ARMAN’s Novel Genes and Unique tRNA Editing

As we have explained many times, being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought to create such a wonder. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought. So today’s falsification, though it falsifies one of evolution’s most treasured predictions, will be no different. Once again, evolutionists have great news.

According to evolutionists, one of the most powerful evidences for their notion that the world just happened to arise somehow on its own, is the underlying unity of biology’s fundamental biochemistry. From information storage in the DNA macromolecule to basic metabolism, the same designs are found across biology’s wide spectrum. As Niles Eldredge put it:

The basic notion that life has evolved passes its severest test with flying colors: the underlying chemical uniformity of life, and the myriad patterns of special similarities shared by smaller groups of more closely related organisms, all point to a grand pattern of descent with modification.

Likewise, Christian de Duve triumphantly declared:

Life is one. This fact, implicitly recognized by the use of a single word to encompass objects as different as trees, mushrooms, fish, and humans, has now been established beyond doubt. Each advance in the resolving power of our tools, from the hesitant beginnings of microscopy little more than three centuries ago to the incisive techniques of molecular biology, has further strengthened the view that all extant living organisms are constructed of the same materials, function according to the same principles, and, indeed, are actually related. All are descendants of a single ancestral form of life. This fact is now established thanks to the comparative sequencing of proteins and nucleic acids.

“The essential macromolecules of life,” explained philosopher Michael Ruse, “speak no less eloquently about the past than does any other level of the biological world.”

And exactly why is it that similarities at the molecular level mandate evolution. Why is it that a conserved DNA code must have arisen spontaneously? Evolutionists cannot explain how the DNA code arose on its own, but they are certain that it must have because it is conserved across the species.

Yes we know, such reasoning does not come from science, but we are getting ahead of ourselves. We can only address one fallacy at a time and the fallacy we are addressing here is not evolution’s hypocritical foundation of metaphysics, nor its illogical affirming of the consequent. Here we are addressing evolution’s failure on modus tollens. Or we might say, its denial of denying the consequent.

Simply and classically put, if P Implies Q, then Not Q Implies Not P. Or in plain English, if a theory makes a prediction, and that prediction turns out to be false, then the theory has a problem. It’s that simple.

To be sure, some predictions are soft and of less consequence. They are more like suggestions than predictions, and if they are found to be false then only minor adjustments are required. But if I insist my theory is confirmed by the success of a prediction, then the failure of that prediction spells trouble for my theory. I cannot claim victory if the prediction works while suffering no consequences when the prediction fails. I can’t have my cake and eat it too.

Not so with evolution. As we saw above the universal DNA code and conserved molecular machinery in all life was claimed to be proof texts for evolution. With such high accolades, one might think that counter indications would pose major problems for evolutionists. Not at all, for this is no ordinary theory.

When the DNA replication apparatus—a rather fundamental biochemical process—was found to be significantly different across different species, evolutionists didn’t miss a beat. Those different versions of DNA replication, we were told, probably evolved independently. Or maybe they diverged. Anyway they evolved, that was for certain.

Another interesting example is the archaeal Richmond Mine acidophilic nanoorganism, or ARMAN, found in microbial mats in the drainage of the acidic northern California mine owned by Ted Arman.

Referred to as enigmatic, the ARMAN species are morphologically unique. They are only a few hundred nanometers across—about a third the size of common bacteria—and some are found strangely attached (actually impaled by a protruding needle) to a nearby larger microbe in apparently some sort of symbiotic or parasitic relationship.

On the inside of this example of lineage-specific biology, the ARMAN species have about two orders of magnitude fewer ribosomes than common bacteria. And their genes don’t map nicely to other organisms. About a fifth of their genes are similar to bacterial genes, and a few of these have never been found except in bacteria. Meanwhile about a third of the ARMAN genes appear to be unique, with no known cousin genes in other species.

Some of the ARMAN species also have some unique molecular machinery. Specifically, they have a unique protein enzyme that edits newly transcribed genes that will become tRNA molecules. tRNA molecules have a three nucleotide reader on one end, and when charged have an amino acid attached to the other end. The type of amino acid corresponds to the type of reader at the other end, and the ribosome uses the tRNAs when translating a messenger RNA molecule according to the genetic code, to construct a protein.

The editing of tRNA genes is one of those fundamental molecular processes hailed by the evolutionists above which were supposed to “point to a grand pattern of descent with modification.” But when we look closely, what we actually find are violations of the pattern. A couple of the ARMAN species, for instance, suddenly show up with their own unique solution.

And if confirming evidence proves evolution, then contradictory evidence must harm evolution, right? Wrong. The first rule one learns for evolution is that all observations are supporting evidence. As the evolutionists concluded, the new finding “represents a new example of the coevolution of tRNA and their processing enzymes.”

You see the “underlying chemical uniformity of life,” such as it is, was never a proof text for evolution because it was never required by evolution. Different DNA codes, one off molecular machines, alternate DNA replication architectures, lineage-specific transcription regulation, unique epigenetic codes, and so forth, will never harm evolution. Contradictory scientific evidence does no damage because evolution never was about following the evidence. It was about interpreting the evidence through a particular theological lens. And like any good lens, this theological lens is transparent to those looking through it.

Religion drives science, and it matters.

Evolution’s Brute Spontaneity

As Michael Ruse and others have pointed out the language evolutionists use can be telling, but what is not discussed is that the language evolutionists do not use is also telling. Anyone familiar with the evolution genre cannot help but notice the curious use of design language. Teleology abounds as natural selection is described as “solving” this or that “problem.” As Ernst Mayr pointed out in Toward a New Philosophy of Biology, “The use of terms like purposive or goal-directed seemed to imply the transfer of human qualities, such as intent, purpose, planning, deliberation, or consciousness, to organic structures and to subhuman forms of life.” Of course for Ruse, Mayr and the evolutionists these are merely interesting asides. The persistence of teleological language in the literature is nothing more than a commentary on how we think and do science. Perhaps it reveals a certain laziness of thought, or perhaps it is a useful way of problem solving, but either way it is nothing more than a fiction. Sure the world looks designed, but we all know that such primitive teleological thinking has long since been exposed and rejected. After all, evolution is a fact.

This brings us to that language that evolutionists do not use. They explain that evolution is a fact, and they give long, flowery descriptions of this process. Organic chemicals coalesced in warm little ponds or along deep sea concentration gradients. Single celled organisms emerged and natural selection proceeded to act on naturally occurring biological variation. The drama unfolded as volcanoes, lightning and comets created just the right mix. Neutral and positive mutations produced innovative solutions to the challenges of the evolving biosphere, resulting in common ancestors and clades. Evolutionists display beautiful, detailed murals depicting this epic history.

But what is not said is that all of this just happened to occur, all on its own. In short, the world arose spontaneously. While evolutionists readily adopt design and teleological language, they eschew accurate, objective descriptions of what their theory actually claims. Evolutionists insist it is a fact that the world arose spontaneously, but they avoid such stark terms. They avoid this because such clarity reveals the absurdity of evolutionary thought.

Spontaneous action is an important concept in science. Everything from thunderstorms and snowflakes to proteins arise spontaneously. Indeed evolutionists often appeal to this phenomena as support. Snowflakes and proteins arise spontaneously, so why not everything else? As I have pointed out this argument fails badly, and in fact merely points out yet more problems for evolution.

But yet another fundamental problem for evolutionists is that the spontaneous formation of things like thunderstorms, snowflakes and proteins occurs within a context. Yes proteins fold spontaneously, but only in the right type of aqueous solution. Even more important, you need an unfolded protein to begin with. That is, you need hundreds of amino acids to be covalently bonded, one to the next, by peptide bonds. And furthermore, it must not be just any arbitrary sequence of amino acids, but from a special class of sequences which, yes, spontaneously folds.

So the right type of amino acid sequence needs to be specified, those amino acids need to be held together by peptide bonds, and the resulting unfolded chain needs to be placed into the right kind of aqueous solution. Then, yes, it will fold spontaneously.

