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.