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!

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Scientists Claim: They Performed Evolution

Geneticists are in the process of engineering molecules which is great science, but when scientists alter molecules which is not found in nature, are they performing evolution which is a mindless unguided process or intelligent design? Is there any evidence for evolution in the experiment?

The abstract in the paper goes like this…

Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution. It involves the storage and propagation of molecular information and the refinement of that information through experience and differential survival. Heretofore, the only molecules known to be capable of undergoing Darwinian evolution were RNA and DNA, the genetic molecules of biology. But on page 341 of this issue, Pinheiro et al. (1) expand the palette considerably.”

“They report six alternative genetic polymers that can be used to store and propagate information; one of these was made to undergo Darwinian evolution in response to imposed selection constraints. The work heralds the era of synthetic genetics, with implications for exobiology, biotechnology, and understanding of life itself. “

Here the paper uses circular reasoning, “Genetics provides a mechanism for molecular memory and thus the basis for Darwinian evolution.” There was no observation of nature selecting the defined structures nor the targets, nor the aptamers! It was an international team of scientists who did the selecting! Not only that but their altered molecules “remains relatively inefficient.” unnatural or designed by scientists are poor polymerase substrates at full substitution.

Molecular memory is not a demonstration of evolution rather it’s an assumption of the data.  Scientists invented their own selection strategy which they call  “compartmentalized self-tagging.”  

The conclusion of the paper says…

Our work establishes strategies for the replication and evolution of synthetic genetic polymers not found in nature, providing a route to novel sequence space. The capacity of synthetic polymers for both heredity and evolution also shows that DNA and RNA are not functionally unique as genetic materials.”

“The methodologies developed herein are readily applied to other nucleic acid architectures and have the potential to enable the replication of genetic polymers of increasingly divergent chemistry, structural motifs, and physicochemical properties, as shown here by the acid resistance of HNA aptamers (fig. S17). Thus, aspects of the correlations between chemical structure, evolvability, and phenotypic diversity may become amenable to systematic study. Such “synthetic genetics” — that is, the exploration of the informational, structural, and catalytic potential of synthetic genetic polymers — should advance our understanding of the parameters of chemical information encoding and provide a source of ligands, catalysts, and nanostructures with tailor-made chemistries for applications in biotechnology and medicine.”

Other media makes wild claims that this experiment produces a more understanding about the origin of life which is nothing more than presupposes the existence of DNA. Because without DNA along with its specified information, and proteins to build DNA, nothing happens! Unless scientists are observing this in nature without their tinkering around, this is not evolution rather they are tinkering with something that was intelligently designed by God.  Even if evolution was true, just because it was done in a lab, doesn’t mean nature does it and altering molecules in a lab is not a demonstration on how evolution works rather just like evolution itself, it’s a man-made up story about the experiment.

Plants Are Not To Be Taken For Granted

We generally don’t think much about plants except what they produce like fruits and vegetables or for decoration. They seem so slow to us and stationary, but actually they move and breath and carry on their lives in truly amazing ways! Did you ever ask, how do plants know when it is spring time or winter time?

In physorg

“Sibum Sung, a molecular biologist at the University of Texas Austin has an idea of how this protective action works on a cellular level. He discovered a special molecule in plants that gives them the remarkable ability to recall winter and to bloom on schedule in the spring. Sung published his results last December in the journal Science Express.”

“While digging through the DNA of a small cabbage-like plant called Arabidopsis, Sung and a colleague discovered that the production of a special molecule could be turned on or off by a string of genetic material. When the plant gets cozy for the winter, this molecule is not produced, repressing a plant’s ability to create flowers. But after 20 days of consistently frigid weather, production of the molecule gets turned back on, signaling another gene to stop repressing flower production and start preparing for spring.”

So how do plants do it? In reviewing a new book, The Restless Plant by Dov Koller (Harvard, 2011), Roger Hangarter’s Plants-in-Motion web site was referenced the site has time-lapse videos of plant movements.

Sarah Wyatt writes in science

“The Restless Plant presents a “guided tour of plant movements.” Koller starts with the classic, rapid leaf movements of the sensitive plant and [Venus] flytrap but then provides a broader understanding of plant movement that includes growth responses, expansion of plant organs, and movements of individual cells and organelles.  The world of plants becomes a fascinating dance with many movements: contractile roots pulling a bulb into the soil; the folding of leaves and flowers at nightfall; leaves and flowers tracking the Sun; roots searching for water and nutrients; the explosion of seeds into the world at large; and growth responses to light, gravity, water, temperature, and touch.”