The same logic applies to thunderstorms, snowflakes and everything else. There is a context within which these things spontaneously form, and the context is crucial. These things don’t just happen spontaneously without the proper context. And so whenever we speak of spontaneous action in science, it is understood that there is an implied context. Molecules A and B spontaneously bond to form molecule AB, but it is understood that molecules A and B are mixed together in the same test tube, at an appropriate temperature, concentration, and so forth.

So in science spontaneous action is not action that is free of context. There is no such thing, we might say, as brute spontaneity. Unless, that is, you are an evolutionist. Here we have yet another absurdity of evolutionary theory. You won’t find this in their beautiful murals or flowery textbook descriptions, but evolutionary thought is based on context-free, brute spontaneity.

Evolutionists appeal to changing allele frequencies, genetic mutations and other means of biological variation as their sources of innovation. And while such mechanisms show little evidence of being capable of designing nature’s incredible array of species, even if they could they would rely on the context of molecular biology—a context which according to evolution arose via, yes, evolution.

But it does not stop here. Molecular biology must have evolved within a context. A terrestrial environment, providing the right mix must have led to the origin of molecular biology, cellular life and the underlying biochemistry.

And again, the terrestrial environment must have evolved within a context of an early earth. And the earth must have evolved within a context of an evolving solar system. And the solar system evolved from a cloud of gas. And the gas evolved from, well, you get the idea.

Ultimately evolution has no starting point except for nothing. For evolutionists there can be no Prime Mover. Everything we see must have arisen from nothing. And while one might, with sufficient wine or song, dream of such unlikely possibilities, evolutionists insist that all of this is a scientific fact that must be acknowledged by all rational parties. Evolution’s absurdity is exceeded only by its confidence.

But in their insistence, evolutionists will never use such clarity. Like the cult that hides its true beliefs to newcomers, evolution covers over its absurdities with beautiful murals and descriptions. They scoff when they hear their theory accurately described. For that is the language that evolutionists do not use.

Religion drives science, and it matters.

The Rapid Origin of Domesticated Chicken

In the early 20th century modern genetics was integrated into evolutionary theory and the resulting neo Darwinism, or New Synthesis, was hailed as a great advance. Darwin didn’t know the details of how biological variation arose but now that gap was filled in—from changing allele frequencies to genetic mutations, modern genetics provided the answer. Biological variation arose from gene sequence variations. But this version 2.0 of Darwin’s theory would go long without its own difficulties, as exemplified yet again by recent research on the origin of the domesticated chicken.

With the onset of the New Synthesis evolutionists wasted little time exploring the power of their new agent of change: DNA mutations. But their expectations were soon dashed as mutations inevitably proved not to be a source of rich new biological innovation but rather of organic chaos and disaster. As usual evolutionists did not doubt their theory, but instead adjusted their hypotheses into the realm of the unfalsifiable. Yes mutations wrought havoc, but there must be those very rare cases that move toward biology’s new and fantastic designs. Wait long enough and the frog turns into a prince. To augment that narrative evolutionists later added another just-so story: mutations that are neutral—neither good nor bad—would accumulate and serve as a rich source of design options when an environmental shift occurred.

Meanwhile scientists were discovering, much to the chagrin of evolutionists, that populations adapt rapidly via intelligent encodings in the genome. It has little to do with random variations as evolutionists had expected, but instead involves incredible biological machinery that rapidly respond to environmental challenges, using an amazing variety of techniques. For example, teams of specially designed proteins chemically attach a carbon atom surrounded by three hydrogen atoms (a methyl group) to the DNA or to the protein hubs around which DNA is wrapped. These methyl groups act as encodings which influence how other proteins react. The result is that they can induce substantial phenotypic change to a population that directly and rapidly responds to environmental shifts.

Evolutionists resisted and denied these findings using the usual tactics of intimidation, dismissal, blackballing, and manipulation of the science. Were not such epigenetic mechanisms limited to physiological change within a lifetime? Of course that was false. Certainly these mechanisms could not establish lasting change. And of course this was also false.

This brings us to recent research that adds yet more evidence to the epigenetics story. The research finds that epigenetic mechanisms may be the cause of the rapid origin of domesticated chickens brought about by breeding, and that these epigenetic changes are reliably and stably inherited, resulting in lasting change in a population.

While this is yet another failure of evolutionary theory, there is more to the story. The new research also found that the inherited methylation differences were sometimes tissue-specific. This indicates yet more complexity of the epigenetic mechanisms, and reminds us of the serendipity underlying evolutionary theory.

If evolution is true, then all kinds of random events must have occurred which much later would serendipitously aid the cause of evolution. In this case, biology’s crucial adaptive change capability arises not from simple, blind DNA mutations, but from immensely complicated epigenetic mechanisms. So complex proteins happened to arise which, when fully assembled as teams, would produce incredible adaptive response mechanisms. Evolution must have constructed evolutionary mechanisms so that evolution could occur. It is yet another example of why it is, frankly, amazing that evolutionists continue in their dogmatic claims.

Richard Dawkins is Sure

The most famous atheist in the world, Richard Dawkins, says that he can’t be sure God does not exist. But in fact Richard Dawkins is sure of a great many religious and metaphysical claims. He is sure there are no miracles, he is sure the recurrent laryngeal nerve would not have been designed, and he is sure our photocells are bad designs. Evolutionists such as Richard Dawkins are quite certain about all kinds of religious and metaphysical claims which drive their so-called science. Whether or not an evolutionist such as Dawkins is an atheist is irrelevant. They believe all kinds of things about God, regardless of whether they believe in God. As Ernst Mayr once said:

People forget that it is possible to be intensely religious in the entire absence of theological belief. [Michael Ruse, Darwin and Design, p. 335]

Indeed, evolutionists are intensely religious. It is the foundation of their theory.

Religion drives science, and it matters.

The Scale of the Universe

Peer through a telescope at larger and larger objects in the universe, or through a microscope at smaller and smaller objects, and you continue to see form and structure. Here is a good illustration, from Cary Huang, of these different worlds (click on the image and once it loads use the wheel on your mouse to zoom in or out):

It is particularly amazing that all of this spontaneously arose.

Flying Squid

When Thor Heyerdahl sailed Kon-Tiki from Peru to the South Pacific islands he noticed that squids occasionally fell onto the ocean-going raft. Did these legendary cephalopods fly through the air? Indeed they do fly hundreds of feet using their patented water gun propulsion system. Like a rocket, the high momentum of the squid’s ejected water translates into impressive acceleration through the air. As one writer explained:

Squids are able to propel themselves out of the water in the same way they swim through the water — by filling their mantle up with water and then forcing it out at very high velocities and pressures. Once a squid has propelled itself above the water, it can contort itself into a rocket — its fins catching the air like wings, the tentacles curled up to create another flat surface in the rear.

So first it was cephalopod’s nervous system that contradicted the expected evolutionary pattern. Then it was their eye that gave yet another example of evolution’s complete failure and left evolutionists with only absurd epicycles to explain it.

Now it is the squid’s propulsion and aerodynamic systems. Yes we know, random mutations just happened to form the mantle, muscles and control systems to eject high pressure water. And other random mutations just happened to shape the fins to catch air like a wing. And yet more random mutations just happened to adjust the tentacles and muscles to enable another aerodynamic surface. And of course more random mutations just happened to give the squid the brains and nervous system to coordinate and control all this.

And how did this massive design serendipity just happen to come together? Evolutionists have no idea, but they are absolutely certain that it did. After all, evolution is a fact. Who needs Jon Stewart for entertainment?

Allopatric Speciation Tested in Martinique

You know the story, mountain ranges formed, rivers changed course, islands formed, and other earth changes split populations into isolated parts which led to divergence, speciation and, well, the rest is history.  Given enough geographic isolation events over enough millions of years, and pretty soon fish turned into amphibians and reptiles and mammals. In short, a fish population had spontaneously turned into a giraffe population. But when islands in the Lesser Antilles coalesced to form Martinique, lizards from the different islands didn’t follow the narrative. In spite of evolutionary expectations the different lizard populations, which had been separated for six to eight millions years, had no difficulty interbreeding as one species. The so-called allopatric speciation never happened. Undaunted as ever, evolutionist now call for “ecological speciation,” which didn’t occur either but it has the virtue that it can’t be falsified.

