DNA Science Disproves Human Evolution

Institute for Creation Science ^ | 06/01/17 | Jeffrey P. Tomkins, Ph.D.

[lasereye]

The Bible describes humans as being created in the image of God—the pinnacle of His creation. In contrast, those who embrace the presupposition of naturalistic origins have put much effort and even monkey business into a propaganda crusade to claim a bestial origin for man.

The idea that humans evolved from an ape-like creature was first widely promoted by Jean-Baptiste Lamarck in the early 1800s and later by Charles Darwin in his 1871 book The Descent of Man—published 12 years after his acclaimed evolutionary treatise On the Origin of Species. Thomas Huxley, a friend of Darwin, also did much to popularize this idea. Since then, the secular scientific community has promulgated the still-hypothetical idea of human evolution as an established fact.1

After the 150-plus years since Darwin’s famous publication, we still have no fossil evidence demonstrating human evolution. Darwin believed such fossils would eventually be found, but that has simply not been the case. The following quotes from evolutionists themselves accurately sum up the current state of affairs regarding the fossil record and its wholesale lack of support for human evolution.

The evolutionary events that led to the origin of the Homo lineage are an enduring puzzle in paleoanthropology, chiefly because the fossil record from between 3 million and 2 million years ago is frustratingly sparse, especially in eastern Africa.2

But with so little evidence to go on, the origin of our genus has remained as mysterious as ever.3

The origin of our own genus remains frustratingly unclear.4

The Evolution of Human-Chimp DNA Research

Although paleontological evidence has been lacking, in more recent times evidence supporting human evolution was thought to have been found in the DNA of living apes and humans. This article will evaluate the popular myth of human-chimpanzee DNA similarity along with recent research showing that a broad and unbridgeable chasm exists between the human and chimpanzee genomes.

DNA is a double-stranded molecule that under certain conditions can be denatured—i.e., “unzipped” to make it single-stranded—and then allowed to zip back up. During the initial stages of DNA science in the early 1970s, very crude and indirect techniques were utilized to unzip mixtures of human and chimpanzee DNA, which were then monitored to see how fast they would zip back up compared to unmixed samples.5 Based on these studies, it was declared that human and chimpanzee DNA was 98.5% similar. But only the most similar protein-coding regions of the genome (called single-copy DNA) were compared, which is an extremely small portion—less than 3%—of the total genome. Also, it was later discovered by an evolutionary colleague that the authors of these studies had manipulated the data to make the chimpanzee DNA appear more similar to human than it really was.6 These initial studies not only established a fraudulent gold standard of 98.5% DNA similarity between humans and chimps but also the shady practice of cherry-picking only the most similar data. The idea of nearly identical human-chimp DNA similarity was born and used to bolster the myth of human evolution, something that the lack of fossil evidence was unable to accomplish.

As DNA sequencing became more advanced, scientists were able to compare the actual order of DNA bases (nucleotides) between DNA sequences from different creatures. This was done in a process in which similar DNA segments could be directly matched up or aligned. The differences were then calculated.

Little progress was made in comparing large regions of DNA between chimpanzees and humans until the genomics revolution in the 21st century with its emphasis on developing new technologies to sequence the human genome. Between 2002 and 2005, a variety of reports was published that on the surface seemed to support the 98.5% DNA similarity myth.

However, a careful analysis of these publications reported by this author showed that the researchers were only including data on the most highly aligning sequences and omitting gaps and regions that did not align.5 Once again, we had the same old problem of cherry-picking the data that support evolution while ignoring everything else. However, at least three of these papers described the amount of non-similar data that was thrown out. When those missing data were included in the original numbers, an overall DNA similarity between humans and chimpanzees was only about 81 to 87%, depending on the paper!

Determining DNA similarity between humans and chimpanzees isn’t a trivial task. One of the main problems is that the current chimpanzee genome wasn’t constructed based on its own merits. When DNA is sequenced, it’s produced in millions of small pieces that must be “stitched” together with powerful computers.