Motors” provide these movements, and, although the use of the term for some of the responses is not without controversy, the analogy is sound. For more rapid, reversible movements, motors involve turgor-driven responses in specific cells (pulvini) that are filled or drained of water as needed for movement.  For the slower growth movements, the tropisms, the motors are growing cells within specific regions of the plant.”

Evolutionists are clueless with plant evolution but not at a loss for using imagination in their explanations! The Moody Institute of Science made one of their most beautiful and intriguing films about plant movements back in the 1990s: Journey of Life! A must see for any video library. Plants are not to be taken for granted!

The Results For Testing Natural Selection On Fruit Flies

During a speech urging the federal government to fully fund the Individuals with Disabilities Education Act (IDEA) then governor, Sarah Palin in October 2008 became critical of spending money for fruit fly research…

She said…

“Where does a lot of that earmark money end up anyway? You’ve heard about some of these pet projects they really don’t make a whole lot of sense and sometimes these dollars go to projects that have little or nothing to do with the public good. Things like fruit fly research in Paris, France. I kid you not.”

Being a conservative and a creationist, she was subjective to all sorts of name calling to “anti-science” rants. However, she was unaware (like most people) that fruit fly research was being used for trying to understand autism. But it’s not the only type of researching going on. A recent study performed an experiment on fruit flies to test the limits of natural selection. It was a major blow to the evolution is an indisputable fact crowd…

The experiment showed only minor changes after 600 generations and what is even more interesting, there was less so-called evolution in these organisms than in similar experiments conducted with microbes, like bacteria and yeast! And success is a lot less likely in the wild than under ideal lab conditions! The paper in Nature is called, “Experimental evolution reveals resistance to change” where it says…

“Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast.  Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development.”

“Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes.  On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development  and pooled controls.”

“On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment.”

“Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed.  More parsimonious  explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants.”

“We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.”

In other words, they were looking for a “signature” of beneficial mutations becoming fixed in the population. Despite their success in creating mutations with the fruit flies, their designed bodies resisted change. And not only that but the fruit flies went in the other direction on what secular scientists call, “reverse-evolution.” Instead of new mutations, there were variants of them. The last paragraph describing the fruit fly research displays disappointment and surprise over this…

“Our work provides a new perspective on the genetic basis of adaptation.  Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.  This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations.”

“Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments.  This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.”

Why are the planets moving backwards? We must figure out why this gap is seemingly the case in the theory of Geocentrism. Perhaps Heliocentrism is a better alternative! Nah, geocentrism is an undisputable fact, eventually this observation will be explained thus preserving it…Ok, that’s not about fruit flies and Darwinian evolution, but you get the idea. Natural selection is presumed to be a miracle worker, that can produce the brain, eyes, ears, nose, and mouth in a step by step process using mutations. However, it doesn’t work theoretically nor historically, nor experimentally. It’s a failed ‘theory’ that relies on story telling.

Sarah Palin was wrong about how valuable fruit fly research can be not only for understanding or fighting diseases, but understanding how variation works within it’s own kind, and how it disproves the idea of evolution as an “indisputable fact.”

Paradigm-shifting With New Discovery About RNA

Pseudogenes are regarded in the evolutionary world that has value with history and claims of being good genes at one point in time then by random chance natural selection didn’t act upon them anymore.  However, advancements in science say otherwise…

“In a study appearing in the June 24, 2010 issue of Nature, the authors describe a new regulatory role for RNA — independent of their protein-coding function — that relies on their ability to communicate with one another. Of potentially even greater significance, because this new function also holds true for thousands of noncoding RNAs, the discovery dramatically increases the known pool of functional genetic information.”

This newly discovered function in RNA unrelated to protein production is vital in fighting tumors! Without this presumed piece of junk with only history in it’s sequences your chances of getting cancer go extremely up!  A complete surprise by evolutionary scientists because if evolution was true it ought to leave junk behind right? Because of this faulty concept that evolution promotes, growth in knowledge has been hindered!

“Defining ‘junk DNA’ is getting trickier.  Pseudogenes, for instance,  have been viewed as non-essential genomic elements and have mostly been ignored.  Well, they shouldn’t be anymore, according to Poliseno and colleagues, who show a clear functional relationship between the tumour-suppressor gene PTEN and its pseudogene PTENP1 (Fig. 1).  This study could have major implications for understanding mechanisms of disease, and of cancer in particular.”

