Monday, February 19, 2018

This Didn’t Evolve a Few Mutations At a Time

Action Potentials

Are there long, gradual, pathways of functional intermediate structures, separated by only one or perhaps a few mutations, leading to every single species, and every single design and structure in all of biology? As we saw last time, this has been a fundamental claim and expectation of evolutionary theory which is at odds with the science.* If one mutation is rare, a lot of mutations are astronomically rare. For instance, if a particular mutation has a one-in-a-hundred million (one in 10^8) chance of occurring in a new individual, then a hundred such particular mutations have a one in 10^800 chance of occurring. It’s not going to happen. Let’s have a look at an example: nerve cells and their action potential signals.

[* Note: Some evolutionists have attempted to get around this problem with the neutral theory, but that just makes matters worse].

Nerve cells have a long tail which carries an electronic impulse. The tail can be several feet long and its signal might stimulate a muscle to action, control a gland, or report a sensation to the brain.

Like a cable containing thousands of different telephone wires, nerve cells are often bundled together to form a nerve. Early researchers considered that perhaps the electronic impulse traveled along the nerve cell tail like electricity in a wire. But they soon realized that the signal in nerve cells is too weak to travel very far. The nerve cell would need to boost the signal along the way for it to travel along the tail.

After years of research it was discovered that the signal is boosted by membrane proteins. First, there is a membrane protein that simultaneously pumps two potassium ions into the cell and three sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell so there is a voltage drop (50-100 millivolt) across the membrane.

In addition to the sodium-potassium pump, there are also sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the decaying electronic impulse travels along the nerve cell tail, it causes the sodium channels to quickly open. Sodium ions outside the cell then come streaming into the cell down the electro-chemical gradient. As a result, the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail.

When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electro-chemical gradient. As a result the original voltage drop is reestablished.

This process repeats itself as the electronic impulse travels along the tail of the nerve cell, until the impulse finally reaches the end of the nerve cell. Although we’ve left out many details, it should be obvious that the process depends on the intricate workings of the three membrane proteins. The sodium-potassium pump helps set up the electro-chemical gradient, the electronic impulse is strong enough to activate the sodium channel, and then the sodium and potassium channels open and close with precise timing.

How, for example, are the channels designed to be ion-selective? Sodium is about 40% smaller than potassium so the sodium channel can exclude potassium if it is just big enough for sodium. Random mutations must have struck on an amino acid sequence that would fold up just right to provide the right channel size.

The potassium channel, on the other hand is large enough for both potassium, and sodium, yet it is highly efficient. It somehow excludes sodium almost perfectly (the potassium to sodium ratio is about 10000), yet allows potassium to pass through almost as if there were nothing in the way.

Nerve cells are constantly firing off in your body. They control your eyes as you read these words, and they send back the images you see on this page to your brain. They, along with chemical signals, control a multitude of processes in our bodies, and there is no scientific reason to think they gradually evolved, one mutation at time.

Indeed, that idea contradicts everything we know from the science. And yet this is what evolutionists believe. Let me repeat that: evolutionists believe nerve cells and their action potential designs evolved one mutation at time. Indeed, evolutionists believe this is a proven fact, beyond all reasonable doubt.

It would be difficult to imagine a more absurd claim. So let’s have a look at the details of this line of thinking. Here is a recent paper from the Royal Society, representing the state of the art in evolutionary thinking on this topic. The paper claims to provide a detailed explanation of how early evolution produced action potential technology.

Sounds promising, but when evolutionists speak of “details,” they have something slightly different in mind. Here are several passages from the paper which reveal that not only is there a lack of details, but that the study is thoroughly unscientific.

We propose that the next step in the evolution of eukaryote DCS [membrane depolarization (through uncontrolled calcium influx), contraction and secretion] coupling has been the recruitment of stretch-sensitive calcium channels, which allow controlled influx of calcium upon mechanical stress before the actual damage occurs, and thus anticipate the effects of membrane rupture.

The recruitment of calcium channels? And exactly who did the recruiting? Here the authors rely on vague terminology to paper over a host of problematic details of just how random mutations somehow performed this recruiting.

To prevent the actual rupture, the first role of mechanosensory Ca++ channels might have been to pre-activate components of the repair pathway in stretched membranes.

“To prevent”? Let’s spell out the logic a little more clearly. The authors are hypothesizing that these calcium channels evolved the ability to pre-activate the repair pathway “to prevent” actual rupture. By spelling out the logic a bit more clearly, we can see more easily the usual teleology at work. The evolution literature is full of teleology, and for good reason. Evolutionists are unable to formulate and express their ideas without it. The ever-present infinitive form is the tell-tale sign. Aristotelianism is dead—long live Aristotelianism.

As another anticipatory step, actomyosin might have been pre-positioned under the plasma membrane (hence the cortical actomyosin network detected in every eukaryotic cell) and might have also evolved direct sensitivity to stretch … Once its cortical position and mechanosensitivity were acquired, the actomyosin network could automatically fulfil an additional function: cell-shape maintenance—as any localized cell deformation would stretch the cortical actomyosin network and trigger an immediate compensatory contraction. This property would have arisen as a side-effect (a ‘spandrel’) of the presence of cortical actomyosin for membrane repair, and quickly proved advantageous.

