Specialized Genes Confirm Creationism

According to evolutionary theory, housekeeping genes are shared with other living things, because of common decent. Evolutionary theory suggests that tiny progressions will eventually lead to other living things. But as scientists sequence more genomes from different animals, they discover something which isn’t that friendly towards evolution and it’s been 20 years and counting for coming up with an explanation which would be more friendly toward evolution.

What scientists have been discovering within the genome project are specialized genes or best known as orphan genes. What is an orphan gene? An orphan gene has coding in it that is unique only to that animal and no other. These DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry. This is why I refer to it as “specialized”. It’s been a surprise for scientists who believe in evolution. Orphan genes are not easily discovered. It takes careful research because the genomic world is very massive. There is also no standardized method in which to use, so it varies from researcher to researcher.

Orphan genes are found in humans too, in fact there was a recent discovery which increased the differences between humans and chimps. Scientists found over 1300 orphan genes which are completely different between humans and chimps. It is possible they may find more as research techniques get better and covering more of the body. In this recent discovery, the focus for these orphan genes were found in the liver, heart, brain, and testes. In ants, researchers have found over 28,000 orphan genes that were specialized only for ants and not other insects.

While orphan genes cause more confusion in the theory of evolution, creationism on the other hand finds these discoveries intriguing because it helps to understand the patterns of genetic diversity related within a created kind. Creationism holds to the view that there are only variants within a kind but no kind changing into a totally different species which is what evolutionary theory claims. Such precise genetic arrangements are truly amazing!

Advertisements

DNA disagrees With Evolutionary Anthropology

Those of us who sat in a public school were taught about evolution. From a biology class to a history class, we all heard the story which includes Neanderthal man. Based on a belief of survival of the fittest, a story about an extinct human species that was believed to be a close relative of modern humans. Creationists believe they are the same species, a group of ancient people. Evolutionists have tried to explain their disappearance by suggesting Neanderthals had a very low-level of intelligence, spoke in grunts, lived in caves most of the time not doing a whole lot, and as a result, not enough for them to survive which is why they say modern humans came along.

As evidence began to surface, this story about Neanderthals which was made up, was not true…Here is one admission from science daily…

“The evidence for cognitive inferiority is simply not there,” said Villa, a curator at the University of Colorado Museum of Natural History. “What we are saying is that the conventional view of Neanderthals is not true.”

“Villa and Roebroeks scrutinized nearly a dozen common explanations for Neanderthal extinction that rely largely on the notion that the Neanderthals were inferior to anatomically modern humans. These include the hypotheses that Neanderthals did not use complex, symbolic communication; that they were less efficient hunters who had inferior weapons; and that they had a narrow diet that put them at a competitive disadvantage to anatomically modern humans, who ate a broad range of things.”

So now they had to readjust their story and came up with a new idea on why Neanderthals disappeared.

“Neanderthals likely interbred and that the resulting male children may have had reduced fertility.”

This conclusion comes with the belief that Neanderthals and modern humans only interbred in the middle east. However, the biggest enemy of their story has been DNA. More DNA has been sequenced. This time from a jawbone which came from a cave in Romania. The reaction to the results was a classic when it comes to falsifications in evolution such as we see in science daily

“Svante Paabo from the Max Planck Institute for Evolutionary Anthropology who led the study. “I could hardly believe it when we first saw the results.” 

In live science

“The large spans of Neanderthal-like segments in Oase 1’s genome indicate that one of his human ancestors interbred with a Neanderthal less than 200 years before he lived.”

This is more confirmation that Neanderthals and modern humans are the same species! Also, to suggest organic material like DNA which degrades rather quickly is going to last that long (40,000 years or more) requires more faith than believing in God! The organic material (DNA) is only a few thousand years old. We don’t need to fund research that makes up stories which has been wrong time and time again. The funding could have gone to fighting cancer or developing new technologies rather than creating fictional stories! Evolution hurts science, rarely do they think outside the box. Creation on the other hand, keeps science moving forward!

Is Evolution Right, When It Is Not?

Usually in other scientific theories when fundamentals are falsified, it eventually withers away and a new theory takes its place. This is something that happens in science but doesn’t happen in evolution. One of the most fundamentals you will find in evolutionary theory is, “common ancestry.”  But within this framework it is claimed that there is gradual accumulation of variations which happens over time through genetic mutations. Thus, making it less common over time.