In large mammalian genomes like the chimpanzee, this isn’t easy, especially since very few genetic resources exist to aid the effort compared to those available for the human genome project. Because of this resource issue, a limited budget, and a healthy dose of evolutionary bias, the chimpanzee genome was put together using the human genome as a guide or scaffold onto which the little DNA sequence snippets were organized and stitched together.7 Therefore, the current chimpanzee genome appears much more human-like than it really is. In fact, a recent study by this author showed that individual raw chimpanzee DNA sequences that had poor similarity to human sequences aligned very poorly (if at all) onto the chimpanzee genome that had been assembled using the human genome as a framework.8 This is a dramatic illustration that it is not an authentic representation of the actual chimpanzee genome.

Another serious problem with the chimpanzee genome is that it appears to contain significant levels of human DNA contamination. When DNA samples are prepared in the laboratory for sequencing, it’s common to have DNA from human lab workers get into the samples. Several secular studies show that many non-primate DNA sequence databases contain significant levels of human DNA.9,10

A recent study by this author shows that a little over half of the data sets used to construct the chimpanzee genome contain significantly higher levels of human DNA than the others.8 These data sets with apparent high levels of human DNA contamination were the ones utilized during the first phase of the project that led to the famous 2005 chimpanzee genome publication.11 The data sets produced after this were added on top of the ones in the initial assembly. So, not only was the chimpanzee genome assembled using the human genome as a scaffold, but research indicates that it was constructed with significant levels of contaminating human DNA. This would explain why raw unassembled chimpanzee DNA sequences are difficult to align onto the chimpanzee genome with high accuracy; it’s because it’s considerably more human-like than it should be.

So, how similar is chimpanzee DNA to human? My research indicates that raw chimpanzee DNA sequences from data sets with significantly lower levels of human DNA contamination are on average about 85% identical in their DNA sequence when aligned onto the human genome. Therefore, based on the most recent, unbiased, and comprehensive research, chimpanzee DNA is no more than 85% similar to human.

What Does 85% DNA Similarity Mean?

So, what does 85% DNA similarity really mean? First of all, it’s important to note that for human evolution to seem plausible, a DNA similarity of 99% is required. This is based on known current mutation rates in humans and an alleged splitting of humans from a common ancestor with chimpanzees about three to six million years ago. This length of time is a mere second on the evolutionary timescale. Any level of similarity much less than 99% is evolutionarily impossible. This is why evolutionists rely on all sorts of monkey business when it comes to comparing human and chimpanzee DNA—they must achieve a figure close to 99% or their model collapses.

So, what if humans and chimpanzees are only about 85% similar in their DNA? Isn’t this pretty close, too, even if it puts evolution out of the picture? In reality, this level of similarity is exactly what one would expect from a creation perspective because of certain basic similarities in overall body plans and cellular physiology between humans and chimpanzees. After all, DNA is not called the genetic code for nothing. Just as different software programs on a computer have similar sections of code because they perform similar functions, the same similarity exists between different creatures in certain sections of their genomes. This is not evidence that one evolved from another but rather that both creatures were engineered along similar basic principles. DNA similarities between different creatures are evidence of common engineered design, and the fact that the differences in these DNA sequences are unexplainable by alleged evolutionary processes is also strong evidence of design.

The Bible says that every living thing was created according to its kind. This fits the clear, observable boundaries we see in nature between types of creatures, as well as the distinct boundaries researchers find in genomes as DNA sequencing science progresses.

In regard to humans, we are not only a distinctly different kind compared to chimpanzees and other apes, but we are also the one part of creation that stands out above all other living forms because the Bible states, “So God created man in His own image; in the image of God He created him; male and female He created them” (Genesis 1:27).

Not only is evolution a false paradigm lacking scientific support, it also directly attacks one of the key paradigms of the Bible. Humanity’s unique creation in God’s image is foundational to why Jesus Christ came to redeem us. Man became corrupt through sin from his original created state—he did not evolve that way from an ape.