An “anticipatory step”? “Pre-positioning”? Actomyosin “evolved” sensitivity to stretch? The position and mechanosensitivity “were acquired”? The network could “fulfil an additional function”? Sorry, but molecular machines (such as actomyosin) don’t “evolve” anything. There is more teleology packed into these few sentences than any medieval tract. And for good measure the authors also add the astonishing serendipity that this additional function “would have arisen as a side-effect.” That was lucky.

Once covering the cell cortex, the actomyosin network acquired the ability to deform the cell by localized contraction.

The actomyosin network “acquired the ability” to deform the cell by localized contraction? Smart move on the part of the network. But may we ask just how did that happen?

Based on the genomic study of the protist Naegleria which has a biphasic life cycle (alternating between an amoeboid and a flagellated phase), amoeboid locomotion has been proposed to be ancestral for eukaryotes. It might have evolved in confined interstitial environments, as it is particularly instrumental for cells which need to move through small, irregularly shaped spaces by exploratory deformation.

Amoeboid locomotion evolved “as it is particularly instrumental.” No infinitive form but this is no less teleological. Things don’t evolve because they are “instrumental.” What the authors fail to inform their readers of is that this would require an enormous number of random mutations.

One can hypothesize that, if stretch-sensitive calcium channels and cortical actomyosin were part of the ancestral eukaryotic molecular toolkit (as comparative genomics indicates), membrane deformation in a confined environment would probably trigger calcium influx by opening of stretch-sensitive channels, which would in turn induce broad actomyosin contraction across the deformed part of the cell cortex, global deformation and cell movement away from the source of pressure.

The concept of a “molecular toolkit” is standard in evolutionary thought, and another example teleological thinking.

One can thus propose that a simple ancestral form of amoeboid movement evolved as a natural consequence of the scenario outlined above for the origin of cortical actomyosin and the calcium–contraction coupling; once established, it could have been further elaborated.

Amoeboid movement evolved “as a natural consequence,” and “once established” was “further elaborated”? This is nothing more than teleological story-telling with no supporting evidence.

It is thus tempting to speculate that, once calcium signalling had gained control over primitive forms of amoeboid movement, the same signalling system started to modify ciliary beating, possibly for ‘switching’ between locomotor states.

Calcium signaling “gained control” and then “started to modify” ciliary beating “for ‘switching’ between locomotor states”? The “for switching” is yet another infinitive form, and “gained control” is an active move by the calcium signaling system. Pure, unadulterated, teleology.

Possibly, in ancestral eukaryotes calcium induced a relatively simple switch (such as ciliary arrest, as still seen in many animal cells and in Chlamydomonas in response to high Ca++ concentrations), which was then gradually modified into more subtle modulations of beating mode with a fast turnover of molecular actors mediated by differential addition, complementation and loss.

“Calcium induced a relatively simple switch”? Sorry, ions don’t induce switches, simple or otherwise. And the switch “was then gradually modified into more subtle modulations”? Note how the passive voice obviates those thorny details. The switch “was modified” conveniently omits the fact that such modification would have to occur via random mutation, one mutation at a time.

Alternatively, control of cilia by calcium could have evolved convergently—but such convergence would then have been remarkably ubiquitous, as there seems to be no eukaryotic flagellum that is not controlled by calcium in one way or another.

“Could have evolved convergently”? And exactly how would that happen? At least the authors then admit to the absurdity of that alternative.

Unfortunately, they lack such sensibility for the remainder of the paper. As we saw above, the paper is based on a sequence of teleological thinking. It falls into the evolutionary genre where evolution is taken, a priori, as a given. This going in assumption underwrites vast stretches of teleological thought, and cartoon-level story telling. Not only is there a lack of empirical support, but the genre is utterly unscientific, as revealed by even a mildly critical reading.

And needless to say, the paper does absolutely nothing to alleviate the problem we began with. The many leaps of logic and reasoning in the paper reveal all manner of monumental changes evolution requires to construct nerve cells and the action potential technology. We are not looking at a narrative of minute, gradual changes, each contributing to the overall fitness. Many, many simultaneous mutations are going to be needed. Even a conservative minimum number of 100 simultaneous mutations leads to the untenable result of a one in 10^800 chance of occurring.

It’s not going to happen. Religion drives science, and it matters.

Saturday, February 10, 2018

Here is How Evolutionists Respond to the Evidence

Unresponsive

Mutations are rare and good ones are even more rare. One reason mutations are rare is because there are sophisticated error correction mechanisms in our cells. So according to evolution random mutations created correction mechanisms to suppress random mutations. And that paradox is only the beginning. Because error correction mechanisms, as with pretty much everything else in biology, require many, many mutations to be created. If one mutation is rare, a lot of mutations are astronomically rare. For instance, if a particular mutation has a one-in-a-million (one in 10^6) chance of occurring in a new individual, then a hundred such particular mutations have a one in 10^600 chance of occurring. It’s not going to happen.

How do evolutionists reckon with this scientific problem?

First, one common answer is to dismiss the question altogether. Evolution is a fact, don’t worry about the details. Obviously this is not very compelling.