Nothing in biology makes sense in the light of evolution.

Worshipping the Creature

Drew Berry explains how that these molecular machines evolved from, well, nothing. Go to the 2:55 mark to skip the introduction and see his animations.

Genes Have Play, Stop and Pause Buttons

You probably remember from biology class that genes hold information that is used to construct protein and RNA molecules which do various tasks in the cell. A gene is copied in a process known as transcription. In the case of a protein-coding gene the transcript is edited and converted into a protein in a process known as translation. What you may not have learned is the elaborate regulatory processes that occurs before, during and after this sequence of transcription, editing and translation. Genetic regulation is fascinating and you can read more here, here, here, here, here, here, here, here, here, here, here, here, here, here, here and here.

Background: Post translation regulation

Regulatory processes are constantly at work in the cell, practically at all levels. Consider the enzymes in the glycolysis pathway which metabolize food intake. There are about a dozen such enzymes and they team up to break down the six-carbon sugar known as glucose into two three-carbon molecules. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work.

In addition to breaking down glucose, glycolysis also produces energy-carrying molecules called ATP. These are in constant demand in the cell as they are used wherever energy is needed. So like most pathways, glycolysis is interconnected with other pathways within the cell. The molecular products of glycolysis are used elsewhere and so the rate at which the glycolysis pathway proceeds is important. Too fast and its products won’t be useful, too slow and other pathways have to slow down.

Glycolysis is regulated in a number of ways. The first enzyme in the glycolysis pathway is regulated by its own product. This enzyme alters glucose to form an intermediate product, but if the rest of the pathway is not keeping up then the intermediate product will build up, and this will cause the enzyme to shut down temporarily. The enzyme is designed to be controlled by the presence of its product.

Two other enzymes in the pathway have even more sophisticated regulation. They are sensitive to a number of different molecules which either increase or decrease the enzyme activity. For example, these enzymes are partly controlled by the energy level of the cell. This makes sense since glycolysis helps supply energy to the cell. A good indicator of the cell’s energy level is the relative concentrations of ATP and spent ATP. High levels of ATP indicate a strong energy supply. Hence the enzyme activity is inhibited (and therefore the glycolysis pathway is slowed) when ATP is abundant. But high levels of spent ATP counteract this effect.

How do these molecules control enzyme activity? The molecules are tiny compared to the big enzymes they control. Just as a small key is used to start up and turn off a big truck, so too these small molecules have big effects on their target enzyme. And just as the truck has an ignition lock that can be turned only by the right key, so too the enzyme has several docking sites that are just right for a particular small molecule, such as ATP, spent ATP, or the intermediate products.

Not only does ATP fit just right into its docking site, but it perturbs the enzyme structure in just the right way so as to diminish the enzyme activity. There is another docking site that only a spent ATP will fit into. And if this occurs then the enzyme structure is again perturbed just right so as to encourage activity and reverse the ATP docking effect.

Background: Pre translation regulation

The regulation of protein enzymes discussed above is the last in a sequence of processes that regulate genes and their products. Just before this there are processes that regulate the very production of proteins.

For instance, some of our DNA which was thought to be of little use actually has a key regulatory role. This DNA is transcribed into strands of about 20 nucleotides, known as microRNA. These short snippets bind and interfere with RNA transcripts—copies of DNA genes—when the production of the gene needs to be slowed. And microRNAs do not only come from a cell’s DNA. MicroRNAs can also be imported from nearby cells, thus allowing cells to communicate and influence each other. This helps to explain how cells can differentiate in a growing embryo according to their position within the embryo.

And MicroRNAs, like instructions of use, can come from the food we eat. In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information—in the form of these regulatory snippets of microRNA—which regulate our gene production.

And while microRNAs regulate the production of proteins from the RNA transcripts, the microRNAs themselves also need to be regulated. So there is a network of proteins that tightly control microRNA production as well as their removal. “Just the sheer existence of these exotic regulators,” explained one scientist, “suggests that our understanding about the most basic things—such as how a cell turns on and off —is incredibly naïve.”

Background: Pre transcription regulation

The next step upstream is the regulation of the transcription process, which copies the DNA gene into an RNA transcript. This is done with the help of transcription factors—proteins that bind to DNA and influence which genes are expressed (transcribed). These transcription factors bind to special, short, sequences of DNA that are before or after the gene they regulate. In so doing the transcription factors influence the huge molecular machine known as RNA polymerase which opens the DNA double helix and makes the RNA transcript copy of the gene.

Exactly how the transcription factors influence the RNA polymerase machine is a complicated topic. Equally complicated is the question of how the transcription factors know when and where to bind to the DNA. One way is with the help of DNA methylation in which a small molecule (a methyl group) is added to the DNA macromolecule at particular locations. Like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on. This DNA methylation is accomplished via the action of a protein machine that adds the methyl group at precisely the right location in the DNA strand.

The methylation occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by protein machines as they move along the DNA. The protein machine binds to the DNA, twists the helix so the DNA base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule to the DNA base.

In bacterial studies it has been found that the short donor molecule does more, however, than just supply a methyl group. It also helps to control the protein. First, the short donor molecule binds to the pocket of the protein so the methyl group is ready for transfer. But the donor molecule also binds to another site on the protein. This binding serves to alter the structure of the protein, enhancing its function. So the protein is designed to do its job when it is charged with a donor molecule.

But not all of the DNA target sequences are methylated. This complex DNA methylation function doesn’t occur if the target sequence is protected by another protein that binds to the sequence. This protein binds to some of these DNA target sequences but not all. The result is a particular DNA methylation pattern which influences which genes are expressed.

Furthermore, the methyl group marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information. For instance, the methyl group can be hydroxylated. And of course a different molecular machine is required for that task, and the information of when and where to go to work is needed.

All of this makes for a complex DNA methylation pattern which is superimposed on the DNA macromolecule. In addition to the DNA macromolecule, methyl groups are also used to tag the histone proteins about which the DNA is wrapped. The histones have a hub, around which the DNA wraps, and a tail that sticks out on which chemical markers are attached. As with DNA methylation, these histone markers are signals for the protein machinery. And like DNA, these tags are removed as well. Such modifications and removal of these chemical tags means that these codes are dynamic, and there are protein inspectors that double-check these complex encodings.

In addition to methylation, histones can also vary by tiny differences in their amino acid sequence. This histone sequence variation serves as yet another type of tag used for gene regulation.

Furthermore, histone variants are not merely static sign posts that influence gene expression. These variants are moved, by other proteins, between different locations in the genome, resulting in migration patterns that occur in the embryonic development phases. DNA methylation can also be transmitted across generations.

And finally this transcription factor binding and methylation patterns are heavily context dependent. In spite of expectations to the contrary, the transcription factor binding sites are not well conserved across different species. In fact, divergence between transcription factor binding sites even shows up in very similar species, such as different species of yeast.

Furthermore the methylation patterns vary substantially across different regions of the DNA and between the two alleles of a given gene and this allele-specific methylation can be tissue-specific. In one type of cell a histone modification may turn off a gene whereas in another type of cell the same histone modification may turn on the gene. As one writer put it, the regulatory architecture has been rewired on a substantial scale. Another explained, these findings “hint at an unimagined complexity of the genome.”

New finding: A pause button

Regulation of genes and their products is complex and occurs at all levels. At the level of transcription where the DNA gene is copied, genes can be turned off and on. It is as though they have a start and stop button. But new research now shows they also have a pause button. That is, transcription factors can not only start and stop the RNA polymerase copy machine, they can also pause the machine after it has begun. And other transcription factors turn off the pause, so the transcription process may continue. This pausing function, which may allow for a more rapid response when needs arise, seems to be a general feature of transcription.