Scientists who believe in evolution are testing this in order to learn more about the variations over time but to their surprise, this is not the case! In a recent study, that compared yeast and humans which should have nothing in common according to evolution, have found lots in common.

Yeast and humans have been evolving along separate paths for 1 billion years, but there’s still a strong family resemblance, a new study demonstrates. After inserting more than 400 human genes into yeast cells one at a time, researchers found that almost 50% of the genes functioned and enabled the fungi to survive.”
“It’s quite amazing,” says evolutionary biologist Matthew Hahn of Indiana University, Bloomington, who wasn’t connected to the study. “It means that the same genes can carry out the same functions after 1 billion years of divergence.
In another article which says it’s not only yeast but other organisms as well…

“We’re a step closer to understanding the microbial community that inhabits the ocean — and it has some striking similarities to the community that lives inside our guts. The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways. In both, there was an almost identical abundance of genes involved in replication, ion transport and cell motility.”

This certainly was rather a big surprise to us because we expected different ecosystems would have microbial communities with functions that would be completely different,” Sunagawa said at a press conference this week.”

One of the things that may have been proof for evolution turns out to be a falsification! Keep in mind, evolution always sounds better within speculation rather than real life. So now what…? Does this mean a fundamental in evolution will wither away and be replaced by another? No! This isn’t normal science. Even though it is believed that genes and proteins should not be conserved but rather a constant state of flux, just adds the opposite (conservation and convergence function) on what it is suppose to predict and observe in real life while maintaining that same fundamental. Sounds confusing, doesn’t it? Not at all logical in any sense of the word.

In creationism, we believe in “common design.” Just like we see with intelligently man-made designed machines. Those machines utilize similar mechanisms in order to achieve that same outcome. There is no need to add the opposite in order to save “common design” from newer observations especially from this latest study and others like it :)

 

Genome Lacks Compliance With Evolutionary Theory

Normally evolution does well with certain models along with assumptions (without observational data).  But according to a new research paper in nature not even models which hold to certain assumptions confirm evolution!

Four  universities conducted research on contemporary human populations in order to discover advantageous mutations, along with the rate of degradation by mutations. Trying to understand diseases from the present is one thing, it’s quite another trying to obtain knowledge of historical evolution which goes by the assumption of many millions of years.

In nature

“Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants…We estimate that approximately 73% of all protein-coding SNVs [single-nucleotide variants] and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.”    

 The researchers used the term “explosive population growth” because of its long age assumption whereby,  “selection has not had sufficient time to purge them from the population.” Researchers then claim that Europeans had stronger genetic drift, than Africans which is strange because genetic drift doesn’t know the difference. Obviously, they are fudging their assumptions in more ways than one!

They give an assessment of their findings…

“More generally, the recent dramatic increase in human population size, resulting in a deluge of rare functionally important variation, has important implications for understanding and predicting current and future patterns of human disease and evolution.”

“For example, the increased mutational capacity of recent human populations has led to a larger burden of Mendelian disorders, increased the allelic and genetic heterogeneity of traits, and may have created a new repository of recently arisen advantageous alleles that adaptive evolution will act upon in subsequent generations.

Advantageous mutations? Where are they? The researchers provide no examples in which they observed! They merely assumed it, because it’s part of evolution! This is what you call, “circular reasoning!” If the supposed evolutionary past doesn’t add up with the present data, how is this shed light on future patterns for evolution? When a theory displays a considerable pattern that shows increasing complexity in its explanation, the theory is not valid!

Rather than observing advantageous mutations, they observed a “larger burden of Mendelian disorders” afflicting mankind which is vital for understanding diseases not evolution. The research does however confirm a creation scientist’s (John Sanford) proposal which is known as genetic entropy where the genetic load increases dramatically. That would be a problem for evolution, because that observation makes it impossible for mankind to survive tens of thousands of years!

Here is more on the genome in this interview with John Sanford…

And here is part two of the interview with John Sanford…

The researchers are baffled by their finding as one can read by what they expected in the evolutionary framework verses what they observed!

“The site frequency spectrum (SFS) of protein-coding SNVs revealed an enormous excess of rare variants (Fig. 1a). Indeed, we observed an SNV approximately once every 52 base pairs (bp) and 57 bp in European Americans and African Americans, respectively, whereas in a population without recent explosive growth we would expect the SNVs to occur once every 257 bp and 152 bp in European Americans and African Americans, respectively (Supplementary Information).”