Second, another common answer is to cast the problem as a strawman argument against evolution, and appeal to gradualism. Evolutionists going back to Darwin have never described the process as “poof.” They do not, and never have, understood the process as the simultaneous origin of tens or hundreds, or more mutations. Instead, it is a long, slow, gradual process, as Darwin explained:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case […] Although the belief that an organ so perfect as the eye could have been formed by natural selection, is enough to stagger any one; yet in the case of any organ, if we know of a long series of gradations in complexity, each good for its possessor, then, under changing conditions of life, there is no logical impossibility in the acquirement of any conceivable degree of perfection through natural selection

The Sage of Kent could find “no such case”? That’s strange, because they are ubiquitous. And with the inexorable march of science, it is just getting worse. Error correcting mechanisms are just one example of many. Gradualism is not indicated.

What if computer manufacturers were required to have a useful, functional electronic device at each step in the manufacturing process? With each new wire or solder, what must emerge is a “long series of gradations in complexity, each good for its possessor.”

That, of course, is absurd (as Darwin freely confessed). From clothing to jet aircraft, the manufacturing process is one of parts, tools, and raw materials strewn about in a useless array, until everything comes together at the end.

The idea that every single biological structure and design can be constructed by one or two mutations at a time, not only has not been demonstrated, it has no correspondence to the real world. It is just silly.

What evolution requires is that biology is different, but there is no reason to believe such a heroic claim. The response that multiple mutations is a “strawman” argument does not reckon with the reality of the science.

Third, some evolutionists recognize this undeniable evidence and how impossible evolution is. Their solution is to call upon a multiverse to overcome the evidence. If an event is so unlikely it would never occur in our universe, just create a multitude of universes. And how many universes are there? The answer is, as many as are needed. In other words, when confronted with an impossibility, evolutionist simply contrive a mythical solution.

Forth, another common response that evolutionists make is to appeal to the fitness of the structure in question. Biological designs, after all, generally work pretty well, and therefore have high fitness. Is this not enough to prove that it evolved? For evolutionists, if something helps, then it evolves. Presto.

To summarize, evolutionists have four different types of responses to the evidence, and none of the responses do the job.

Religion drives science, and it matters.

Saturday, January 27, 2018

Early Complexity: A Case Study of Evolutionary Theory

No Matter How Perplexing

Nature does not make jumps. That old canon of natural history, as Darwin called it, goes back centuries and was heartily endorsed and adopted by evolutionary theory. Here are representative quotes from Origin, 1st edition, explaining important this doctrine was to Darwin:

I have been astonished how rarely an organ can be named, towards which no transitional grade is known to lead. The truth of this remark is indeed shown by that old canon in natural history of "Natura non facit saltum." We meet with this admission in the writings of almost every experienced naturalist; or, as Milne Edwards has well expressed it, nature is prodigal in variety, but niggard in innovation. Why, on the theory of Creation, should this be so? [194]

On the theory of natural selection we can clearly understand the full meaning of that old canon in natural history, "Natura non facit saltum." This canon, if we look only to the present inhabitants of the world, is not strictly correct, but if we include all those of past times, it must by my theory be strictly true. [206]

The canon of "Natura non facit saltum" applies with almost equal force to instincts as to bodily organs. [210]

the canon in natural history, of "natura non facit saltum" is applicable to instincts as well as to corporeal structure, and is plainly explicable on the foregoing views, but is otherwise inexplicable,—all tend to corroborate the theory of natural selection. [243]

As natural selection acts solely by accumulating slight, successive, favourable variations, it can produce no great or sudden modification; it can act only by very short and slow steps. Hence the canon of "Natura non facit saltum," which every fresh addition to our knowledge tends to make more strictly correct, is on this theory simply intelligible. We can plainly see why nature is prodigal in variety, though niggard in innovation. But why this should be a law of nature if each species has been independently created, no man can explain. [471]

In these and other passages Darwin explained the fundamental evolutionary view and prediction that evolution and natural selection produce gradual change with no sudden changes or jumps.

At this point, more than a century and a half later, that fundamental prediction of evolution has been falsified so many times by the empirical evidence it is a wonder there is anyone left believing in the theory.

One way that this prediction has been falsified, among many, is in the finding of early complexity. Evolutionists of course expected that the history of life would reveal a gradual increase in complexity. But as I have discussed many times here, life does not fit this evolutionary expectation. Instead the very earliest life forms reveal high complexity.

For example, as science writer (and evolutionist) Amy Maxmen explains, Amoebas contain hundreds of times more DNA than humans, and this “just didn’t make sense.”

amoebas date back farther in time than humans, and simplicity is considered an attribute of primitive beings. It just didn’t make sense.

The amoeba versus human comparison was just one example of how genome size contradicts evolutionary theory. What about the number of genes? Here again, evolution makes a clear prediction, as Maxmen explains:

Simple, early organisms would have fewer genes than complex ones, they [evolutionists] predicted

And here again, the evolution prediction was demolished by the science. For example, evolutionists were surprised to find sea anemones have more genes than insects, in spite of arising earlier. That, admits Maxmen, “meant animals might have been genetically complex from the start.”

These sorts of findings also contradict the evolutionary tree. Your high school biology book said that the new genetic data perfectly corroborated the traditional morphological data. Evolutionists have triumphantly celebrated the confirmation that the molecular sequence data provided to pre-existing evolutionary trees.

But that celebration was premature. In fact, study after study have found there is no such corroboration. In fact, as I have documented many times, morphological data across the species contradict the evolutionary tree (i.e., they do not fall into an evolutionary common descent pattern), and the new molecular data simply continued that trend.

