Sunday, February 26, 2012

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.

Saturday, February 25, 2012

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.

Tuesday, February 21, 2012

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?

Saturday, February 18, 2012

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.

Tuesday, February 14, 2012

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.

Saturday, February 11, 2012

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 na├»ve.”

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.

Thursday, February 9, 2012

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.

Wednesday, February 8, 2012

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.

Saturday, February 4, 2012

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.

Wednesday, February 1, 2012

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.