Thus, the European American and African American samples contain approximately fivefold and threefold increases in SNVs, respectively, attributable to explosive population growth, resulting in a large burden of rare SNVs predicted to have arisen very recently (Fig. 1b).”

“For example, the expected age of derived singletons, which comprise 55.1% of all SNVs, is 1,244 and 2,107 years for the European American and African American samples, respectively. Overall, 73.2% of SNVs (81.4% and 58.7% in European Americans and African Americans, respectively) are predicted to have arisen in the past 5,000 years. SNVs that arose more than 50,000 years ago were observed more frequently in the African American samples (Fig. 1b), which probably reflects stronger genetic drift in European Americans associated with the Out-of-Africa dispersal.”

 Their findings conflict with the whole long ages notion which comes from the ‘theory’ of evolution but does shed light on understanding diseases better while containing evidence for a population that has been around for 5,000 to 10,000 years! Which confirms what? Yes! It confirms creationism!

Has The Assumption Of A Unique Genome Been Overthrown

Consensus in the scientific community told us that every cell in our body has a copy of our unique genetic code.  It is an interesting proposal but practically impossible to verify with current technology until now. There has been advances in sequencing technology taking place which make it possible to check this assumption.

Researchers studying induced pluripotent stem cells (iPSC’s) (adult stem cells reprogrammed back to embyro stem cells used for medical treatments) have discovered copy number variations (CNV) in cells derived from skin cells. Most assumed these changes occurred in the process of inducing them to the pluripotent state but Yale researchers checking to see whether CNV’s are also found in the somatic cells from which the iPSC’s were derived.

Their paper published in nature says…

“Using PCR and digital droplet PCR, we show that at least 50% of those CNVs are present as low-frequency somatic genomic variants in parental fibroblasts (that is, the fibroblasts from which each corresponding human iPSC line is derived), and are manifested in iPSC lines owing to their clonal origin. Hence, reprogramming does not necessarily lead to de novo CNVs in iPSCs, because most of the line-manifested CNVs reflect somatic mosaicism in the human skin….”

“Overall, we estimate that approximately 30% of the fibroblast cells have somatic CNVs in their genomes, suggesting widespread somatic mosaicism in the human body. Our study paves the way to understanding the fundamental question of the extent to which cells of the human body normally acquire structural alterations in their DNA post-zygotically.” 

What do they mean by “Somatic mosaicism? It’s basically jargon telling you that genomes differ from cell to cell! But not only in copy number variations (CNV’s), but they discovered it in single nucleotide polymorphisms (SNP’s) also. The long held assumption about you having only one genome is thus falsified. This discovery is telling us we have numerous genomes!

How is this going to affect genetics and evolutionary studies? Ever since the Human Genome Project published its epochal map of “the human genome,” there have been maps of other animals including chimps. But from what we know now about genome variations do those maps reflect reality in nature and are these maps depended upon which somatic cell was sequenced?

Geneticists have been aware of variations between individuals of a species which is why various ethic groups have been included in studies but this new discovery is finding significant variation within an individual’s own cells! It is not known at this time on how significant these changes are considering their study was based only on skin cells. But it is quite possible this could be a game changer…

“The prevailing wisdom has been that every cell in the body contains identical DNA. However, a new study of stem cells derived from the skin has found that genetic variations are widespread in the body’s tissues, a finding with profound implications for genetic screening, according to Yale School of Medicine researchers.”

As far as the story of evolution, it has been claimed for years about small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? If there is a difference then that means any conclusions about human-chimp similarities would prove unreliable. Which cells should be averaged? Will the averages converge or diverge, depending on which cells are selected? Philosophers of science can have fun with this one!

Creationists have taken some of the claims about evolutionary similarities and differences based on genetics with a grain of salt and now this belief has been confirmed by this scientific study! This is going to be one of the more interesting areas in science!

Skeptics of ENCODE’s Discovery of Function

In 1972, geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in reference to  pseudogenes but the meaning expanded to non-coding DNA as well. Ohno stated, “The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?

Out of a span of 30 years or so, scientists didn’t do much research on what was considered “fossil remains” of DNA.  Then a group of scientists called, ENCODE discovered something very interesting in 2007. DNA is transcribed into RNA!

Ewan Birney, a coordinator of ENCODE said, “The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.” 