Then molecular analyses did something else. They rearranged the order of branches on evolutionary trees. Biologists pushed aside trees based on how similar organisms looked to one another, and made new ones based on similarities in DNA and protein sequences. The results suggested that complex body parts evolved multiple times and had also been lost.

In other words, the scientific data contradict the theory. The result is that evolutionists have had to concoct increasingly complex and bizarre epicycles to try to explain the data. This includes complex structures evolving, then disappearing, then re-evolving, all in the same lineage, as well as independently evolving in a separate lineage. As Maxmen explains:

Furthermore, the idea that complex parts like a brain and nervous system—including nerve cells, synapses, and neurotransmitter molecules—could evolve separately multiple times perplexes evolutionary biologists because parts are gained one at a time. The chance of the same progression happening twice in separate lineages seems unlikely—or so biologists thought.

This is a tautology. Whatever we observe, evolution somehow created it, no matter how ridiculous the narrative becomes. An unfair criticism? Consider Maxmen’s conclusion:

When new data suggests a rearrangement, it must be considered no matter how perplexing the conclusion seems.

In other words, the plausibility of evolution is not a consideration. No matter “how perplexing” are the data, we must find a way to force fit it into the theory.

Religion drives science, and it matters.

Tuesday, January 23, 2018

Embryonic Development Reveals Staggering Complexity

Oh My

I recently cited a paper on the evolution of embryonic development and how the evidence contradicts evolutionary theory and common descent. Even the evolutionists, though in understated terms, admitted there were problems. Evolutionary analyses are “reaching their limits,” it is difficult to “conclude anything about evolutionary origins,” genetic similarities “do not necessarily imply common ancestry,” and “conserved regulatory networks can become unrecognizably divergent.” In other words, like all other disciplines within the life sciences, embryonic development is not working. The science contradicts the theory.

But there is much more to the paper, and as a reader noticed, the authors give a rather blunt admission of the magnitude of the problem, not often seen in the literature:

One of the main reasons for Duboule’s pessimism about the return of the EvoDevo comet is the staggering complexity and diversity of cellular and developmental regulatory processes. The configuration space for realistic models of such systems is vast, high dimensional, and potentially infinitely complex.

Staggering complexity? Staggering diversity? The configuration space is vast and high-dimensional?

And it is potentially infinitely complex?

And we are to believe this is the product of random mutations?

Religion drives science, and it matters.

Sunday, January 21, 2018

About That RNA World Hypothesis

It Just Doesn’t Make Sense

Given its widespread popularity and acceptance you might not have realized that the so-called RNA-World hypothesis suffers from some dramatic problems. At the top of the list is the rather awkward fact that there is, err, no evidence for it. While skeptics have pointed this out for years, we now see evolutionists coming clean on this inconvenient truth as well. To wit, here is how Peter Wills and Charles Carter open their recent BioSystems paper:

The RNA World is a widely-embraced hypothetical stage of molecular evolution, devoid of protein enzymes, in which all functional catalysts were ribozymes. Only one fact concerning the RNA World can be established by direct observation: if it ever existed, it ended without leaving any unambiguous trace of itself.

Even this is a bit of an understatement. Because without the prior assumption of evolution, which can and has underwritten a wide range of speculation, there is precisely zero reason to believe this wild hypothesis. No organisms have ever been discovered that demonstrate the RNA World hypothesis in action. Nor have scientists ever constructed any such organisms in their laboratories. This is not too surprising because no one has even produced anything remotely close to a detailed design of how such organisms could function.

Wills and Carter also point out negative evidences such as catalysis (RNA enzymes lack the ability to function over a wide range of temperatures) and the “impossible obstacles” to the hypothetical yet necessary transition from the RNA World to something resembling today’s extant cells. As Carter explains:

Such a rise from RNA to cell-based life would have required an out-of-the-blue appearance of an aaRS [aminoacyl-tRNA synthetase]-like protein that worked even better than its adapted RNA counterpart. That extremely unlikely event would have needed to happen not just once but multiple times—once for every amino acid in the existing gene-protein code. It just doesn’t make sense.

Indeed, it just doesn’t make sense. And yet in spite of these obvious problems, the RNA World has been a textbook staple, presented as a plausible and likely example of how early life evolved.

Religion drives science, and it matters.

Friday, January 19, 2018

How Embryonic Development Bears on Evolution

Follow the Theory

In order for evolution to have occurred, the intricate embryonic development stages of species must have evolved. Indeed, the developmental pathways of the species would be crucial in such a process. If we are to believe the evolutionary claim that the species spontaneously arose, then untold embryonic development pathways must have somehow undergone massive change. But while evolutionists expected the study of such evolution of development to yield great insight into the evolutionary process and history, it has underwhelmed. This shortcoming is well known, as exemplified in this 2015 paper:

First, traditional comparative approaches to the evolution of development—whether focused on the morphological or on the molecular/genetic level—are reaching their limits in terms of explanatory power.

Except that this is an overstatement. To say that comparative approaches “are reaching their limits in terms of explanatory power” is to suggest that there was, at one time, some significant level of explanatory power provided. That would be a very optimistic interpretation of the data.

The paper continues:

The more we learn about the evolution of pattern-forming gene networks, or the ontogeny of complex morphological traits, the more it becomes clear that it is less than straightforward to conclude anything about evolutionary origins or dynamics based on such comparisons alone.