With each new research study we learn more about evolution’s capabilities. There is, of course, no question that evolution created all of these regulatory processes and mechanisms because evolution is well known to be a fact. What is not known is the extent of evolution’s capabilities. No one would have thought evolution could have produced such elaborate designs. But as science advances so too does our knowledge of this incredible process.

Frog Genome Shares Substantial Similarities With Mammalian Genomes

Ten years ago work began on sequencing the first amphibian genome. The organism of choice was Xenopus tropicalis, a two inch frog native to Sub-Saharan Africa. And when the finished product was analyzed it was found to share substantial similarities with mammalian genomes, including our own. As one headline put it, “Frogs and humans are kissing cousins.” As the report explains:

What's most surprising, researchers say, is how closely the amphibian's genome resembles that of the mouse and the human, with large swathes of frog DNA on several chromosomes having genes arranged in the same order as in these mammals. …

"There are megabases of sequence where gene order has changed very little since the last common ancestor" of amphibians, birds and mammals about 360 million years ago, says bioinformaticist Uffe Hellsten at the US Department of Energy's Joint Genome Institute in Walnut Creek, California, a co-author on the study. …

Such conservation has important evolutionary implications. "By comparing the genomes of these different animals, you can really tell what the ancestral complement of genes may have been," says Richard Harland, a molecular and developmental biologist at the University of California, Berkeley, who also took part in the study.

In addition, says Harland, it belies the view that genomes as a rule evolve quickly. "I think the old expectation was that there was a lot of chromosome rearrangement, but I think increasingly we are finding that chromosomal translocations are pretty rare."

So much for another “old expectation” based on evolutionary thinking. After all, it is not as though evolutionists had no reason for their prediction. Other vertebrate genomes are known to vary substantially more than this. But now we must believe in remarkable genetic conservation over 360 million years.

This of course will not be the last surprise. You can bet new genomes will be found that have more differences but yet have far less time to evolve those differences. This will leave evolutionists saying remarkable genetic similarity is conserved over hundreds of millions of years yet is lost over tens of millions of years. It all depends on which species you examine.

Nothing in biology makes sense in the light of evolution.

Did Fish Evolve From Terrestrial Creatures? Science 1, Mr. Limpet 0

If you thought it strange that those incredible whales and dolphins are supposed to have evolved from freshwater and ultimately terrestrial environments then you’ll be amazed to hear that evolutionists are now saying the same is true for the majority of fish in the ocean. As they explain:

Remarkably, trait reconstructions (for both living and fossil taxa) suggest that all extant marine actinopterygians were derived from a freshwater ancestor …

Another evolutionist speculates that these new results may point to a more general pattern. Perhaps most major groups of vertebrates ultimately came from land-based ecosystems. If so, then the incredible Mr. Limpet had it all wrong. Most fish didn’t crawl out of the ocean, they crawled into the ocean:

Have you given much thought to the Devonian Period?
The what?
The Devonian Period of the Paleooic Era. You know, it followed the Silurian and preceded the Carboniferous Eras.
I try not to think of things like that.
I've given it a lot of thought. Do you realize our ancestors were fish?
Maybe your ancestors, Henry, not mine. Maybe you ought to try to find a new hobby. Maybe go in for parakeets.
I'm not joking. I can explain.
He sure can. He's read many books on the subject. He claims years ago there was nothing but fish in the world.
That's right. Then some of those creatures became amphibians. They crawled out on land. Millions of years later they became men.
I know some who ought to crawl back.
Doesn't it give you a thrill of hope?
Hope for what, Henry?

But while Mr. Limpet has been falsified, evolutionists are of course undeniably correct. True, evolution doesn’t always make sense, but there are always just-so stories to explain the contradictions. In this case the evolutionists are now saying that freshwater environments form an “arc of survival” that act to reseed the oceans. Makes perfect sense.

Religion drives science and it matters.

Mouse-to-Elephant: Evolution in Action

An international team of evolutionists reported this week that mice evolved into 33,000 pound elephants in 24 million generations. They also looked at other evolutionary transitions such as from a slightly larger, rabbit-sized, mammal to an elephant (10 million generations), and going in the other direction from a large elephant to smaller dwarf versions (100,000 generations). This relatively fast rate of reduction was a surprise for the evolutionists, as the lead research explained:

The huge difference in rates for getting smaller and getting bigger is really astounding—we certainly never expected it could happen so fast!

What is also surprising is that evolutionists could even make such measurements. One report explained that the evolutionists “measured large-scale evolution in mammals” and another explained that they “have for the first time measured how fast large-scale evolution can occur in mammals.”

It looks like yet another impressive proof text for evolution. To first order the timeframe, and number of generations, to morph mice into elephants has actually been measured? One might wonder how evolutionists could achieve such an accomplishment. The complexities of such an undertaking seem overwhelming. The very idea seems to be unscientific, and yet here we have not only an understanding of the process, but we even have sufficient detail to measure such large-scale evolution. Surely this is ground-breaking research.

Well, as usual, there’s a catch. In spite of the claims, the evolutionists did not actually make any such measurement. Not in any scientific, objective way, at least. What the evolutionists did was to compare various fossils and, assuming they evolved into each other, computed the time required.

Assuming the evolved into each other? Yes, behind all the headlines and hoopla, there is that minor caveat. Evolution was assumed from the beginning. Evolutionary rates were “measured” by first taking evolution as a given. That’s just the stuff of good solid scientific research.

Religion drives science, and it matters.

Evolutionist Accuses Others of Lying

According to evolutionist Jeffrey Martz “creationism is based on lies and misrepresentations of science.” But why isn’t Martz concerned about the “lies and misrepresentations” of evolutionists? Evolutionists say their idea is a scientific fact, on par with gravity and the round shape of the earth. Why does Martz not work to correct that tall tale? Look in any evolution textbook and you can see many more such misrepresentations. Yet evolutionists such as Martz just look the other way.

Neil deGrasse Tyson: No engineer would design that, at all. Ever!

Evolutionist Neil deGrasse Tyson has pointed out that notions of creationism and intelligent design ignore a fundamental and important problem—the fact that the universe, and most of the things in it, would never have been designed. As Tyson explains:

Star formation is completely inefficient. Most places in the universe will kill life instantly—instantly! People say “Oh, the forces of nature are just right for life.” Excuse me. Just look at the volume of the universe where you can’t live. You will die instantly. That is not what I call the Garden of Eden, alright. … We’re on a collision course with the Andromeda galaxy—gone is this beautiful spiral that we have. And of course we’re on a one-way, expanding universe as we wind down to oblivion, as the temperature of the universe approaches absolute zero. 

The inner solar system is a shooting gallery. And look how long it took for multicellular life to evolve—3.5 billion years! Obviously not a good design. Then there are the earthquakes, volcanoes, floods, tornadoes, hurricanes, tsunamis, and one of Darwin’s favorites, lightning strikes. 99% of all life that ever lived is now extinct. “None of this,” Tyson explains, “is any sign that there is a benevolent anything out there.”

And consider all the natural diseases. Lukemia, hemophilia, sickle cell anemia, multiple sclerosis, epilepsy, and ALS. The list goes on and on. But that’s not all. Our limited human vision system can only perceive a narrow band of the entire electromagnetic spectrum. As Tyson makes clear:

Anyone who has seen the full breadth of the electromagnetic spectrum will recognize how blind we are.

We have to eat constantly because we’re warm-blooded. So we’re always looking for food. And what about carbon monoxide? You can’t smell it or taste, but you breath it in and “your dead.”

The problem, Tyson explains, is that we tend to ignore these obvious problems:

This is all simply stupid design. The problem is, if you look for what is intelligent, and yes you can find some things that are really beautiful, and really—“hey, that’s clever,” such as the ball-socket of the shoulder. There are a lot of things you can point to, but then you stop looking at all the things that confound that revelation. And so, if I came upon a frozen waterfall, and it just struck me for all its beauty, I would then turn over the rock and try to find a millipede, or some kind of deadly newt, and put that in context, and realize, of course, the universe is not here for us.

