is true. Nothing like contradicting the science. Skinner admits that a paradigm shift is needed.
Unfortunately for Skinner and his readers that is where the light ends and smoke begins. Qua evolutionist, Skinner must present this contradictory biology as, somehow, consistent with evolution. The first sign that Skinner will firmly plant himself in the Stage Three lie (Rename and incorporate) is the opening sentence:
The unifying theme for much of modern biology is based on Charles Darwin�s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive.
Evolution is the unifying theme for much of modern biology? This not so secret handshake is such an over-the-top misrepresentation that it hardly seems worthwhile to dignify it with a rebuttal. Given how evolutionists are consistently surprised by biology, one would hope they at least could stop with this lie. But there it is.
Unfortunately it doesn�t stop there. Skinner�s next Big Lie, and the thesis of his article, is that the long rejected epigenetics will now fit conveniently into evolutionary theory. It was all a big misunderstanding and rather than rejecting epigenetics, we should see it as merely another component in the ever increasingly complex theory called evolution.
This is Stage Three: Rename, recast, retool, reimagine, and incorporate the new idol into our modern-day Epicureanism.
With enough massaging and story-telling evolutionists will forget the contradictions and convince themselves, and their fawning audiences, that the fit is perfect and epigenetics is, in fact, yet more proof of evolution.
There�s only one problem. This is all absurd.
What Skinner and the evolutionists won�t tell you is that all of this makes no sense on their theory. With epigenetics the biological variation evolution needs is not natural. It is not the mere consequence of biophysics�radiation, toxins or other mishaps causing DNA mutations. Rather, it is a biological control system.
It is not simple mistakes, but complex mechanisms.
It is not random, but directed.
It is not slow, but rapid.
It is not a single mutation that is selected, but simultaneous changes across the population.
This is not evolution.
And as Skinner inconveniently realizes, such epigenetics are found across a wide range of species. They are widely conserved and, for evolution, this is yet more bad news. It means the incredible epigenetics mechanisms must have, somehow, arisen very early in the history of evolution.
What the evolutionists will never admit is that epigenetics contradicts evolutionary theory. Not only must such incredibly complex mechanisms have evolved early on, and not only must they have arisen from chance mutation events, and so not only must evolution have created evolution, but they would have persisted in spite of any fitness advantage.
The whole idea behind the evolution mythology is that natural selection saves the day by directing the blind, chance mutations. Setting aside the silliness of this idea which we have discussed many times, the problem with epigenetics is that if they were to arise from chance mutations (and �oh what a big if�), they would not increase the organism�s fitness.
Epigenetics mechanisms are helpful at some future, unknown, time when the environmental challenge finally presents itself. They are useless when they initially arise, and so would not be preserved by evolution�s mythical natural selection.
Of course evolutionists will contrive yet more complex, silly, just-so stories about how epigenetics mechanisms arose from pre existing parts used for other purposes (the ridiculous co-adaptation argument), and about how they just happened to provide some other functions so as to improve fitness.
Skinner�s presentation of how to integrate epigenetics with evolution is entirely gratuitous. He has empirical evidence for the former, and religious dogma for the latter. There is no scientific need for the addition of evolution�it is a multiplied entity and is gratuitous. But Skinner needs it.
These are all the usual lies, which will be trotted out as yet more �facts.� Evolutionists must tell these lies. Otherwise they would have to move beyond Stage Three, and admit the science contradicts the theory.
And that is not going to happen. Old scientists don�t change their minds, they just die.
Religion drives science, and it matters.
Tim Ingold�s Question For Andy Gardner Says It All
A Not So Hidden Agenda
Anyone who has interacted with evolutionists knows this moment all too well. The metaphysics and religion are always there for evolutionists, crouching at the door and ready to strike at any moment. Whether in lecture, seminar, or writings, the agenda is painfully obvious. As Eva Jablonka put it, �Not God�we�re excluding God.�
Evolution isn�t about the science�it never was. It doesn�t matter what the science shows, evolution must be true. Religion drives science, and it matters.
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