“Less than straightforward”? Let’s be clear—a more accurate descriptor would be “impossible.” In fact, the evidence does not reveal an evolutionary history, but rather is supported by the theory. Evolutionary theory does not follow the data, as Huxley prescribed, but rather the data follow the theory.

The paper continues:

On the one hand, homoplasy or convergent evolution abounds at all levels of investigation. One of the most lauded major insights of EvoDevo is that a common toolkit of genes and signaling pathways is reused over and over again to create a large diversity of different body plans, shapes, and organs.

Most lauded major insights? That would be the mother of all euphemisms. Evolutionists are always rationalizing devastating contradictions as teachable moments, and here we have yet another example. To cast the nonsensical finding of a “common toolkit” as a “major insight” is laughable.

This becomes clear as the paper continues:

Because of this, similarities in gene expression patterns or morphological structure often do not necessarily imply common ancestry, since they may as well reflect the frequent reuse of the same regulatory or morphogenetic modules.

Profound similarities “do not necessarily imply common ancestry.” We have now entered a Lewis Carroll world, as Sober would put it. The whole point of evolution was that such similarities revealed and mandated common descent. But now, we have the exact opposite, as similarities cannot be due to common descent, but must have arisen independently. And this is an “insight”? A fundamental prediction is demolished and evolutionists do not skip a beat. This is not science.

But it gets worse:

On the other hand, developmental system drift allows conserved networks to change considerably in terms of their component genes and regulatory interactions without changing the phenotypic outcomes such systems produce. This means that even functionally conserved regulatory networks can become unrecognizably divergent at the molecular and genetic level, especially across large evolutionary time spans.

We have now reached the height of absurdity. First, profound developmental similarities were found which could not be ascribed to common descent. Now we find that those developmental pathways which can (theoretically) be ascribed to common descent are profoundly different.

When will this bad dream end? The science contradicts the theory. Over. And over. And over. And over.

It never ends. Religion drives science, and it matters.

[h/t: El Hombre]

Wednesday, January 17, 2018

Allmon and Ross Demolish Evolution

It Gets Worse

Last time we saw, in a new paper, evolutionists Warren Allmon and Robert Ross reformulate the argument for evolution from homologous structures. The paper makes several mistakes, but is important because it is a rare case of evolutionists (i) recognizing the religion in evolutionary thinking, and (ii) trying to do something about it. In this case the religion is in the claim that God would not have created non optimal homologies (such as vestigial structures). Allmon and Ross attempt to remove the religion by restating the claim as: God did not have to create such homologies. It is good that evolutionists are finally recognizing the religion, after having been in denial for so many years. But Allmon and Ross’ solution fails on several counts.

The first failure of Allmon and Ross’ solution is that it strips the power of the argument. The traditional religious arguments (i.e., God would not create those structures) at least had the virtue of providing a strong argument for evolution. Granted it was a religious argument, and granted one had to agree with that particular religion. And granted it ignored the problems of process and pattern (more below on that). And granted it turned evolution into, as Elliott Sober hinted, a “Lewis Carroll world in which down is up,” because the argument required evidence that is unlikely on evolution. The more unlikely, the better. Such is the logic of evolution’s religion. But after all those caveats, at least it provided a strong argument for evolution.

With design refuted, evolution had to be true, no matter how many problems it had. But with Allmon and Ross’ reformulation, design is not refuted. Now the advantage for evolution is not that the alternative is false or even highly unlikely, but that the alternative does not specify what we observe whereas evolution does. Allmon and Ross triumphantly conclude their new formulation is a powerful argument for evolution. They apparently think their reformulation is merely a minor tweak, and that their new argument is just as strong as the traditional argument. It isn’t. There is no free lunch. What Allmon and Ross fail to understand is that this is a much weaker argument.

But it gets worse.

The second failure of Allmon and Ross’ solution is that it never did get rid of the religion as they had hoped. Allmon and Ross naively assume that the claim God may or may not create these homologies is merely an obvious point of fact. This is a deep subject into which Allmon and Ross have rushed in, but suffice it to say that it is not at all clear that God can go with either world. Leibniz undoubtedly would disagree. The Lutheran polymath would argue that because of His perfection and other attributes, God cannot just create any old world. The bottom line, and one which Allmon and Ross are blissfully na├»ve of, is that like it or not, claims about God are religious.

But it gets worse. Much worse.

Not only did Allmon and Ross utterly misapprehend and expose the homology argument, they have, in fact, altogether demolished evolutionary theory. Remember, with their reformulation it becomes utterly crucial that evolution predicts what we observe. In other words, evolution must predict the pattern of similarities and differences we observe across the species. This is because their new formulation was that while design can explain a common descent pattern or other patterns, evolution is narrowly restricted to the common descent pattern.

With that the two Harvard trained Epicureans just inadvertently blew up evolution. This is because what we actually observe is not the common descent pattern.

The actual comparisons between the species have contradicted the common descent pattern over and over. It is, as we have documented here so many times, not even close.

If evolution predicts the common descent pattern, then by modus tollens, evolution is false.

Religion drives science, and it matters.

Monday, January 15, 2018

Warren Allmon on the Argument from Homology

An Enormous Concession

I once debated two evolutionists on the campus of Cornell University. In that debate I raised several fundamental problems with evolutionary theory. The problems that I pointed out fell into two broad categories: process and pattern. In the latter category, I pointed out that the keystone argument for evolution from homology had badly failed. Unfortunately, that failure was waved off and went unaddressed by the evolution professors. That may not have been the case had Warren Allmon been able to participate. Allmon, Director of the Cornell University-affiliated Paleontological Research Institution (PRI), has thought more deeply about the homology argument than most evolutionists. Now in 2018, he has published, along with adjunct professor Robert Ross, a new paper containing a very important concession.