References

1. Menton, D. 2016. Did Humans Really Evolve from Ape-like Creatures? In Searching for Adam: Genesis & the Truth About Man’s Origins. T. Mortenson, ed. Green Forest, AR: Master Books, 229-262.
2. Kimbel, W. H. 2013. Palaeoanthropology: Hesitation on hominin history. Nature. 497 (7451): 573-574.
3. Wong, K. 2012. First of Our Kind: Could Australopithecus sediba Be Our Long Lost Ancestor? Scientific American. 306 (4): 30-39.
4. Wood, B. 2011. Did early Homo migrate “out of” or “in to” Africa? Proceedings of the National Academy of Sciences. 108 (26): 10375-10376.
5. Tomkins, J. and J. Bergman. 2012. Genomic monkey business—estimates of nearly identical human-chimp DNA similarity re-evaluated using omitted data. Journal of Creation. 26 (1): 94-100.
6. Marks, J. 2011. The Rise and Fall of DNA Hybridization, ca. 1980-1995, or How I Got Interested in Science Studies. In Workshop on “Mechanisms of Fraud in Biomedical Research,” organized by Christine Hauskeller and Helga Satzinger. The Wellcome Trust, London, October 17-18, 2008.
7. Tomkins, J. P. 2011. How Genomes are Sequenced and Why it Matters: Implications for Studies in Comparative Genomics of Humans and Chimpanzees. Answers Research Journal. 4: 81-88.
8. Tomkins, J. 2016. Analysis of 101 Chimpanzee Trace Read Data Sets: Assessment of Their Overall Similarity to Human and Possible Contamination with Human DNA. Answers Research Journal. 9: 294-298.
9. Longo, M. S., M. J. O’Neill, and R. J. O’Neill. 2011. Abundant Human DNA Contamination Identified in Non-Primate Genome Databases. PLoS One. 6 (2): e16410.
10. Kryukov, K. and T. Imanishi. 2016. Human Contamination in Public Genome Assemblies. PLoS One. 11 (9): e0162424.
11. The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 437 (7055): 69-87.

    
    * Dr. Tomkins is Director of Life Sciences at the Institute for Creation Research and earned his Ph.D. in genetics from Clemson University, where he worked as a research technician in a plant breeding/genetics program. After receiving his Ph.D., he worked at a genomics institute and became a faculty member in the Department of Genetics and Biochemistry at Clemson.

[exDemMom]

[[Either provide an example of my engaging in Christian bashing, or refrain from making that claim.]]

LOL with the demands- your posts are rife with them- knock yerself out- Bearing false witness lol- that’s rich-

Since you can’t refrain from doing so- I’m done with you- dealt enough with your kind in the past-

I get it. You are not gracious enough to admit that you made a false accusation or to apologize after being called out for it.

If there were an ignore function, I would just ignore you now. Do not expect me to answer any more of your posts.

[BroJoeK]

exDemMom: " I believe the proper term for that is the "Gish gallop"--named after another scientist who found the allure of delving into pseudoscience irresistible."

Wow, you sound like my daughter, though she is no doubt younger than you.
Great, great post.

"The Gish Gallop (also known as proof by verbosity[1]) is the fallacious debate tactic of drowning your opponent in a flood of individually-weak arguments in order to prevent rebuttal of the whole argument collection without great effort.
The Gish Gallop is a belt-fed version of the on the spot fallacy, as it's unreasonable for anyone to have a well-composed answer immediately available to every argument present in the Gallop.
The Gish Gallop is named after creationist Duane Gish, who often abused it."

[BroJoeK]

from the article: "Since then, the secular scientific community has promulgated the still-hypothetical idea of human evolution as an established fact.1"

As a scientist Thomkins certainly knows the differences between hypotheses, theories & facts.
He also knows that much of basic evolution theory is observed confirmed fact -- i.e., descent with modifications and natural selection.
Those are facts because we can see them.
The theory part is what we can't see -- deep time, long term speciations leaving many clues in the fossil record, but not directly observable.

And yes, there are many unconfirmed hypotheses related to evolution, especially in the area of abiogenic origins of life on Earth.
On this much fascinating advanced work has been done since Miller-Urey in 1952, but it's mostly still hypothetical speculations.

from the article: "After the 150-plus years since Darwin’s famous publication, we still have no fossil evidence demonstrating human evolution.
Darwin believed such fossils would eventually be found, but that has simply not been the case...
'The evolutionary events that led to the origin of the Homo lineage are an enduring puzzle in paleoanthropology, chiefly because the fossil record from between 3 million and 2 million years ago is frustratingly sparse, especially in eastern Africa.2 ' "

This is a most astonishing claim, amounting to deliberate self-inflicted blindness in the face of glaring evidence:

Smithsonian: "From skeletons to teeth, early human fossils have been found of more than 6,000 individuals.
With the rapid pace of new discoveries every year, this impressive sample means that even though some early human species are only represented by one or a few fossils, others are represented by thousands of fossils."

from the article: "The Bible says that every living thing was created according to its kind.
This fits the clear, observable boundaries we see in nature between types of creatures, as well as the distinct boundaries researchers find in genomes as DNA sequencing science progresses."