Evolutionists insist it looks like the wind blew it together, rather than intelligently designed. The Darwin crowd should not be so surprised by these discoveries, there is a pattern of junk DNA having some kind of function. Instead of assuming it’s junk, they better start asking other questions like why has it been placed there, for what purpose? When unable to answer, it shouldn’t be considered junk for history value rather no known function has been found but continue research. If evolutionary geneticists think outside the box of Darwinian evolution, they will discover even more amazing things!

New Research On Neanderthals Puts Old Assumption To Rest

What has been deemed to be an astonishing implication puts to rest the evolutionary story about Neanderthals and vindicates creationism…

A blogger points out…

“Michael states that Neanderthals “are quite human like the rest of us.” Persuasive genetic evidence from the recent sequencing of several Neanderthal genomes shows that they were not human, but a separate species that branched off about 700kyr ago, and did not thereafter interbred with humans…It is only the popular press that portrays Neanderthals as dim witted. And their physiognomy allowed them to survive in climates that humans could not easily tolerate.

This dedicated blogger who believes in the story of evolution makes the assumption that persuasive genetic evidence from sequencing  had already vindicated his position back in January 2010. He is not the only one as other articles that pertained to this subject have been written. But not so fast!  The research was only beginning when these assumptions were being made. Last week a paper with a more thorough analysis of Neanderthal’s genome which was summarized by science daily said this to the contrary…

“Although we are both hominids, the fossil record told us long ago that we differ physically from Neandertals, in various ways. But at the level of genes and the proteins that they encode, new research published online May 6 in the journal Science reveals that we differ hardly at all.”

“It also indicates that we both — Neandertals and modern humans — differ from the chimps in virtually identical ways…In short, Hannon says, “the news, so far, is not about how we differ from Neandertals, but how we are so nearly identical, in terms of proteins.”

Keep in mind there is more research to go with the Neandertal’s genome because only 60 percent has been recovered so far while a third of it has yet to be sequenced. Also, more research includes gene regulation which could reveal even more similarities which deal with function rather than sequence.

What is more revealing, Europeans and Asians share about 1% to 4% of their nuclear DNA with Neanderthals, indicating that there was substantial interbreeding that went on between the two groups in the past.

This is very important evidence because when a species can interbreed like in this case Neanderthals and modern humans then they are the same species! Creationism vindicated once again!

More articles on Neanderthals published in science

“A Draft Sequence of the Neanderthal Genome” by Green et al.1  Some 55 authors are listed on the paper, including Svante Paabo, who has advanced theories about Neanderthal interbreeding for years.

The NY Times, a militant publication for evolution attempts to keep the old assumption alive by suggesting we are still distinct from Neandertal man. But even in places like John Hawk’s blog who is an  Associate Professor of Anthropology at the University of Wisconsin answered his own question if this means Neanderthal man belongs in our species and the answer was a resounding, “yes”.

Neanderthal research through the years has never been a search for unbiased truth about the history of humans rather it was about looking for that evolutionary story using artistic reconstructions as the main prop on how a cell became a specialized complex human being. Fictional stories were invented telling us about how Neanderthals split 650,000 years ago only to encounter modern humans to interbreed with 100,000 years ago.

Logic would seem to indicated that the time span of 550,000 years would have drifted Neanderthals so far apart that interbreeding would have been impossible with modern man. What was our hominid ancestors doing for 150,000 years and then invented agriculture and domestication so recently and so abruptly? Do you see how absurd these evolutionary time frames are in relation to the evidence?

So who were these Neanderthals?  No, they didn’t live 650,000 years ago. They were people who migrated after the Flood, like everyone else. They became a very close-knit tribe which separated themselves from others. Inbreeding of tribes led to accentuated features. Physical characteristics or traits could have been caused by their diet custom or a harsh environment, age, or disease.

Neanderthals did not arise out of such things as population bottlenecks caused by major diseases nor massive murders carried out through the centuries which reduces the gene pool. It explains why the percentage of Neanderthal DNA found in modern humans is small.  In the Book of Genesis it advocates a world of distinct reproductive groups varying within their kinds which we observe today.

The amazing new research reveals what creationism expected so after 150 years of  being taught the wrong things about Neanderthal man because of the storytelling in evolution, it’s time to put the old evolutionary assumption about Neanderthals which is long overdue to rest!