As is typical, the new Allmon/Ross paper makes several serious scientific errors, either through ignorance, denial, confirmation bias, or whatever. The paper also relies heavily religious claims and arguments, which again is typical.

I have covered this religiously-driven phony science here many times. And in future posts I will address the specifics in the Allmon/Ross paper.

But most importantly, the paper does accomplish something new. The paper takes several turns, but in the end Allmon and Ross do recognize, at least somewhat, the presence of religion in evolutionary thought. To remedy this, they downsize the argument from homology.

In its canonical form, this keystone argument proves evolution by the process of elimination. That is, it refutes design and independent creation, leaving naturalistic evolution, in one form or another, as the only solution. God wouldn’t have created these lousy designs, according to evolutionists, so the designs must have arisen naturalistically. As usual, it is the religion that provides the certainty.

This isn’t science.

Rather than deny this obvious fact (see here for examples of such denial), Allmon and Ross ultimately admit to it (after appealing to it repeatedly), and seek to reformulate the argument from homology without the religion. They do this as follows.

Rather than claiming God would not have created non optimal homologies (such as vestigial structures), Allmon and Ross walk back the claim to say merely that God did not have to create such homologies. Under independent, divine, creation, God could have done it differently. Allmon and Ross then contrast this with descent with modification which, they say, necessarily would have resulted in such homologies.

So you have Theory A (design) which can accommodate Observation X or ~X (not X). And you have Theory B (evolution) which requires Observation X, and cannot accommodate ~X. Our observation of X, therefore, makes Theory B more probable.

Readers here will know there are enormous problems with this argument. It fails badly, right out of the gate. And I will discuss these failures in the future. But before we get to that, it is important to understand the implications of the argument, even without its problems.

In their attempt to save the theory, what Allmon and Ross have done is to provide an enormous concession. What traditionally has been an iron-clad, unquestionable, textbook proof of evolution, now becomes a minor Bayesian term, slightly improving the probability of evolution.

This is a monumental concession, neutering the keystone argument for evolution. Why should anyone believe in the heroic claim that the biological world arose by itself if the strongest argument merely increases its probability by some unspecified amount?

Sunday, December 24, 2017

Evolutionist: “Jesus had nothing to say about … abortion”

And So This Is Christmas

On this 2017 Christmas holiday an evolutionist has proclaimed that the man whose birthday is celebrated today did not come out against abortion. She wrote:

Jesus had nothing to say about … abortion … He did have quite a lot to say about the poor and the vulnerable, and maybe that’s a good place to start.

Readers shouldn’t need a lengthy explanation of the problem here. Theologians refer to this as imposing an idea onto Scripture rather than reading it out of Scripture. To say that Jesus said nothing about abortion but—in the very next breath—admit that He did instruct us to protect the vulnerable, does not make sense.

It would be like saying Jesus said nothing about stabbing people in the back, though he did admonish us not to murder, but that’s different.

Or again, it would be like saying Jesus said nothing about being nice to people, though he did tell us to do to others as we would have them do to us. But that’s different.

No, it isn’t different.

The problem here is that babies are, if anything, “vulnerable.” One need not stretch definitions to see the problem. One does not need an imagination here to get it.

Babies. Are. Vulnerable.

It is not that this writer made a minor slip here. This assertion is nothing short of absurd.

In fact, the claim is so silly and ridiculous, I would not normally bring it to the attention of readers. If you showed me this quote, I would assume it is from some phony troll or chatroom.

But it isn’t, and this is where the problem becomes more important. The quote is from a newspaper article. And it is not from just any old newspaper. It is from, err, the top newspaper in the world—The New York Times.

Nor is the article deeply buried somewhere. It is prominently displayed above the fold, top right on the website.

Nor is the author someone who accidently slipped a piece into The Gray Lady. In fact, the piece was written by, err, Contributing Op-Ed writer Margaret Renkl.

Renkl’s point is that followers of Jesus need to get with the program, and drop the whole pro life thing. After all, Jesus had nothing to say about abortion.

Right?

The argument isn’t even wrong, and yet there it is. Complete absurdity parading as words of wisdom, as if in some Hans Christian Andersen story.

Religion drives science, and it matters.

Sunday, December 17, 2017

Evolutionists: Our Findings Suggest That Similarities in Bilateria Evolved Independently

Not Even Wrong

This week one of the top scientific journals in the world published what would seem to be a ground breaking paper. The paper claims to have found evidence for the independent evolution of nervous system similarities across the Bilateria. As the abstract explains:

Our findings … suggest that the similarities in dorsoventral patterning and trunk neuroanatomies evolved independently in Bilateria.

By the end of the manuscript the authors are even more confident:

Therefore, the expression of dorsoventral transcription factors evolved independently from the trunk neuroanatomy at least in certain bilaterian lineages

This is a monumental claim, but there is only one problem: It is blatantly false. The paper’s findings did not “suggest” the evolution, independent or otherwise, of the transcription factor expression patterns. They certainly did not demonstrate, show or find such an incredible conclusion.