But in fact, there are no such boundaries, as both morphological and DNA analyses demonstrate.
I could cite any number of examples -- consider Polar Bears & Brown Bears once classified in separate genera until viable cross-breeds discovered.
Now they are separate species within the same genus.

Similar reclassifications happened with zebra and giraffes, among many others, where sub-species became species and visa versa based on DNA comparisons.

Even among pre-humans, interbreeding with different species has left its marks in our DNAs including Neanderthals and Denisovans.
So species "kinds" lines are not as sharply drawn in nature as our author here suggests.

from the article: "the Bible states, “So God created man in His own image; in the image of God He created him; male and female He created them” (Genesis 1:27). "

But in chapter 2 Genesis tells us just a bit more about how God did it:

"And the Lord God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul."

To me that sounds like evolution, "from mud to man", at the end of which God performs His pinnacle of creation by breathing the "breath of life" and making Adam the first truly "living soul".

That's why I see no problem with it.

[ifinnegan]

“”And the fact that “junk” fell from over 90% in, say, 1975 to just 65% now doesn’t much impress you.”

Empty rhetoric.

Provide a reference.

[ifinnegan]

“guess you missed the part where I said that my Ph.D. is in the field of biochemistry and molecular biology. “

No, I didn’t. It makes your shocking ignorance of the last 20 years quite sad.

“ase pairs on the chromosome, but the coding region is only 2547 base pairs—meaning that 96.6% of that gene is junk that the cell excises and discards “

You’re not in the field anymore, are you?

Genomic studies and the understanding of the importance of chromatid structure has shown “junk DNA” to be an obsolete non-useful idea.

You really still think that protein coding regions are all that matter?

And don’t be slandering Phil Sharp m

[ifinnegan]

“You, of course, keep bringing up more and more details that are outside of the scope of this discussion—I know, the tactic is meant to trip me up”

Paranoid much?

[ifinnegan]

“I can’t help but observe that a “discussion” with a creationist is much like...”

Interesting how you judge and pre-judge.

I assume you believe in God the Creator (maybe you’re atheist, I don’t know). If so, there are plenty of people who would pre-judge and dismiss you.

[itsahoot]

As for God, I frankly don't think He objects to evolution theory, just so long as we "get" Who is the Master of evolution --

And just what part of the current instruction on evolution, would encourage anyone to believe there even was a God? Whether God is interjected into the argument or not no data that would point to any other explanation for the Origin of Species is allowed in any institution of higher learning.

'Truth is stranger than fiction, but it is because Fiction is obliged to stick to possibilities; Truth isn't.' Mark Twain -

Look into how 97% of scientists believe man made global warming is true. Then see if any scientific journal will let anyone contest that statement in their peer reviewed publications, they won't. The government is involved in this scam 100%.

The question is why? Money and control which creates several subsets of reasons but basically it comes down to the two, always. Of course there are some true believers that actually think they are saving the world. Marxists referred to these people as useful Idiots.

[BroJoeK]

Ifinnegan: "Empty rhetoric. Provide a reference."

Non-responsive.

See links in my post, or do your own googling.
All my data is readily available to anybody who looks for it.

[ifinnegan]

So asking someone to back up assertions I “non-responsive”?

My response was clear. It’s empty rhetoric.

You seem not to understand 1) that it is empty rhetoric and 2) why it’s empty rhetoric.

“And the fact that “junk” fell from over 90% in, say, 1975 to just 65% now doesn’t much impress you.”

This is just an uninformed ludicrous, even senseless comment.

When were introns discovered? What year?

[ifinnegan]

You both seem to have big issues with Creationists and with popular arguments over “junk DNA”m

You also both seem to know little more of DNA than that it codes for proteins, and the old idea that, therefore, all other sequences are non-functional filler.