And so the final verdict: “No engineer would design that, at all. Ever!” As Hume’s character Philo put it more than two centuries ago,

Here, Cleanthes, I find myself at ease in my argument. Here I triumph. Formerly, when we argued concerning the natural attributes of intelligence and design, I needed all my skeptical and metaphysical subtlety to elude your grasp. In many views of the universe and of its parts, particularly the latter, the beauty and fitness of final causes strike us with such irresistible force, that all objections appear (what I believe they really are) mere cavils and sophisms; nor can we then imagine how it was ever possible for us to repose any weight on them. But there is no view of human life, or of the condition of mankind, from which, without the greatest violence, we can infer the moral attributes, or learn that infinite benevolence, conjoined with infinite power and infinite wisdom, which we must discover by the eyes of faith alone. It is your turn now to tug the laboring oar, and to support your philosophical subtleties against the dictates of plain reason and experience.

Tyson has more evidence than Hume ever had, and it confirms that age old message. Complexity and beauty may suggest design, but dysteleology and evil refute it. The world must have evolved. Religion trumps science every time.

Evolution Professors: Evolution is Simply Genetic Change (And a Fact)

As we saw here, here, here and here Randy Moore and Sehoya Cotner, in their new book Arguing for Evolution: An Encyclopedia for Understanding Science, list altruism as an evidence for evolution, make religious arguments that prove evolution, say that evolution predicts “There will be anatomical similarities among related organisms,” begin the book with a bogus prediction claim, define science as strictly naturalistic and say it would be perverse not to accept the scientific fact of evolution.

Of course Moore and Cotner are not saying anything new. These types of arguments are standard in evolutionary thought. They can be found throughout evolutionary apologetics. After all, the book is meant to be an encyclopedia. So the book is a useful compendium of evolutionary thought.

And as the book reveals, the most serious problems in evolutionary thought lie not in the scientific details that are brought forth as evidence, but in how those details are interpreted and arranged. Everyone agrees on the scientific observations, but how are we to understand those observations? It is here that the main problems arise, and it is here where one begins to learn the essence of evolutionary thought.

The underlying religious motivation drives evolutionary thinking into several common, predictable patterns. These include the construction of bogus predictions, the ignoring of substantial scientific problems, and misrepresenting how the evidence bears on the theory.

This is all in support of the false claim that evolution is a scientific fact. Evolution may have occurred or it may not have occurred. People can argue over the this, but there is no question that evolution is not a scientific fact. That is to say, the scientific evidence, no matter how generously interpreted, does not make evolution a fact. Not even close. There are significant scientific problems with the theory.

So evolutionists have a problem. The science contradicts their theory yet they say it is a fact.  One strategy evolutionists use to rationalize their claims is to make undefendable demarcation claims about what science is. Though they have made metaphysical claim after metaphysical claim, they then hypocritically say science must be strictly naturalistic. And if science is strictly naturalistic, then the species must have arisen naturalistically, at least according to science.

So evolutionists both rely on and eschew metaphysics. Not surprisingly Moore and Cotner follow in this tradition. For instance, they tell us that “Nonnatural, or supernatural explanations, are neither scientific nor evidentiary.” Yet elsewhere they approvingly quote Darwin who wrote that “nothing can be more hopeless than to attempt to explain this similarity [pentadactyl pattern] … by utility or by the doctrine of final causes.”

So when convenient, metaphysics are allowed, but when not convenient metaphysics are ruled out as “not scientific.” After all, we all know metaphysical claims are not scientific (except when we make them).

As if sensing a problem, evolutionists deploy yet another backstop. To rationalize their rationalizations, they lower the bar and reduce evolution to mere change over time. This way, no one can argue that evolution is not a fact. Change occurs over time, therefore all of biology arose spontaneously, strictly by the play of natural laws.

For instance, Isaac Asimov once wrote that mere color changes in the peppered moth prove evolution. How could such trivial change prove evolution? Of course it doesn’t—this is an equivocation on evolution.

Similarly Steve Jones wrote that the changes observed in HIV (the human immunodeficiency virus) contain Darwin’s “entire argument.” According to science writer Jonathan Weiner, the changes in the beaks of birds show us “Darwin’s process in action.”

Likewise Professor Marta Wayne tells us that “Evolution is change in gene frequency” and science writer Emily Willingham defines evolution as “a change in population over time.” Professor Pamela Bjorkman states that a mutating virus is “evolution at work” and that “In the same way, people have evolved, but over a much slower time scale.”

So it is not surprising that Moore and Cotner follow this tradition of equivocation. After approvingly quoting Stephen Jay Gould that it would be perverse not to accept the fact of evolution, they next inform the reader that “Most simply, evolution is any change in a population’s genetic composition over time.”

All of this would be laughable if it weren’t so real. The book’s promotional material states that:

The book shows how scientists have tested the predictions of evolutionary theory and created an unshakeable foundation of evidence supporting its truth. As such, it demonstrates how evolution serves as a case study for understanding the scientific method and presents a logical model for scientific inquiry.

Unfortunately the truth is close to the exact opposite. This new book by Moore and Cotner does not demonstrate the truth of evolution any more than previous apologetics have. Nor do Moore and Cotner help reveal anything about “the scientific method” or “scientific inquiry.”

There’s nothing wrong with exploring new or unlikely ideas, but evolution is about the manipulation and misrepresentation of science to prove a preconceived conclusion. Evolutionists do not merely explore an unlikely idea, they insist it is a fact in spite of the science.

Moore and Cotner are not demonstrating the scientific method, they show yet again how evolution abuses science. They do not reveal the truth of evolution, but rather how unfounded are its proofs. Evolutionary thought is a Trojan Horse that has infected science. This new book from Moore and Cotner is simply one more example.

Religion drives science, and it matters.

Evolution Professors: Science Must be Naturalistic and Testable (Can You Find the Fallacy?)

As we saw here, here and here Randy Moore and Sehoya Cotner, in their new book Arguing for Evolution: An Encyclopedia for Understanding Science, list altruism as an evidence for evolution, make the typical religious arguments that prove evolution, say that evolution predicts “There will be anatomical similarities among related organisms,” and begin the book with a bogus prediction claim.

But this is only the beginning. In their next move Moore and Cotner attempt to precondition the reader by mandating naturalism. In a section entitled “Definitions of Science and Scientific Theory,” Moore and Cotner inform the reader that:

Nonnatural, or supernatural explanations, are neither scientific nor evidentiary (i.e., they cannot be supported by scientific evidence). Scientific hypotheses must be testable and falsifiable. Making conclusions that cannot be tested through experimentation and observation is not scientifically valid.

So if the ground rules are that science must be strictly naturalistic—if science must not stray from the naturalism paradigm—then science cannot test naturalism. Naturalism, insofar as science would be concerned, cannot be falsified. Therefore, according to the evolutionist’s logic, the naturalism ground rule is not scientifically valid.

Next Moore and Cotner explain that the theory of evolution has been, in the words of Stephen Jay Gould “confirmed to such a degree that it would be perverse to withhold provisional assent.”

Perverse?

In fact the naturalistic origin of all of biology (and everything else for that matter) is not even testable. Of course it has been confirmed, for there is no other choice. We don’t know how the entire biosphere could have arisen spontaneously, and evolutionary predictions have fallen one after the other, but one way or another, evolution must be the answer. It would be perverse to think otherwise. That’s just the Stuff of Good Solid Scientific Research.

Religion drives science and it matters.

Professors: Evolution Predicts Unknown Moth

As we saw here and here Randy Moore and Sehoya Cotner, in their new book Arguing for Evolution: An Encyclopedia for Understanding Science, list altruism as an evidence for evolution, make the typical religious arguments that prove evolution, and say that evolution predicts “There will be anatomical similarities among related organisms.” That religion is doing the heavy lifting behind the phony science is not news, but Moore and Cotner’s book gives us yet another example of this hypocrisy.

