DNA researcher, Andras Pellionisz gives favorable review to a shredding of Dawkins and TalkOrigins

DNA researcher Andras Pellionisz has found unwitting friends in the ID community. He observed that while Darwinists like Richard Dawkins are dismissive of his field of scientific research, ID proponents are surprisingly enthusiastic about his work and that of his colleagues. We have thus found here at Uncommon Descent a friend from quarters I would have never guessed in Dr. Pellionisz and his colleagues.

Pellionisz lamented here that it is the ID proponents who show more interest than people like Dawkins in the highly important areas of research within biology [and imho, evolutionary biology is not a highly important field of research, SYSTEMS Biology is]. Pellionisz then added:

the issue of “Junk” DNA itself is much more vital for human kind, since hundreds of millions are dying of “Junk DNA diseases” while the urgency of plunging into active research is overlooked because on ANY ideological grounds.

Those looking at

http://www.junkdna.com/junkdna_diseases.html

will realize that for those to whom SCIENCE of “junk” DNA is still not the “mainstream” are socially guilty because of putting priority on ideology over survival.

Hundreds of millions of patients don’t appreciate delay of medicine by ideology.

It appears elements within the anti-Design community are institutionally biased against the important research Dr. Pellionisz and his colleagues are performing on behalf of science. And it is the ID community that is far more friendly to this important work than the communtiy of evolutionary biologists.

Pellionisz gives a favorable review of a pro-ID article. The article is: How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schaer.

Dr. Pellionisz gives his review at junkdna.com

From the Shauer’s Article:

Richard Dawkins writes:

And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, “tandem repeats”, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself.
…

Panda’s Thumb also finds it important to argue for “Junk DNA”
….

Tandem Repeats are a class of repetitive DNA unique in every individual, which is why they are used in DNA forensic evidence, etc. … Talk Origins also has this to say about Tandem Repeats: “scientists view tandem repeat sequences as resulting from accidental DNA duplications.”

Now let’s look at what the scientific evidence is telling us about Tandem Repeats:

They Silence and Activate Genes

Tandem repeat sequences are frequently associated with gene silencing phenomena.

This region contains the major and minor promoters of the Tsix gene, which runs antisense to Xist, and the

DXPas34 tandem repeat lying close to the Tsix major promoter.

Our results identify a function for DXPas34 in murine XCI and demonstrate the critical role of Tsix transcription in preventing XCI in differentiating male ES cells and in normal functioning of the counting pathway.

Transfection studies in mouse mesenchymal C3H10T1/2 cells showed that it is the tandem repeat of the C/EBP binding site in PPARgamma2 promoter region that regulates dexamethasone-mediated PPARgamma2 gene activation.

These observations establish that a dinucleotide tandem repeat sequence, capable of self-association, forms part of a cell-specific silencer element in a mammalian gene.

They [tandem repeats] Determine the Length of a Dog’s Nose

Breeds with collie-like noses had more of a particular tandem repeat, while those with pug-like faces had more of a different tandem. And when the researchers compared bull terrier DNA, they found that terriers have one more repeat unit than they did in the 1950s, which could explain why the nose used to be droopier, the researchers note.

They [tandem repeats] Determine a Cow’s Milk Fat Percentage

In addition to this, another polymorphism in the 5′-regulatory region of this gene, the DGAT1 variable number of tandem repeat (VNTR), also showed a strong association with milk fat percentage.

These research finding show that, far from being junk, Tandem Repeats have important functional roles in the genome. More interestingly, the unique copy number in individuals seems not to be caused by random mutations, but rather by a built-in program that occurs during the combination of male and female DNA. While children will tend to inherit Tandem Repeat numbers similar to those of their parents, this variable component makes every child unique. The fact that Tandem Repeats are so well correlated to racial classifications shows that they have a role in determining what each individual looks like. Tandem repeats appear to be the major factor in what determines the size of your nose, the amount of body fat you have, your height, skin color, etc.