One cites Phil Sharp’s 1977 discovery of introns, which would put the non-coding portion on mammals at 98% or so, another says it was 90% in 1975 (before introns were ever discovered).

There’s no reason not to laugh or make fun of both or either of you.

But I don’t and know you are FRiends.

So I will try to walk you through the most recent findings in the amazing world of nucleic acids and the key importance of non-coding DNA.

This is great stuff and reflects how intricate, multifunctional and complex DNA is.

We can start with a 2017 articles from Phil Sharp.

https://www.ncbi.nlm.nih.gov/pubmed/28283057

Cell. 2017 Mar 9;168(6):1000-1014.e15. doi: 10.1016/j.cell.2017.02.015.
Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis.

Suzuki HI1, Young RA2, Sharp PA3.

Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function. CRISPR/Cas9 genomics revealed that super-enhancer constituents act cooperatively and facilitate Drosha/DGCR8 recruitment and pri-miRNA processing to boost cell-specific miRNA production. The BET-bromodomain inhibitor JQ1 preferentially inhibits super-enhancer-directed cotranscriptional pri-miRNA processing. Furthermore, super-enhancers are characterized by pervasive interaction with DGCR8/Drosha and DGCR8/Drosha-regulated mRNA stability control, suggesting unique RNA regulation at super-enhancers. Finally, super-enhancers mark multiple miRNAs associated with cancer hallmarks. This study presents principles underlying miRNA biology in health and disease and an unrecognized higher-order property of super-enhancers in RNA processing beyond transcription.

[BroJoeK]

itsahoot: "And just what part of the current instruction on evolution, would encourage anyone to believe there even was a God?"

None, because it's science and science, by definition, only covers natural causes for natural processes.
As soon as you bring supernatural God into the picture, it's no longer natural science.
That's why you don't want government union employees teaching your children your religious beliefs.
You and your church should do that.

Now, in the proper church-school setting, your pastor can explain Genesis and answer any questions about evolution or science your children may ask.
Then you can be certain your own religious beliefs are being passed on to your family.
But that can never happen in government schools, never, and you absolutely don't want it to.

How is that not plain & clear?

itsahoot: "Look into how 97% of scientists believe man made global warming is true.
Then see if any scientific journal will let anyone contest that statement in their peer reviewed publications, they won't.
The government is involved in this scam 100%."

Well, first, I don't for a minute believe that 97% number.
At least not if applied to the AlGore "inconvenient truth" political agenda nonsense.
Sure, 97% of "scientists" will say that it's warmer today than it was at some time in the past -- for example, in January.
But the full throated Leftist One World Big Government socialist agenda is not approved by 97% of anybody regardless of how often AlGore claims otherwise.

Second, there are peer-reviewed reports, including even some from the government itself, which say AGW is not the great boogeyman Leftist claim.

And third, a point I always make on this: looking at the geological record of past ice-ages, it appears we are today past due for the next one, and when ice ages arrive they arrive very quickly, in a matter of decades.
Now I don't know what might trigger ice-ages, but it still seems to me that a little "global warming" might help delay the next one by even a few centuries.
That would be good!

itsahoot: "Marxists referred to these people as useful Idiots."

Totally agree!

[BroJoeK]

ifinnegan: "There’s no reason not to laugh or make fun of both or either of you."

{sigh} You're hopeless.

[ifinnegan]

To follow up on your obsession with “junk DNA” and paranoia that somehow “junk DNA” having function would be a victory for “ creationists” (an odd concern for a scientist), let’s look at “junk DNA”.

Junk DNA was always a non-technical and informal term.

One notes that Phil Sharp did not use such a term in his Nobel speech (https://www.nobelprize.org/nobel_prizes/medicine/laureates/1993/sharp-lecture.pdf), nor are there any articles by him with the term “junk DNA” as per PubMed search.

And it’s quite something that Sharp went on after his Nobel work to study “junk DNA” for its important regulatory properties.

The term was always descriptive, informal and not meant to be taken literally.

