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!

What Creates Innovation?

We sometimes like you use “creativity” for “innovation” or “innovation” for “creativity” but these two words contain separate meanings.  Creativity is an idea, while innovation is bringing that idea to life.

Creationists view DNA including so-called, “Junk DNA” as creativity while evolutionists view junk mutations as “innovation” thus skipping the “creativity” part because evolution has no idea, because it’s considered to be a mindless process.  Well, maybe not! However, evolutionists continue to seek something in mutations that can define “creativity” (without the idea part of it if that makes any sense) as found in such articles as this recent one in phys.org...”Insects show how DNA mistakes become evolutionary innovation.”

It continues…

“In two recently published projects, however, scientists show how typos can indeed lead to improvements. In numerous species of insects, they document the DNA errors that led to changes that are not only beneficial but also brilliant. Various species of beetles, aphids, butterflies, and moths have independently acquired genetic errors that allow them to eat highly toxic plants and then use the toxins to defend themselves against predators.”

What did Faye Flam (the reporter) offer as proof for this assumption? Mutations (copy errors in the DNA) caused the cardenolides not to bind to the enzymes required by the insects’ sodium pump. Notice, the insects are still the same species, and there was no increase in novel genetic information, or even specified complex structures.  So the mutations themselves lack the ability to explain origin like how did the sodium pump and the enzyme come into existence in the first place? Do you know what I mean?

By removing one of your fingers to slip out of the handcuffs or even removing one of your arms so your hands could never be handcuffed ever again would not be considered a new innovative mechanism but it’s only a reduced vulnerability! The article celebrated this experiment as an “evolutionary trick” that produced “convergent evolution” in different insect lineages.

The author of the article seems to forget that evolution should be producing novel information (rather than reducing a vulnerability) that leads to new species.  Flam (the author of the article) could not claim that the varieties able to ingest the toxins were new species; but rather he confessed at the end, “The way new species are born is another longstanding puzzle in evolution that DNA is helping scientists to solve.”  In other words, comeback for promised evidence of innovation without the idea behind it.

Where is the really big innovation attributable to mutations? Duplications are a form of mutation, but just because you get a second copy of your twitter feed,  doesn’t mean the second one will evolve into a new, or better feed when cosmic rays hit it. Mutations can change existing information while decaying the information but there is no evidence that it can produce novel information!

So what creates innovation? The answer is simple, nothing creates innovation, creativity is the idea that innovation brings to life and ideas as we observe them come from intelligence! Whether it be artwork, a car engine, your computer, your smartphone, or nature itself! Without creativity there is no innovation.

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!

Most Ambitious Human Genetics Project To Date

New science is putting the so-called leftovers from our supposed evolutionary past to shame! When the first study of the genome was published about 11 years ago, scientists were surprised to find that only about 3% of it coded for proteins and the rest was considered, “junk DNA.”

Then of course new science discoveries came to be where researchers discovered coded information in the “epigenome,” which includes RNAtranscripts that regulate the code.  New results from the most ambitious human genetics project to date,  show at the least, 80 percent of the genome has a function! A remarkable turnaround in slightly over a decade.

The turnaround has become one of the major stories for science discoveries this year and could be the best breakthrough study out of them all in science for this year as well! Numerous publications have been writing about it. Over 20 papers were published in various publications like Genome Research and Genome Biology, along with reviews in The Journal of Biological Chemistry. Even my local newspaper made this front page news and described what it means for possible future medical uses.

It also has Darwinists putting to rest the notion of  leftovers from our supposed evolutionary past which had been heavily promoted by militant evolutionists who lobby hard against creationism and intelligent design such as  P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and British atheist, Richard Dawkins.

It has been part of the creationism model and ID proponents who have argued for years that function will be discovered for much of our DNA that was once considered to be useless with better science and indeed it has!

In an article in Nature

“The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification.”

These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation.

“Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.”  

Was the evolutionary explanation helpful with this discovery? Nope.  In this article in Nature, it says…“Why evolution would maintain large amounts of ‘useless’ DNA had remained a mystery, and seemed wasteful,” Barroso wrote.  “It turns out, however, that there are good reasons to keep this DNA.”

Language like  “evolutionary constraints” and “evolutionarily conserved” used in many of the articles is another indication that evolution was useless when it came to this discovery. Both of those terms of course refer to lack of evolution rather than showing evolution which is why the likes of P.Z. Myers, Nick Matzke, Jerry Coyne, Kenneth Miller and Richard Dawkins advocate junk DNA very heavily! Perhaps it will modify their position, anything left which is considered “junk DNA” they will begin to focus on. Or they could hold the position what New Scientist is now advocating with their skepticism of finding function with non-coding DNA.