Transposons/Retrotransposons

Here’s what Talk Origins says about Transposons:
In many ways, transposons are very similar to viruses. However, they lack genes for viral coat proteins, cannot cross cellular boundaries, and thus they replicate only in the genome of their host. They can be thought of as intragenomic parasites.…finding the same transposon in the same chromosomal location in two different organisms is strong direct evidence of common ancestry, since they insert fairly randomly and generally cannot be transmitted except by inheritance….

So is there evidence that Transposons have function?

They [transposons] are Necessary for Embryonic Development

The research, published in the October issue of Developmental Cell, suggests that retrotransposons may not be just the “junk DNA” once thought, but rather appear to be a large repository of start sites for initiating gene expression. Therefore, more than one third of the mouse and human genomes, previously thought to be nonfunctional, may play some role in the regulation of gene expression and promotion of genetic diversity. Dr. Barbara B. Knowles and colleagues from The Jackson Laboratory in Bar Harbor, Maine, found that distinct retrotransposon types are unexpectedly active in mouse eggs, and others are activated in early embryos. Surprisingly, by acting as alternative promoters, retrotransposon-derived controlling elements drive the coordinated expression of multiple mouse genes. The researchers think that expression of retrotransposons during very early stages may contribute to the reprogramming of the mammalian embryonic genome, a prerequisite for normal development.

They [Transposons] Format the Genome File System…

Generic repeated signals in the DNA format expression of coding sequence files and organize additional functions essential for genome replication and accurate transmission to progeny cells. Retroelements comprise a major fraction of many genomes and contain a surprising diversity of functional signals.

That is just the beginning. Now let’s examine specific classes of Transposons mentioned in the two Talk Origins Articles.

SINE/Alu Sequences

The Talk Origins view of SINEs/Alu:

…current evidence suggests that only a very few Alu sequences are active sources of transcripts; perhaps transcription from most copies is inhibited by the chromosomal environment of the insertion

Further, the excellent health of individuals who lack particular Alu insertions supports the view that these insertions do not serve any important function in human physiology.

What does the recent scientific evidence say about SINEs/Alu?

Alu can turn a single gene into multiple proteins

Through a process called alternative splicing, humans create multiple versions of a gene and, consequently ,multiple proteins. It’s a way of constructing a new protein, while keeping a backup copy of the original version.For example, the researchers found that the ADAR2 enzyme contains 40 amino acids in its active site that arederived from an Alu element. The addition changes the activity of the enzyme.

“The excitement about the exonization of Alu is the ability to explain what is unique in our genome,” Ast says. The mouse genome contains 2.5 billion nucleotides, the human genome around 3 billion. “The quarter of a billion nucleotides, [or] the difference between human and mouse, is mostly [due to] retrotransposable elements like Alu,” he says.

They [Alu] affect Micro-RNA processing

Although Alu was originally thought to represent ‘junk’ having no biological functions, the presence of Alu sequences within protein-coding genes can affect the processing of mRNAs at multiple levels

Highly Conserved Vertebrate SINEs with unknown function

Extensive conservation of V-SINEs can, however, be more easily explained by the hypothesis that the central conserved domain may somehow “earn its keep” in the genome.

The observed conservation strongly indicates that the central domain of these transposable elements have been exapted, i.e., have become a functional component of the mammalian genomes.

The close copies of the ultraconserved element scattered around vertebrate genomes have changed less than would be expected over evolutionary time, indicating that they are functionally important. But relatively few of the copies contain parts that code for proteins, which suggests they [ultraconserved elements] instead are helping to regulate when genes are turned on and off.

“Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality.”

So many SINES have been shown to be FUNCTIONAL, counter to the Talk Origins claims. Alu sequences are unique to primates and seems to be particularly active in the human brain.

LINES

Talk Origins has this to say of LINES:
LINEs thus have several properties expected of “selfish” DNA sequences that can spread in the host DNA simply because they encode their own machinery for spreading.

In other words, they don’t serve a purpose other than to copy themselves, according to Talk Origins.