If we do a search on current literature, we do find “junk DNA” referenced, in most cases using the term ironically to underscore the folly of the concept.

https://www.ncbi.nlm.nih.gov/pubmed/?term=%22Junk+dna%22

Some selected articles from a “junk DNA” PubMed search.

---

Ann Transl Med. 2017 Mar;5(6):147. doi: 10.21037/atm.2017.01.20.
The importance of being ncRNAs: from bit players as “junk DNA” to rising stars on the stage of the pharmaceutical industry.

Di Mauro V1,2,3, Catalucci D1,2.

(Excerpt)

For many years it has been assumed that only functional proteins, encoded by genomic sequences containing open reading frames (ORFs), were accountable in playing crucial roles in almost all biological processes, including cardiac physiology and pathologies (3). However, only 2% of the eukaryotic genome codes for proteins, which is why the formerly called “junk DNA” has become an expanding area of interest. Indeed, the latest advances in sequencing technologies and initiatives such as ENCODE (Encyclopedia of DNA Elements) have highlighted that the mammalian genome is actively transcribed into a myriad of non-coding transcripts, collectively defined as ncRNAs (4). In the context of the cardiovascular system, only recently it has become evident how these ncRNAs may play a crucial role in the gene regulatory networks that control physiological and pathological development (5).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395473/

---

BMC Genomics. 2017 Feb 23;18(1):200. doi: 10.1186/s12864-017-3566-0.
Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development.

Ge SX1.
Author information

Abstract
BACKGROUND:
Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study the complex gene regulation in mouse pre-implantation development (PD).
RESULTS:
Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time.
CONCLUSIONS:
Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3566-0

[ifinnegan]

And I post this one separately so it doesn’t get lost in the mix. Chromatin structure and regulation is essential for all aspects of biology. Ultimately this is what determines a species, eg why a human and ape genome can be so similar, especially in coding regions, but something causes one to be human, one ape.

The article below is representative of this type of work where the regulatory importance of the worst of the worst “junk DNA” is being elucidated and is crucial at a fundamental level.

—/

Chromosome Res. 2017 Mar;25(1):77-87. doi: 10.1007/s10577-016-9547-3. Epub 2017 Jan 11.
The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals.

Nishibuchi G1, Déjardin J2.
Author information

1
Biology of Repetitive Sequences, CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France.
2
Biology of Repetitive Sequences, CNRS UPR1142, 141 rue de la Cardonille, 34000, Montpellier, France. jerome.dejardin@igh.cnrs.fr.
Abstract
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes. Genetic and biochemical studies have revealed that histone methylation at H3K9 and its recognition by heterochromatin protein 1 represent the fundamental mechanism by which heterochromatin forms. Although this molecular mechanism is highly conserved from yeast to human cells, its detailed epigenetic regulation is more complex and dynamic for each distinct constitutive heterochromatin structure in higher eukaryotes. It can also vary according to the developmental stage. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis is a powerful tool to investigate the epigenetic regulation of eukaryote genomes, but non-unique reads are usually discarded during standard ChIP-seq data alignment to reference genome databases. Therefore, specific methods to obtain global epigenetic information concerning repetitive elements are needed. In this review, we focus on such approaches and we summarize the latest molecular models for distinct constitutive heterochromatin types in mammals.

KEYWORDS:
Constitutive heterochromatin; endogenous retrovirus; interspersed repetitive element; pericentromere; retrotransposon; tandem repeat; telomere

PMID: 28078514 DOI: 10.1007/s10577-016-9547-3

[ifinnegan]

“{sigh} You’re hopeless.”

Please read what I’ve written to you.

Going back to last night and the idea that only coding is DNA’s function.

A key is DNA itself, in it’s very structure, its’ electro-chemical properties, has function.

Regions well outside any gene or coding region have shapes that are recognized by regulatory events, can be protein alone or RNA alone or complexes of protein-RNA.

How and where the chromatin is wound or unwound is central to regulating gene expression patterns.

This is ultimately more important than protein coding in that proper regulation of gene expression determines everything.

Indeed many cancerous transformations can be accounted for by an acquired defect in this sort of proper regulation. Transformed cells lose their function and become differently-differentiated, no longer carrying out their physiological role. Yet they continue to code for proteins and churn them out without regard for their functional utility so that the cancer simply grows and uses resources without producing physiological benefit.

