Evolution Breakthrough: Enzymes Evolved “Very Early” in the Evolution of Life

After a massive study of the evolution of enzymes—which as usual was really nothing more than a comparison of enzymes, with precisely zero explanation of how the amazing protein machines actually are supposed to have arisen all by themselves as evolutionists insist must be true—the evolutionists did what evolutionists always do, sweep the problem under the proverbial origin-of-life rug:

Although, of course, new enzymes must have evolved at some stage, probably very early in the evolution of life.

Yes, very, very early, because, after all, we have no idea how it could have happened. In the beginning, everything that is important somehow rapidly evolved by lateral evolution between interacting communities. From there the rest, as they say, is history. The details are left up to the student.

Top Microbiologist: Darwin was a priest

Didier Raoult, whom even the evolutionists admit is “the most productive and influential microbiologist in France,” explains that Charles Darwin “was a priest,” in a personal profile story this week.

Raoult’s popular book, Dépasser Darwin (Beyond Darwin) questions several tenets of modern evolutionary theory, including the importance of natural selection. Evolution’s tree of life, explains Raoult, should be replaced by a network of interconnected species.

And how do evolutionists respond? David Moreira of the University of Paris-Sud in Orsay explains that “It’s dangerous to say those things.” It’s not that Raoult is wrong, but that he provides creationist groups with ammunition. As usual, evolutionary dogma takes precedence over science.

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.