“The ENCODE project has revealed that 80 per cent of our genome does something, but doing something is not the same as doing something useful…there are still very good reasons for thinking that most of our DNA is far from essential.”

You can tell that this discovery is not good for evolution when you have a publication like New Scientist that confuses “essential” with “adaptive” and then begs the question whether something useful must be essential. On the other side, ID proponents are jumping for joy, Casey Luskin writes

“We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let’s simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called “junk” DNA. ENCODE researchers use words like “surprising” or “unprecedented.”

“They talk about of how “human DNA is a lot more active than we expected.” But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted.” 

While this breakthrough in science has caused a problem for the story of evolution, Darwinists have pushed back the idea of forcing the data into their evolutionary framework for future researchers such as in this article, “Evolution and the Code” where one scientist mentions it, but the other three did not which doesn’t mean they didn’t go along with the assumption in the same paper in which they co-wrote together.

Here is a video, where it suggest there might be more than 80 percent function with the genome. “There are probably things that we have no idea what they’re doing and yet they’re going something important.” A logical assumption considering the pattern of discoveries being made so far!

 

Evolution has hurt this part of research for years with its assumption of junk DNA but not anymore. Now researchers are looking for more functions than ever before! Here is more quotes by scientists…

“I don’t think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle.  He is referring to researchers who believe in evolution, other scientists have anticipated a lot more sequence that ENCODE.

“It’s a treasure trove of information,” says Manolis Kellis, a computational biologist from Massachusetts Institute of Technology (MIT) in Cambridge who analyzed data from the project.

“Regulation is a 3D puzzle that has to be put together,” Gingeras says. “That’s what ENCODE is putting out on the table.”

What an amazing time we live in! Wow! Unless there is a cure for cancer or someone lands on Mars, this is no doubt the science breakthrough for 2012 which confirms creationism and will also help improve the health of mankind!

Denisovan Genome Disproves Human Evolution

In a Siberian cave, far from Europe, scientists discover a finger bone and two teeth. What were they? According to the story of human evolution, these people were a less-known group called the Denisovans.

Scientists who believed in human evolution were surprised not just by discovering another group of ancient humans, because with just meager fragments, 70 percent of the DNA still remained in what they considered to be 82,000 years old! What? Let me say that again, the DNA remained in what they considered to be 82,000 years old! Does soft tissue really last that long even at 30,000 years old? No! But if you believe in human evolution one has to suspend logic for a story.

In nature news a revised take on the story with new twists with the discovery in mind…

“Unfortunately, the Denisovan genome doesn’t provide many more clues about what this hominin looked like than a pinky bone does. The researchers will only conclude that Denisovans likely had dark skin. They also note that there are alleles “consistent” with those known to call for brown hair and brown eyes. Other than that, they cannot say.”

“Yet the new genetic analysis does support the hypothesis that Neandertals and Denisovans were more closely related to one another than either was to modern humans. The analysis suggests that the modern human line diverged from what would become the Denisovan line as long as 700,000 years ago—but possibly as recently as 170,000 years ago.”

How could have ancient humans who lived in a Siberian cave who were considered lower than Neanderthals interbreed with modern humans? Before the  sequencing of the genome took place it would have been considered, impossible! But in human evolution, falsifications are confirmations as shown below…

“Going back further in time will be exciting.  There’s a huge race on—it’s exciting” says John Hawkins.

Rather than admitting their evolutionary story had been wrong with real-time observations, it’s now a race to get to the finish line.  Not only that but it is implausible that this bone contained 70% of its original DNA after 82,000 years! Who would believe such preservation of soft tissue? It’s a stretch to say the least. It’s much more likely that this individual lived a few thousand years ago at most.

Who would believe that the Denisovan people who stayed isolated from the rest of the world, who never thought of making tools to build a town or even ride a horse for over a hundred thousand years but being able to travel vast distances to court with modern humans in Europe every now and then.  Talk about a bizarre story in human evolution!

While a new sequencing technique now available to researchers that can be used to discern a genome from one DNA strand rather than both is quite remarkable but trying to explain it in historical terms which is forced into a particular framework known as human evolution, is not remarkable, it’s not even science.

We live in an exciting time, since the earth is actually thousands of years old, we are able to learn more about the past rather than loosing valuable information which comes from DNA if the earth was older!