In fact the book begins with yet another silly claim that evolutionists find to be significant. In 1862 Darwin examined an orchid, originating from Madagascar, with an incredible foot-long nectary. How could an insect reach all the way down to the base of the tube where the nectar was? The logical conclusion was that there must be a moth species, somewhere in Madagascar, with a very long proboscis with which to pollinate the freak orchid. Darwin may have been an evolutionist, but he could also come to common sense conclusions.

Such a moth was eventually found, and of course evolutionists interpret the orchid-moth pair as a result of evolutionary change. But Darwin’s successful prediction was hardly an evolutionary one. One need not believe orchids and moths (and everything else) just happened to spontaneously arise due to chance in order to reason that for every orchid there must be a pollinator.

Moore and Cotner, however, tell the reader otherwise. They begin their volume with this example on arguing for evolution as though it is an example of the success of evolutionary thinking. This is not unusual. Evolutionists often claim, as successes, predictions and findings where evolution is, in fact, gratuitous. This is understandable if one begins with the assumption that evolution, one way or another, must be true.

Religion drives science and it matters.

Evolution Professors: There Will be Anatomical Similarities Among Related Organisms

What exactly is a scientific prediction? Philosophers have long since pointed out that many so-called scientific predictions do not qualify. For instance, sometimes a prediction is made after the fact. Other times the prediction is too broad or vague. In some cases a failure of the prediction can be too easily accommodated, using minor adjustments to the theory. In fact sometimes the prediction is not even required by the theory. It is simply used to make the theory look good. These textbook examples from the philosophy of science can be found in abundance in evolutionary theory. Consider, for example, Randy Moore and Sehoya Cotner who, in their new book Arguing for Evolution: An Encyclopedia for Understanding Science, state that evolution predicts “There will be anatomical similarities among related organisms.” It is a typical example of how evolutionists commit even obvious fallacies in their apologetics.

The evolutionary prediction that “There will be anatomical similarities among related organisms” is, for starters, an after-the-fact prediction. It has been known since antiquity that species are not simply randomly designed, but instead share at least some patterns. And the prediction is incredibly vague. It could mean just about anything. But this is only the beginning.

The prediction that “There will be anatomical similarities among related organisms” is not even binding. Biology is full of falsifications of this prediction. We humans and squids, yes squids, share similar vision systems. It is an incredible anatomical similarity among very different species. On the other hand, different frog species have completely different development pathways to form their vision systems. These are just two of biology’s many examples of unrelated organisms with striking similarities and related organisms with striking differences. When confronted with such falsifications, evolutionists respond that “evolution does that too.” As the philosopher warned, sometimes prediction failure can be too easily accommodated.

In fact, evolution’s ability to accommodate such massive contradictions to the prediction shows that the prediction was not even required by the theory in the first place. Evolutionists have no problem explaining violations of their expected pattern. Evolution, they say, can temporarily speed up, thus creating big change and erasing the expected similarities. This and other just-so explanations reveal that this prediction never really was a genuine prediction in the first place. It is just there to make the theory look good.

Religion drives science, and it matters.

Is Evolution an Enabler of All Kinds of Absurdities?

New Book on Arguing for Evolution

Did you know that helping is evidence for evolution? As Randy Moore and Sehoya Cotner explain in their new book Arguing for Evolution: An Encyclopedia for Understanding Science, this and most everything else in biology proves evolution to be an undeniable fact. Altruism, they explain, may seem to be a “problem” for evolution. (They put “problem” in quotes because, of course, there are no real problems for evolution. All those false predictions are simply explained by adjusting the theory.) In this case, most acts of so-called altruism are “anything but.” If an individual sounds an alarm to warn the others or dies to save the group, it is really just another evolutionary calculation. Does not such risky behavior maximize the chances that the all important genes will be propagated to the next generation? And so falling on hand grenades may seem to be a noble, heroic act, but actually it is simply a product of natural selection. As John Haldane once put it, “I would lay down my life for two brothers or eight cousins.”

But how did such complex behaviors evolve in the first place? How do we decide which behaviors maximize gene propagation versus simply terminating such propagation? Even something as seemingly simple as bacteria suicide is enormously intricate and complex. It is an elaborate molecular choreograph that isn’t going to arise by a few chance mutations.

Remember that selection cannot induce such designs. It can only select them once they have been randomly produced by those epicurean veering atoms. But chance mutations can’t create real-life complexities. There is no gradual path of tiny changes that morphs a tricycle into a jet airliner. Even simple molecular machines don’t show signs of gradual buildup.

There is also the “problem” of the many altruistic behaviors that don’t fit the evolutionary model. Such non reciprocal altruism hardly helps get one’s gene into future generations. Why does Mother Theresa help the needy in far away countries?

These and other thorny “problems” are not seriously addressed. Instead, Moore and Cotner present the usual non scientific, metaphysical proofs that mandate evolution. As philosopher Elliott Sober has pointed out, the strong evidences for evolution come from metaphysical rebukes of creationism.

For example, Moore and Cotner point to the pentadactyl pattern which is:

difficult to explain if the organisms originated independently of (and were therefore unrelated to) each other, for such an origin would not require pentadactyl limbs or, any other shared traits.

Why are such similarities difficult to explain if the organisms are not related by common descent? Because the organisms should not share any similarities. And how do evolutionists know that the organisms should not share any similarities? Because such similarities are not required. And what is the basis for these requirements? Evolutionary fitness, of course. But the pentadactyl pattern is presented as evidence for evolution and as such, it needs to be interpreted objectively. Otherwise the argument is circular.

Of course what is lurking behind all this is the usual evolutionary metaphysics. It is what Sober calls Darwin’s Principle. And if there was any doubt that evolution is a religious theory the authors dig deeper into the metaphysics:

Creationists have explained these developmental and structural similarities as the handiwork of a Creator who saved time and work by varying a basic theme. Darwin, however, considered such explanations to be useless, noting that “nothing can be more hopeless than to attempt to explain this similarity … by utility or by the doctrine of final causes,” and that the similarities are “inexplicable” by traditional views of creationism.

Final causes is hopeless? Creationism is inexplicable? Well then yes, evolution is a fact. So while the evidence is unlikely on evolution, as Sober points out, it ironically makes evolution a fact:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Evidence and Evolution, p. 314]

No matter that the evidence doesn’t fit evolution very well. Creationism is inexplicable, so evolution is a fact.

Religion drives science, and it matters.

This Just In: Everything Came From Nothing and if You Don’t Agree You Know Nothing

Evolution professor Lawrence Krauss is now saying that the universe, and everything in it, came from nothing. Not only that, but there are probably billions and billions of universes that have spontaneously arisen. Occasionally a universe happens to have all the right properties for life to arise spontaneously within it, and that would be us.



Krauss, a theoretical physicist and head of The Origins Project at Arizona State University, is not the first evolutionist to defy the age-old wisdom that something does not come from nothing. World-famous physicist Stephen Hawking popularized the idea in a recent book he co-authored entitled The Grand Design.

Krauss and Hawking use gravitational theory and quantum mechanics to argue that, in fact, such spontaneous creation is all but inevitable. Their narratives appeal to graduate-level physics which most people do not understand, but the basic idea of a strictly naturalistic creation story goes back centuries.

The intellectual necessity of naturalism

In the seventeenth and eighteenth centuries, with the rise of modern science and the Enlightenment, the urge for strict naturalism was promoted by various Christian traditions. Both in England and on the continent, Christians were refining a range of theological views that required science to describe the world’s origins strictly in terms of natural law. The dozen or so views that emerged fell into two broad categories. One category dealt with the divine attributes while the other dealt with epistemology and man’s knowledge. For short, we may refer to them as the “greater god mandate” and the “intellectual necessity” for naturalism.

In each category a foundational theological view supported various specific arguments for naturalism. One argument from the intellectual necessity view, which became more clear in the eighteenth century, was that special divine action (or primary causation) interfered with scientific progress, or even made science impossible.