Then on September 5, 2012, the guardian reports…

“Long stretches of DNA previously dismissed as “junk” are in fact crucial to the way our genome works, an international team of researchers said on Wednesday.

It is the most significant shift in scientists’ understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture.”

80 percent of the genome is now regarded to having function which is a major shift considering most of it was considered junk. The discovery has caused quite a stir with those who advocate “junk DNA” being necessary for evolution (having a critical role in ensuring the survival of biological lineages) while using it for evidence against creationism or intelligent design.

P.Z Meyers has been a skeptic of ENCODE and a huge advocate of junk DNA, (but admires their work) here he writes the following in his blog called, “The ENCODE Delusion.” 

“The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.”

“That isn’t function. (says PZ Myers) That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.”

Nick Matzke in Panda’s Thumb, reiterates what Myers spewed out…

“The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.”

“However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”.

“People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.”

ENCODE defines function by activity meaning, the transcription into RNA which makes 80% of our DNA functional which is a perfectly logical conclusion. However, PZ Myers suggests in his sarcasm…”Oh, jeez, straining over definitions—ultimately, what he ends up doing is redefining “functional” to not mean functional at all, but to mean simply anything that their set of biochemical assays can measure.” 

ID proponent and scientist says…”Non-protein-coding DNA even provides spacers to regulate the timing of protein production; and focusing light in rod cells in the retinas of nocturnal mammals.”  –Biologist Jonathan Wells.

Skeptics of ENCODE, are just one angry bunch of men because one of their weapons they have used for many years is being taken away from them as a result of better science. There is nothing to suggest that the majority of scientists even agree with them just rumblings on facebook and twitter. That is not to say the majority in the science community is always right, (many times they are wrong concerning evolution) but they have always advocated the majority to creationists as being logically conclusive and right in science. But we know that is nothing more than a straw man’s argument along with circular reasoning.

How Richard Dawkins Fights For Evolution

One has observe it in the pages of research, now one has observed it in the realm of debate. Back in 2009, Richard Dawkins thought he was putting it to the creationists and the modern intelligent design movement with his argument about junk DNA.

Here is what he says in his book, The Greatest Show on Earth (pp. 332-333)…

“It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene — a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something — unless he was deliberately setting out to fool us.”

Now here, Dawkins believes that pseudogenes are genetic relics that have lost their original protein-coding function which had been possessed by some ancestral creature. Thus, Dawkins contends that pseudogenes provide convincing evidence for evolutionary history rather than an intelligent designer namely, God!

Then Dawkins goes on to say in his book…

“Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes…useful for. . . embarrassing creationists.”

Dawkins statement was embarrassing not creationists but rather the ENCODE project which back in 2007, two years before his book was published…was the remarkable and unexpected discovery (by evolutionists but predicted by creationists and proponents of intelligent design) that vast regions of non-coding DNA (formerly known as junk) were transcribed into RNA, This included what? Yes! This included a significant amount of pseudogenes!

There were other papers also being published that Dawkins failed to accept at the time like Balakirev and Ayala who wrote two papers back in 2003 and 2004 (here and here) on discovering functions with pseudogenes.

The two papers talk about pseudogenes being involved with gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity.

“Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over non-synonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles.”

The modern Intelligent Design Movement had also predicted function in junk DNA even though it was the prevailing viewpoint in evolutionary theory to oppose it…Here is their trailer about this very subject…

Even this gal in her youtube  program, “Ask A Biologist” who is very smart also predicts function with junk DNA…

So there was research refuting one of Dawkins arguments against creationism and yet he decided to try to stick it us.  Ok, fast-forward to 2012…

Wait a minute! Dawkins not only acknowledges that what was considered junk DNA, does in fact have function like pseudogenes and that but evolution predicted it all along….lol My question to Richard Dawkins is when and why he changed his mind? I know why he hasn’t admitted his mistake because he doesn’t want to look weak in front of creationists and his choir. But the reality of it is in black and white.

So this is how Richard Dawkins fights for evolution, he is not totally honest with the public about his position. One has to keep in mind, many of them use a similar slant for debate. I have never seen a top-notch creation scientist debate like Richard Dawkins does and that is because they are honest! It’s not like creation scientists don’t make mistakes, they are human too which is something Richard Dawkins should think of himself, human who makes mistakes! He is wrong about evolution!