Here’s what some recent scientific evidence says about LINES:

Human LINE-1 sequences being investigated for function

Long interspersed elements (LINE-1, L1s) are the only active autonomous retrotransposons in mammals, covering as much as 18% of their genomes. L1s’ activity results in a great repertoire of actions, such as gene disruption, transcriptional regulation, alternative splicing, creation of exons and gene coding regions and amplification of the processed pseudogenes and the Alu SINE family.

A LINE-2 sequence which functions as a potent T-cell-specific silencer

In summary, we have identified a LINE-2 fragment named ALF that is a potent T-cell-specific silencer. We also show that agonists that down-regulate ALF-containing genes in T cells induce a factor that binds to a sequence within ALF. These findings are in contrast to other reports associating enhancer or promoter activities with repetitive elements (16,17), because ALF has the potential to function as a cell-type-specific silencer. We favour the hypothesis that this is not an arbitrary activity, and that ALF contributes to gene regulation in vivo.

LINE-1 sequences modify RNA expression

Because L1 is an abundant and broadly distributed mobile element, the inhibition of transcriptional elongation by L1 might profoundly affect expression of endogenous human genes. We propose a model in which L1 affects gene expression genome-wide by acting as a ‘molecular rheostat’ of target genes. Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome.

LINE-1 may have a role in DNA Repair

Thus, our results suggest that LINE-1s can integrate into DNA lesions, resulting in retrotransposon-mediated DNA repair in mammalian cells.

Extrapolating these findings to the 600,000 copies of L1 in the genome, we predict that the amount of DNA transduced by L1 represents ~1% of the genome, a fraction comparable with that occupied by exons. So again, there are plenty of examples now of functional LINES.

Endogenous Retroviruses and LTR retrotransposons

Talk Origins has this to say of Endogenous Retroviruses:
Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous retroviral sequences. Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes.

Here’s what some recent scientific evidence says about Endogenous Retroviruses:

They [Endogenous Retroviruses] show up expressed in many cell tissues

Human tissues that lack HERV transcription could not be found, confirming that human endogenous retroviruses are permanent components of the human transcriptome. Distinct activity patterns may reflect the characteristics of the regulatory machinery in these cells, e.g., cell type-dependent occurrence of transcriptional regulatory factors.

They [Endogenous Retroviruses] are required for placental development?

In particular, a class of endogenous retroviruses, known as endogenous retroviruses related to Jaagsiekte sheep retrovirus or enJSRVs, are critical during the early phase of pregnancy when the placenta begins to develop.

They [Endogeneous Retroviruses] impact gene expression

Indeed, the LTR is the dominant promoter in the colon, indicating that this ancient retroviral element has a major impact on gene expression

EBR LTR promotes a significant proportion of the total EBR transcripts, and transient transfection results indicate that the LTR acts as a strong promoter and enhancer in a placental cell line. They are highly conserved between the mouse and distantly related species…. On account of their abundance, LTR retrotransposons are believed to hold major significance for genome structure and function.…High sequence similarity between several LTR retrotransposons identified in this study and those found in distantly-related species suggests that horizontal transfer has been a significant factor in the evolution of mouse LTR retrotransposons.

Did they cause the human/chimp split or are they simply one more indicator that humans are unique?

The discovery that human-specific retroviruses emerged at the same time other researchers believe humans and chimps diverged was startling.…McDonald said it is increasingly clear that organisms need the viral elements and that their apparent continual backdoor assaults on normal genes may, in truth, be more like a vast, sophisticated chess game on an enormously complex board. Admittedly, most of the scientists involved in the above studies of Endogenous Retroviruses still assume that they were parasites that somehow were incorporated into the genome with functional roles. However, since many of these perform similar functions in different species, one cannot prove common descent based upon the idea that shared retroviruses are shared errors.

Pseudogenes

Both the Talk Origins and Panda’s Thumb websites spend a lot of time on Pseudogenes.

I did not cite the full article here, but I encourage the serious readers to read Shauer’s article, Pellionisz review, and visit Pellioisz website.

I wish to thank Dr. Pellionisz for alerting me us to this wonderful compilation by Wade Schauer.

To quote a line from a famous movie, “I think this is the beginning of a beautiful friendship…”