As Baden Powell had insisted, all of science depends on the principles of uniformitarianism. Darwin’s confidant J. D. Hooker was more direct. Though he found special creation and evolution at an empirical standoff, neither theory with a clear advantage, he opted for the latter for its “great organizing potential.” It was not that evolutionary theories were “the truest,” he wrote to William H. Harvey in 1859, “but because they do give you room to reason and reflect at present, and hopes for the future, whereas the old stick-in-the-mud doctrines … are all used up. They are so many stops to further inquiry; if they are admitted as truths, why there is an end of the whole matter, and it is no use hoping ever to get any rational explanation of origin or dispersion of species—so I hate them.”

A law-like origins of the world, on the other hand, supported the accrual of knowledge. Darwin enunciated this view when he explained that acceptance of his theory of evolution was less important than the rejection of special divine action:

Whether the naturalist believes in the views given by Lamarck, by Geoffroy St. Hilaire, by the author of the ‘Vestiges,’ by Mr. Wallace or by myself, signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable: for he who admits this as a great truth has a wide field open to him for further inquiry.

The rejection of special divine action was equated with scientific progress. Here Darwin extrapolated his metaphysical argument to arrive at the ultimate proof against creation. His main point, that no creator ever would have intended for this world, was now protected against counter arguments because such counter arguments would be unscientific.

Darwin repeatedly used metaphysical arguments against creation to prop up evolution, but now he declared that counter arguments would be out-of-bounds since they were unscientific. Darwin correctly observed that creation and its supporting arguments hinge on one’s concept of God, but he conveniently forgot that arguments against creation equally hinge on one’s concept of God. For Darwin, it was fair game to argue against creation but not for it. Thus, evolution was the correct scientific conclusion. In fact, what good science required was a naturalistic explanation, regardless of what particular explanation was used.

Since Darwin this theological argument has gained strength. For Niles Eldredge, the key responsibility of science—to predict—becomes impossible when a capricious Creator is entertained:

But the Creator obviously could have fashioned each species in any way imaginable. There is no basis for us to make predictions about what we should find when we study animals and plants if we accept the basic creationist position. … the creator could have fashioned each organ system or physiological process (such as digestion) in whatever fashion the Creator pleased.

In his text Paul Moody explains that without strict naturalism one does not have an explanation at all:

it amounts to saying, ‘Things are this way because they are this way.’ Furthermore, it removes the subject from scientific inquiry. One can do no more than speculate as to why the Creator chose to follow one pattern in creating diverse animals rather than to use differing patterns.

Likewise Tim Berra warns that we must not be led astray by the apparent design in biological systems, for it “is not the sudden brainstorm of a creator, but an expression of the operation of impersonal natural laws, of water seeking its level. An appeal to a supernatural explanation is unscientific and unnecessary—and certain to stifle intellectual curiosity and leave important questions unasked and unanswered. ” In fact, “Creationism has no explanatory powers, no application for future investigation, no way to advance knowledge, no way to lead to new discoveries. As far as science is concerned, creationism is a sterile concept.”

Lawrence Krauss and the intellectual necessity

And so it is not surprising to hear Lawrence Krauss, at the 3:14 mark in the above lecture, rehearse the same, centuries-old, intellectual necessity theology in support of his conviction that something, in fact the entire universe, just happened to spontaneously arise from nothing:

I am going to a talk about our modern picture of cosmology and how it has changed our view of the universe—the past and the future, and in some sense how that picture is clearly remarkable. And far more remarkable than the fairly tales that are made up in most religious situations.

But the key point is mystery. That is one of the things that makes science so special I think. It is that scientists love mysteries. They love not knowing. That’s a key part of science. The excitement of learning about the universe. And that again is so different than the sterile aspect of religion where the excitement is apparently knowing everything, although clearly knowing nothing.

There you have it. Without naturalism there is not only no excitement, there is no knowledge. We are left “apparently knowing everything” but “clearly knowing nothing.” Given this truth, then of course, we must have evolution.

Everything came from nothing and if you don’t agree, then you know nothing. Religion drives science, and it matters.

Rib Development Interdependencies: More Complicated Than We Would Have Imagined

Research published last year out of Portugal shows that the development of ribs is more complicated than evolutionists imagined. It turns out that in the developing embryo, rib growth is promoted by one pathway and inhibited by another. The end result is a delicate balancing act between the two to construct the proper design.

And on top of that, the balancing act is further complicated by its coordination with muscle development. As one writer explained:

The researchers went on to unpick the genes involved in this process, and came up with yet another surprising finding: that the whole process relies on first hitting so-called muscle genes in the embryo, which then provide signals to switch on the 'rib' genes to make both ribs and muscle, in a coordinated process.

Did evolution get lucky again by randomly constructing another complex, interdependent process that needs all the major components? Who knows but who cares. After all, evolution is a fact. As the lead researcher assures us, the perplexing result “makes perfect sense” from an evolutionary perspective. And why is that true? Because:

it is no good to make ribs without muscle, so, in the embryo, the production of both ribs and their associated muscles is under the control of a single and coordinated mechanism.

Of course. It is all so clear now. Evolution constructed incredible complexity because ribs are no good without muscles. That’s just the Stuff of Good Solid Scientific Research.

Religion drives science, and it matters.

Evolution Professor: I Wrote a Thoughtful Response

An evolution professor who wrote a profanity-laced diatribe in response to a question about evolution is now saying it was a “thoughtful response.” He writes:

I wrote, what I thought, was a thoughtful response to a question I was asked regarding math and evolution and creationists.

But as I pointed out here, here and here, aside from the foul language the professor’s response contained several scientific blunders. And now those blunders are being amplified in the professor’s next response. But as usual a straightforward discussion about the science won’t be easy.

Evolution is a religiously driven theory that is weak on the science, so you can guess where the discussion goes. Here is how the professor begins his next “thoughtful” response:

In my original post, I pointed out one creationist argument against the theory of evolution misuses probability. The argument goes like this: using these assumptions, the odds of life originating is infinitesimally small therefore god and Jesus and homosexuals can not visit each other in the hospital.

Aside from the usual mocking that evolutionists rely on, the misuse of probability is not a “creationist argument.” Again, this is typical. Evolutionists think they can cover over the problems with their theory by raising the “Creationist” alarm and turning to ridicule.

The professor’s first mistake was his misuse of probability. They say there are lies, damn lies, and then there are statistics. We might now add probability to the list. A problem with evolution, and the origin of life, is that they are astronomically unlikely. They have low probability.

The professor attempted to explain this away by arguing that all outcomes are equiprobable. Incredibly complex cellular life arising on its own is no different than a blob of mud. After all, all possible outcomes have a probability of 1/#Outcomes. This is an old, and frankly pathetic, trick. Laplace explained the problem centuries ago and I elaborated on it here.

Using the professor’s rationale, we would credulously accept all manner of bizarre events. If all our roulette wheel bets turned out winners, if our poker hands always gave a royal flush, if random letters spelled out CONSTANTINOPLE, it all would be just another equiprobable event.

But not surprisingly all of this was lost on the professor. He writes:

Instead of dealing with the fact that creationist assumptions are pure fiction …

That would be difficult to do since the professor gave no specifics to deal with. The professor gave no references, no citations, no links, not even any names. In fact the professor’s characterization of “creationist assumptions” was a convenient strawman rather than a serious criticism.

For instance, the professor characterizes creationists as assuming evolution occurs instantaneously. I’m not up on the creationist literature so perhaps they do say this. But if so, this hardly addresses the serious problems with evolution. (More on this below). The professor continues:

Cornelius takes a different tact. Poker and scrabble. See the odds of three players each getting an amazing poker hand at the same time is a really small number therefore evolution can not be true or the odds of pulling out scrabble tiles in order that spell out CONSTANTINOPLE is a really small number therefore evolution can not be true.