New Paper Advocates The “Genetics First” Hypothesis

Last year, William Dembski who is one of the key figures in the modern intelligent design movement recently debated Lewis Wolpert who is a developmental biologist. It was an interesting debate, but they were not the only ones butting heads, there was another ID proponent who reviewed the debate and found it to be not that impressive, he states…

“I am afraid I will have to disagree with the impression of the debate. While I give Wolpert a failing grade or at best a D, I cannot give Bill Dembski’s responses better than a C…”

“One glaring example was when Bill was asked whether Chemistry was designed. There was hesitation and then an attempt to get into the design of the universe. The better answer would have been that the laws of Chemistry flow from the characteristics of the elements and that these flowed from the basic laws of physics. To try to move it immediately to the design of the laws of physics left the impression that there was a designer behind every door.”

Dembrski takes issue with a fellow contributor of ID…

“Jerry, We have some history in which you find fault with my presentations, and in which you cite your Duke and Stanford degrees and experience in business communications as qualifications for offering up your criticisms.

As I point out in the debate, the arrangement of stones can signify design even if the stones themselves can’t be said to be designed. The same point can be made for chemistry — basic chemistry may be undesigned (I don’t believe this) but chemical arrangements might be. Thus there are nuances to the design question in chemistry and physics that I was not willing to slide over in my discussion with Wolpert.”

Obviously, Dembski went into is comfort zone which is physics rather than chemistry. Most likely Stephen Meyer could have addressed the chemical aspect. But this brings up the “Genetics First” hypothesis (chance formation of nucleic acids) verses metabolism coming into existence first. The later has been rising in popularity in certain camps. Evolutionists believe replication of chemicals must be in play before natural selection can pick the best material so it can build it into elephants, sharks, humans, you name it.

Two Darwinian schools of thought on origins butting heads and falsifying each other. Three European scientists who published a paper in PNAS, said stated the following…

“A basic property of life is its capacity to experience Darwinian evolution.  The replicator concept is at the core of genetics-first theories of the origin of life, which suggest that self-replicating oligonucleotides or their similar ancestors may have been the first “living” systems and may have led to the evolution of an RNA world.”

“But problems with the nonenzymatic synthesis of biopolymers and the origin of template replication have spurred the alternative metabolism-first scenario, where self-reproducing and evolving proto-metabolic networks are assumed to have predated self-replicating genes.  Recent theoretical work shows that “compositional genomes” (i.e., the counts of different molecular species in an assembly) are able to propagate compositional information and can provide a setup on which natural selection acts.”

“Accordingly, if we stick to the notion of replicator as an entity that passes on its structure largely intact in successive replications, those macromolecular aggregates could be dubbed “ensemble replicators” (composomes) and quite different from the more familiar genes and memes.”

We know metabolism-first scenario is plagued with many problems of its own as indicated in this paper. Anyone can generalize the notion of a replicator up to a system or network of molecules instead of requiring a genetic code but replication has to be accurate! In a designed world we live in, there is not much room for error, in the story of evolution there is plenty room for errors which supposedly result in updates or upgrades.

The “Genetics First” hypothesis have it’s problems as well. Leslie E. Orgel of the Salk Institute for Biological Studies who has spent a lifetime studying origins from an evolutionary framework.  His final paper published in 2007 in PLOS, was not very encouraging for evolutionists, it was called; “The Implausibility of Metabolic Cycles on the Prebiotic Earth.”

The caption reads like this…“In this essay, the final contribution of his scientific career, Leslie Orgel explores the severe difficulties that arise when these proposals are scrutinized from the standpoint of chemical plausibility.”

Their hope is fading, the story of  complex polymers to arise naturally. Rather, they are starting to settle for more on untested ideas such as simple compounds arising instead. Orgel in his final criticisms of the field are so broad and so damaging to the ability of natural processes to produce life at all by any method.  He states…

“It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility.”

Does this sound familiar? I have repeated this theme many times in various topics when it comes to the scientific method concerning data. Just because there is a claim that it could happen, doesn’t mean it ever will. For example, some might believe O2 levels increased sizes of animals and could test O2 levels in tanks to see if it had effects on smaller animals. Then say well we haven’t found it yet, but we believe it will show results. This doesn’t mean certain O2 levels can evolve by a million-fold.

“Whatever the original input, one would finish with an equilibrium mixture, the composition of which is determined by thermodynamics.” Equilibrium means you are at a standstill and nothing more will happen.

Back to the ID debate which I opened up with. Even though Jerry was vague in his assertion that the laws of chemistry  should have been included in the debate for ID, it’s certainly in the debate for creationism. Science has said “no” countless times to evolutionary prediction, assumptions, and other stories. But science has said “yes” to a creator, an intelligent designer, namely God!