All due to dysregulation of regulatory elements which are non-coding “non-functional” regions of DNA.

The structure or shape of DNA in and of itself is functional.

[ifinnegan]

Per your reference to 65%

http://rationalwiki.org/wiki/Junk_DNA

That is not a scientific site and has no scientific references or merit at all.

It reflects the irrational obsession over the term junk DNA, though.

It has nothing to do with biology except in as much as it attempts to exploit it.

My advice- drop the crevo crud.

[ifinnegan]

These were like my bibles in grad school.

[ifinnegan]

“You base that claim on what, exactly? On the fact that I do not repeat creationist pseudoscience nonsense, and only stick with the actual scientific papers published in journals like Science...”

http://www.sciencemag.org/news/2016/08/junk-dna-tells-mice-and-snakes-how-grow-backbone

(Excerpt)

‘Junk DNA’ tells mice—and snakes—how to grow a backbone
By Diana CrowAug. 1, 2016 , 11:45 AM
Why does a snake have 25 or more rows of ribs, whereas a mouse has only 13? The answer, according to a new study, may lie in “junk DNA,” large chunks of an animal’s genome that were once thought to be useless. The findings could help explain how dramatic changes in body shape have occurred over evolutionary history.

Scientists began discovering junk DNA sequences in the 1960s. These stretches of the genome—also known as noncoding DNA—contain the same genetic alphabet found in genes, but they don’t code for the proteins that make us who we are. As a result, many researchers long believed this mysterious genetic material was simply DNA debris accumulated over the course of evolution. But over the past couple decades, geneticists have discovered that this so-called junk is anything but. It has important functions, such as switching genes on and off and setting the timing for changes in gene activity.

Recently, scientists have even begun to suspect that noncoding DNA plays an important role in evolution. Body shape is a case in point: “There’s an immense amount of variation in body length across vertebrates, but within species the number of ribs and so forth stays almost exactly the same,” says developmental biologist Valerie Wilson of the University of Edinburgh. “There must be some ways to alter the expression of those [genes] regulating evolution to generate this massive amount of variation that we see across the vertebrates.”

To explore this question further, researchers led by developmental biologist Moises Mallo of the Gulbenkian Institute of Science in Oeiras, Portugal, turned to an unusual mouse. Most mice have 13 pairs of ribs, but a few strains of mutant mice bred by Mallo and colleagues have 24 pairs. Their rib cages extend all the way along their backbone, down to the hind legs, similar to those of snakes.

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And some fun stuff.

http://blogs.sciencemag.org/pipeline/archives/2015/03/09/the_junk_dna_fight

The Junk DNA Fight
By Derek LoweMarch 9, 2015

In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. “We don’t use that term anymore,” Collins replied. “It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, “turns out to be doing stuff.”
For Gregory and a group of like-minded biologists, this idea is not just preposterous but also perilous, something that could yield bad science. The turn against the notion of junk DNA, they argue, is based on overinterpretations of wispy evidence and a willful ignorance of years of solid research on the genome. They’ve challenged their opponents face to face at scientific meetings. They’ve written detailed critiques in biology journals. They’ve commented on social media. When the N.I.H.’s official Twitter account relayed Collins’s claim about not using the term “junk DNA” anymore, Michael Eisen, a professor at the University of California, Berkeley, tweeted back with a profanity.

[exDemMom]

Even among pre-humans, interbreeding with different species has left its marks in our DNAs including Neanderthals and Denisovans. So species "kinds" lines are not as sharply drawn in nature as our author here suggests.

And then there are the retroviruses that have inserted themselves into human (and other mammalian) DNA throughout evolution and become a permanent part of our genome. A sizeable fraction of our DNA is, in fact, viral DNA. One fascinating consequence of the viral DNA contained within our genome is that a protein essential for placenta formation is, in fact, viral in origin. Which begs the question, if it were not for viruses inserting themselves into the mammalian genome tens of millions of years ago, would mammals carry around some sort of egg inside, and give birth only when the egg hatches? Some fish reproduce in that manner.

At this time, there is a retrovirus spreading among koalas. The indication is that the retrovirus is making itself a permanent part of their genome.

The process of evolution is truly amazing.