Here the professor avoids the problem and instead distorts what I said. The problem is not that “evolution cannot be true,” which of course I never said. The problem is that evolution is unlikely, and his equiprobable argument doesn’t help. After failing to address the problem, the remainder of the professor’s response degrades further:

So if flipping a coin or the lottery are not sufficient evidence, then poker and scrabble will be? Poker and scrabble did not even exist 10,000 years ago, therefore the world can not be that old (if I understand Cornelius' way of thinking). The problem isn't getting small numbers. That's easy, I brought up two ways and now we have two more. The problem is the assumptions creationists make, they are not reality.

10,000 years ago? The world can not be that old? The assumptions creationists make? Where did that come from? Later the professor contrived more opponents to attack:

He is stuck on the idea that scientists think a cell just poofed into existence, regardless of what we say, he refuses to accept it and keeps harping the same lie over and over. … Cornelius' world-view is that the Bible (as he interprets it) is correct and the universe must fit into that tiny little corpuscle of his imagination.

Poofed into existence? Of course I never said any such thing. The professor is simply contriving strawmen to knock down. Unfortunately this is typical. Try discussing the science with evolutionists and too often they attack imagined motives. The irony is that while they promote the religiously-driven theory of evolution, they criticize everyone else for the same. Sorry, but misrepresenting science and resorting to various fallacies is not “thoughtful.”

Religion drives science, and it matters.

Evolution Professor: You’re Quote-Mining Elliott Sober

It is well known that evolution is a religious theory except, that is, to evolutionists. Amazingly, they make their religious claims but then immediately turn around and deny ever having done any such thing. And those who are in a position to expose this denial, professional philosophers, too often are of little help. Evolutionists literally deny their religious premises right after making them and philosophers fail to point out the problem. That is why a peer-reviewed paper on this topic by leading philosopher Elliott Sober, in a leading journal, was helpful. Sober analyzes arguments in great detail and in the paper he points out how evolutionary reasoning entails metaphysical premises. According to evolutionists the scientific evidence falsifies creation and so evolution, of one sort or another, is the only alternative. As Sober has pointed out elsewhere, this contrastive logic works even though evolution itself fares so poorly on the scientific evidence:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Evidence and Evolution, p. 314]

But the contrastive logic entails religious assumptions. This is not about science. In the journal paper Sober explains how this argument works and how Darwin used it to rebuke creationists. The paper is a valuable contribution to our understanding of how religion has penetrated science, and of the evolutionist’s denials.

But, not surprisingly, evolutionists are not only in denial of the religion in evolution, they are even in denial of Sober’s assessment. One evolutionist professor, for example, criticized me for quote-mining and mis reading Sober’s paper. He explained that Sober was merely pointing out the failure of creationism as a sidebar:

It's ridiculous to say that the mere mention of creationists necessarily implies something about a creator. Sober's just saying that creationists hold the idea that species don't differentiate beyond certain fixed boundaries, and that that idea was shown wrong. There's no statement about any creator there.

But how could Darwin show that creationism had become untenable if he hadn’t assumed something about the creator? Not a problem, the professor explained. For Darwin used two models, adaptation for common ancestry and chance for separate ancestry:

[Darwin] considers the possible causes for unrelated organisms to share certain character. These would be adaptation and pure chance.

But if the separate ancestry model doesn’t represent creationism, then how can this show creationism to be so improbable? Again, the professor answered that religious assumptions were incidental to Darwin’s logic:

Sober mentioned creationists because they postulated separate ancestry. Whatever else they'd have thought is irrelevant. If we remove the reference to them, the logic of the paper remains the same.

The professor was clearly in denial of the religious premises Sober had pointed out in the paper. One cannot rebuke creationism without modeling creationism. I tried again to explain this:

the evolutionists cannot evaluate Pr(O|separate ancestry) without a model of separate ancestry. Unless that model is based on creationism, they cannot refute creationism. If that model is based on some other notion of separate ancestry, then it carries no force against creationism.

At this point the professor’s denialism became more obvious as he simply rewrote Sober’s explanation of the evolutionary argument, saying it has nothing to do with divine intent:

There's no relationship of necessity between [separate ancestry] and divine intervention. One can consider the former separately. …

it refutes [separate ancestry], not divine intent. The argument explained by Sober in the paper cannot conclude that divine intervention is unlikely. It cannot do that, though you wish Sober said it does. … nobody's interested in your precious creationism in that paper.

But if there is no relationship between separate ancestry and divine intervention, and if Darwin’s logic refuted separate ancestry but not divine intent then, I reminded the professor, Darwin could not rebuke creationism as Sober had explained.

At this point the evolutionist’s denial of his own religious premises were exposed as he simply refused to acknowledge the Sober paper. Sober explained that Darwin had shown to be a myth the creationist notion that species or “kinds” are separated from each other by walls. But one cannot show this creationist notion to be a myth without assuming something about that creationist notion.

The evolution professor had accused me of quote-mining the Sober paper and interpreting it according to personal biases, but in fact this is what the professor was doing.

At this point the professor changed his tack with a new argument and again blamed the problem on me:

What it rebukes is the "species separated by walls" thesis of creationism, but not "creation theory" as a whole, nor the most important claim of creationism: divine intervention in the origin of species. Again, you're equivocating a single creationist thesis with "creation theory" with all of its postulates.

But of course whether the evolutionary logic rebukes a particular thesis of creationism or creationism as a whole is irrelevant, as I explained:

If Darwin rebukes even just some creation theories using religious assumptions, that still amounts to the use of religious assumptions. You’re raising red herrings.

Of course none of this is new. It is just another example of the denialism that comes with evolution. You can see more examples here and here (from Jerry Coyne), here (from PZ Myers) and here (from Douglas Theobald).

Evolutionists say the world arose spontaneously, by itself, they claim this is a scientific fact beyond any shadow of a doubt in spite of massive empirical problems, they make religious arguments to prove their claim, and then they deny it. Evolution is a truly amazing movement in the history of thought. If this wasn’t fully documented by the evolutionists themselves one would never believe it.

Religion drives science, and it matters.

University of Toronto Conference: The Wise Scientist

The Institute for the History and Philosophy of Science at the University of Toronto is hosting a conference this summer entitled “The Wise Scientist: Historical and Philosophical Reflections on the Place of Wisdom in Science” and their first suggested topic is: “Case studies which highlight particularly wise (or spectacularly unwise) scientists.” I think I have an idea. Here is my abstract:

In 1859 Charles Darwin presented his theory of evolution which stated that the species originated spontaneously. From whatever initial conditions existed in the early earth, millions upon millions of species arose by themselves. Indeed, from biochemistry to anatomy, the entire biological world arose on its own. Not surprisingly the theory was met with a degree of skepticism from some scientists. But Darwin’s idea was greeted by theologians and soon was hailed as an undisputable fact. In spite of its heroic claims and a long series of failed predictions, the theory of evolution became entrenched orthodoxy in the twentieth century. As evolutionist Ernst Mayr explained, the fact of evolution is so overwhelmingly established that it would be irrational to call it a theory. Even consciousness, evolutionists insist, is merely an emergent result of the seemingly limitless complexity which spontaneously arose.

But evolutionary thinking did not begin with Darwin and is not limited to biology. The theory that the world arose by itself traces back to antiquity, and in modern times was promoted by cosmologists centuries before Darwin. As Kant explained, a strictly naturalistic origins was based on “incontrovertible principles” which left no doubt of the conclusion. Recently the cover of the venerable Scientific American informed its loyal readers that “Infinite Earths in Parallel Universes Really Exist” and the internationally renown physicist Stephen Hawking proclaimed that even the universe arose on its own.

It would be difficult to overstate the sheer intellectual strength and academic credentials of these leading evolutionists. They are the best and the brightest the world has to offer. Similarly, it would be difficult to overstate the enormous chasm that separates their dogmatic truth claims and reality. While evolutionary theories have been called unwise, evolutionary thinking is undoubtedly the most “spectacularly unwise” movement in history. It would be difficult to imagine a more unlikely science proclaimed with more certainty. Brilliance and intelligence are not necessarily accompanied by wisdom.

Think they will accept it? Religion drives science, and it matters.