It would be difficult to overstate how misleading this paper is. It provided literally zero evidence for any such evolution. Nothing. Nada.

There simply is no such scientific evidence in the paper. The claim that they found that the expression of dorsoventral transcription factors evolved independently in certain bilaterian lineages is not even wrong.

Let’s be clear about this. I am not saying their claim is weak. I am not saying their claim is faulty. I am not saying they failed to make their case conclusively. The problem is they don’t have any case at all.

We cannot criticize the science because, well, there is no science. For a paper entitled “Convergent evolution of bilaterian nerve cords,” one would have expected at least some evidence and explanation for the evolution of bilaterian nerve cords.

Unfortunately papers such as this inform journalists and science writers. They report that scientists have now discovered yet another aspect of evolution. It is yet another example of how science proves evolution.

In fact, if one is looking for a meaningful takeaway, what the study did find is that the expectations of evolution—that nervous system similarities would align with the evolutionary tree—turned out to be, like so many other of evolution’s predictions—false. But that doesn’t fit the narrative.

Religion drives science, and it matters.

Monday, November 6, 2017

Protein Mutations Are Highly Coupled

A Rugged Fitness Landscape

A new study from Michael Harms’ laboratory at the University of Oregon finds that potential amino acid substitutions in protein sequences are highly coupled. That is, if one residue mutates to a new amino acid, the swap impacts the other possible substitutions—they now have a different impact on the protein tertiary structure. As the paper explains:

Proteins exist as ensembles of similar conformations. The effect of a mutation depends on the relative probabilities of conformations in the ensemble, which in turn, depend on the exact amino acid sequence of the protein. Accumulating substitutions alter the relative probabilities of conformations, thereby changing the effects of future mutations. This manifests itself as subtle but pervasive high-order epistasis. Uncertainty in the effect of each mutation accumulates and undermines prediction. Because conformational ensembles are an inevitable feature of proteins, this is likely universal.

This coupling leads to a “profound unpredictability in evolution,” and the authors conclude that “detailed evolutionary predictions are not possible given the chemistry of macromolecules.”

This finding seems to confirm what many evolutionists have said for decades—that evolution is a contingent, not law-like, process:

These [macro]evolutionary happenings are unique, unrepeatable, and irreversible.” – Theodosius Dobzhansky, 1957.

Laws and experiments are inappropriate techniques” for explaining evolutionary events and processes. – Ernst Mayr

What science needs are “plausible scenarios for a fully material universe, even if those scenarios cannot be currently tested.” – Victor Stenger, 2004

any replay of the tape would lead evolution down a pathway radically different from the road actually taken. – Stephen Jay Gould

All of this is in direct contradiction to the science, which reveals undeniable patterns in biology that have been repeated over and over. From the pervasive instances of convergence, recurrence, and all kinds of other “ence’s”, to the non adaptive patterns discussed by Michael Denton, the biological is anything but haphazard or random. Clearly, the same solution, for whatever reason, is used repeatedly across a wide range of species, in various patterns.

This is a clear falsification of an evolutionary expectation expressed across many years, and widely held by a consensus of experts.

But there is another problem with these protein findings. In addition to confirming the complexity and coupling of protein folding, the findings also seem to corroborate what theoretical and experimental studies have shown for years, that the fitness landscape of macromolecules in general, and proteins in particular, is rugged.

The problem of evolving a protein is difficult for several reasons. First, protein function drops off rapidly with only a few mutations. Very quickly a protein loses its function as you move away from the native sequence.

Second, random or starting sequences are stuck in a flat and rugged fitness landscape. There is little sign of a the kind of smooth and gradually increasing fitness landscape that would aid evolution’s enormous task of figuring out how proteins could evolve.

These problems are just getting worse, and this new finding a good example of that trend.

Religion drives science, and it matters.

Blindness in Cave Fish is Due to Epigenetics

Evolutionists Say “We See”

A recent paper out of Brant Weinstein’s and William Jeffery’s laboratories on eye development, or the lack thereof, in blind cave fish has important implications for evolutionary theory (paper discussed here). The study finds that the loss of eyes in fish living in dark Mexican caves is not due to genetic mutations, as evolutionists have vigorously argued for many years, but due to genetic regulation. Specifically, methylation of key development genes represses their expression and with it eye development in this venerable icon of evolution. But the finding is causing yet more problems for evolutionary theory.

Darwin appealed to the blind cave fish in his one long argument for evolution. It is a curious argument in many ways, and the first sign of problems was in Darwin’s presentation where he flipped between two different explanations. At one point he explained the loss of vision in the cave fish as an example of evolutionary change not due to his key mechanism, natural selection. Instead, the Sage of Kent resorted to using the Lamarckian mechanism or law of “use and disuse.” Privately Darwin despised and harshly criticized Lamarck, but when needed he occasionally employed his French forerunner’s ideas.

Elsewhere Darwin hit upon a natural selection-based mechanism for the blind cave fish, explaining that elimination of the costly and unneeded vision system would surely raise the fitness of the hapless creatures.

This latter explanation would become a staple amongst latter day evolutionary apologists, convinced that it mandates the fact of evolution. Anyone who has discussed or debated evolutionary theory with today’s Epicureans has likely encountered this curious argument that because blind cave fish lost their eyes, therefore the world must have arisen by itself.

Huh?

To understand the evolutionary logic, or lack thereof, one must understand the history of ideas, and in particular the idea of fixity, or immutability, of species. According to evolutionists, species are either absolutely fixed in their designs, or otherwise there are no limits to their evolutionary changes and the biological world, and everything else for that matter, spontaneously originated.

Any evidence, for any kind of change, no matter how minor, is immediately yet another proof text for evolution, in all that the word implies.

Of course, from a scientific perspective, the evidence provides precisely zero evidence for evolution. Evolution requires the spontaneous (i.e., by natural processes without external input) creation of an unending parade of profound designs. The cave fish evidence shows the removal, not creation, of such a design.

The celebration of such evidence and argument by Darwin and his disciples reveals more about evolutionists than evolution. That they would find this argument persuasive reveals their underlying metaphysics and the heavy lifting it performs. It is all about religion.

We are reminded of all this with the news of Weinstein’s new study. But we also see something new: The insertion, yet again, of Lamarck into the story. The irony is that the epigenetics, now revealed as the cause of repressed eye development in the cave fish, hearkens back to Lamarck.

Darwin despised Lamarck and later evolutionists made him the third rail in biology. Likewise they have pushed back hard against the scientific findings of epigenetics and their implications.

The environment must not drive biological change.

False.

Well such biological change must not be transgenerational.

False.

Well such inheritance must not be long lasting, or otherwise robust.

False again.

This last failure is revealed yet again in the new blind cave fish findings.

False predictions count. A theory that is repeatedly wrong, over and over, in all of its fundamental expectations, will eventually be seen for what it is.

The rise of epigenetics is yet another such major failure. Evolutionists pushed back against it because it makes no sense on the theory, and that means it cannot now be easily accommodated.

One problem is that epigenetics is complex. The levels of coordination and intricacy of mechanism are far beyond evolution’s meager resources.

It’s not going to happen.

Another problem is the implied serendipity. For instance, one epigenetic mechanism involves the molecular tags places on the tails of the DNA packing proteins called histones. While barcoding often seems to be an apt metaphor for epigenetics, the tagging of histone tails can influence the histone three dimensional structures. It is not merely an information-bearing barcode. Like the tiny rudder causing the huge ship to change course, the tiny molecular tag can cause the much larger packing proteins to undergo conformational change, resulting in important changes in gene accessibility and expression.

This is all possible because of the special, peculiar, structure and properties of the histone protein and its interaction with DNA. With evolution we must believe this just happened to evolve for no reason, and thus fortuitously enabled the rise of epigenetics.

Another problem with epigenetics is that it is worthless, in evolutionary terms that is. The various mechanisms that sense environmental shifts and challenges, attach or remove one of the many different molecular tags to one of the many different DNA or histone locations, propagate these messages across generations, and so forth, do not produce the much needed fitness gain upon which natural selection operates.

The incredible epigenetics mechanisms are helpful only at some yet to be announced future epoch when the associated environmental challenge presents itself. In the meantime, selection is powerless and according to evolution the incredible system of epigenetics, that somehow just happened to arise from a long, long series or random mutations, would wither away with evolution none the wiser.

These are the general problems with epigenetics. In the case of the blind cave fish, however, there is possible explanation. It is a longshot, but since this case specifically involves the loss of a stage of the embryonic development, evolutionists can say that genetic mutations caused changes in the methylating proteins, causing them to be overactive.

This explanation relies on the preexistence of the various epigenetic mechanisms, so does not help to resolve the question of how they could have evolved. What the explanation does provide is a way for evolutionists to dodge the bullet presented by the specter of the cave fish intelligently responding to an environmental shift.

Such teleology in the natural world is not allowed.

So the evolutionary prediction is that these proteins will be found to have particular random changes causing an increase in their methylation function, in particular at key locations in key genes (i.e., the genes associated eye development).

That’s a long shot, and an incredible violation of Occam’s Razor.

My predictions are that (i) this evolutionary prediction will fail just as the hundreds that came before, and (ii) as with those earlier failures, this failure will do nothing to open the evolutionist’s eyes.

Religion drives science, and it matters.

Monday, October 23, 2017

World’s Oldest Tree is World’s Most Complex Tree

Makes Perfect Sense

We have often discussed the problem of “early complexity,” and how as we peer back in time—whether in the geographic strata or by phylogenetic reconstruct—things don’t get simpler. This makes no sense on evolution and this week’s news of a fossil specimen in northwest China, revealing and ancient, and highly complex, tree, just makes it worse. As one of the authors admitted:

This raises a provoking question: why are the very oldest trees the most complicated?

Fortunately evolution is a fact.

Thursday, October 12, 2017

Welcome to Alt-Science

Expelled

Sometimes it’s obvious, as in the case of the scientific research paper that was rejected after it was accepted. While the paper was well accepted and given positive comments from peer reviewers, certain members of the editorial board of a seemingly scientific journal noticed that the results had negative implications for evolution. And so months after the editor had told the authors he was happy “to proceed with publication,” the paper suddenly was, “on further reflection and discussion,” summarily rejected.

And what exactly was the “discussion” about? That “the unspoken implication of the article is that, probabilistically, random undirected evolution is impossible.”

And that, dear scientists, is not allowed.

Random undirected evolution is, by definition, a fact. Break that ground rule, and pay the price. This isn’t about science or truth. This is the alt-science that seeks to control everything from publications and textbooks to careers and funding.

Religion drives science, and it matters.