'smORFs': Functional Little Genome Gems Confront Evolution (article)

Institute for Creation Research ^ | Oct. 14, 2013 | Jeffrey Tomkins, Ph.D.

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'smORFs': Functional Little Genome Gems Confront Evolution

by Jeffrey Tomkins, Ph.D. *

Until recently, thousands of tiny, potential protein-coding regions in the genome called "small open reading frames" or "smORFs" have been difficult to identify. They are now getting well-deserved attention for the important biochemical functions they play in the cell—like making your heart beat.1

In the present study published in Science, researchers found two smORF-encoded proteins in fruit fly genomes that were 28 to 29 amino acids in length and involved in regulating calcium transport and calcium intake in muscle and heart cells.1 And based on these proteins' 3-D shape and function in flies, the researchers found two counterparts in humans, which they also characterized and found to be involved in calcium uptake and heart muscle function as well.

Based on their 3-D shape, the researchers claimed that the human smORF proteins evolved from fly smORFs over a span of 550 million years, despite the fact that the DNA sequences that encode them showed virtually no similarity. The authors of the report revealed this contradiction burying it in the middle of their report where they said, "We searched for conservation of these smORFs in other species by using Basic Local Alignment Search Tool (BLAST) and only identified them in other Drosophilids [other fruit flies] (page 1118)."1 In other words, the DNA sequences for these smORFs were specific only to fruit flies and showed no evolutionary relationship to humans or any other creature. For all practical purposes, the evolutionary story behind this discovery was marginal all along.

Most of the proteins produced in the human genome are about 500 amino acids long on average. The proteins encoded by smORFs are only about 10 to 30 amino acids long and have been largely found by happenstance while studying gene mutations. Noted Harvard University physiologist, Alan Saghatelian (not an author on the current study) said, "These things have fallen through the cracks of traditional gene-finding algorithms, and most of the ones we know about have been serendipitously discovered."2

Interestingly, the smORF-related genes that contain segments that encode these small proteins—called long non-coding RNAs or lncRNAs—are often quite long (much like protein-coding genes), are complexly regulated, and highly multifunctional.1 These lncRNA genes occupy the regions of the genome once thought to be nothing but junk DNA. However, lncRNAs have been found to be highly cell and tissue specific in their function and also encode other important regulatory molecules like micro RNAs. Some lncRNAs also combine with various proteins to make different types of important cell machinery and are key players in epigenetic modifications (chemical tagging) in controlling the genome's function.3 Amazingly, lncRNAs are also proving to be key players in DNA repair, 3-D chromosomal positioning in the nucleus, and overall genome stability and function.4

Since no real DNA sequence-based evolutionary relationships exist for these human and fruit fly smORFs encoded within lncRNA genes, the most important news about this discovery is the continuing revelation of pervasive design and function in the genome—further negating the weak evolutionary paradigm of junk DNA.

References

Magny, E. et al. 2013. Conserved Regulation of Cardiac Calcium Uptake by Peptides Encoded in Small Open Reading Frames. Science. 341 (6150): 1116-1120.

Yong, E. Hidden Treasures. The Scientist. Posted on the-scientist.com August 22, 2013, accessed September 20, 2013.

Rinn, J. L. and H. Y. Chang. 2012. Genome Regulation by Long Noncoding RNAs. Annual Review Biochemistry. 81:145–166.

Ohsawa, R. J. H. Seol, and J. K. Tyler. 2013. At the intersection of non-coding transcription, DNA repair, chromatin structure, and cellular senescence. Frontiers in Genetics. 4 (36). doi:10.3389/fgene.2013.00136.

*Dr. Tomkins is Research Associate at the Institute for Creation Research and received his Ph.D. in genetics from Clemson University.

Article posted on October 14, 2013.

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ICR article image.

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"A three-dimensional model representing the molecular interaction between the smORF peptides and the calcium pump, superimposed over a microscopy image showing the cellular location of these same proteins in the muscles of an adult fruit fly."

Image from physorg...

Read more at: http://phys.org/news/2013-08-tiny-fruit-science-heart-human.html#jCp"

[AndyTheBear]

Ok trying to put this in context. The job of the evolutionary scientist is to find the most plausible way to explain the diversity of life based on the assumption that it all started from a common cell long long ago. The explanation of how that cell came about is beyond the scope of their work, and there is no clear way it could have happened, but never-the-less it must be assumed since the alternative would be philosophically devastating to dogmatic materialism. The job of biologists who hold to short term creation is to show that it all happened in a hurry from a few thousand years ago and that fossils are much younger than they have been traditionally dated--and that species started from various kinds that had the essential information of they needed, and have since fairly rapidly diversified from there. And finally the job of other biologists studying the matter without either assumption is to try to categorize the species to see which kinds are related through natural processes and which are not.

Is this a fair characterization?

[Toddsterpatriot]

"small open reading frames" or "smORFs"

I don't remember seeing this in the Bible, how do you know they exist?

[fishtank]

I will give a very serious answer.

This is why I post these articles:

Romans 1: 19-20

“Because that which is known about God

is evident within them;

for God made it evident to them.

For since the creation of the world

His invisible attributes, His eternal power and divine nature,

have been clearly seen,

being understood through what has been made,

so that they are without excuse.” NASB translation

qwerty

>> Or, to put it another way,

the ability to see God’s handiwork

in the created world

is not delusional.

It is logical.

[UCANSEE2]

[UCANSEE2]

Papa Smorf and the baby Smorfs.

[Hostage]

The short term creation belief is likely a shoe-horn fit of misinterpreted biblical lore with fossil evidence.

The flaw in creationism that dictates a 6000 year old Earth is rooted in the assumption that Adam’s life in years began its count when he was created and not at the Fall (when he was expelled).

The Bible says nothing of Adam’s time in Eden. As an immortal perfect spiritual being for all that anyone knows Adam may have been in the Garden for hundreds of thousands if not millions of years. Thus, 6000 years is a possible time frame from his expulsion not his creation.

Further, nothing in the Bible contradicts a supposition that Adam and Eve bore children while in Eden, children not born in sin. As wild a conjecture such a supposition could be, it is neither confirmed nor denied in biblical scripture.

All of the suppositions on both sides of the argument are unverifiable in the sense that the biblical account cannot be discounted and the creation account of a 6000 year old Earth cannot be upheld. Each side loses but the Bible stands.

The remarkable fact is that the Bible is not contradicted by fossil evidence; it continues to stand on its own.

[Boogieman]

Aw shucks, we must all be innorant if’n we read the buy-bull, yessiree.

[fella]

“Harvard University physiologist, Alan Saghatelian (not an author on the current study) said, “These things have fallen through the cracks of traditional gene-finding algorithms, and most of the ones we know about have been serendipitously discovered.””

So the research is being done with computer modeling like global warming predictions. GIGO, garbage in/garbage out.

[I want the USA back]

Amazing how little the scientists really know, but how much they profess to know.

[onedoug]

I think Adam was the first human to abstract God with his mind. Highly intelligent, he must have seemed like God to those around him. Which also goes somewhat as to why the progeny of Adam and Eve didn’t have to commit incest to procreate.

[Toddsterpatriot]

I didn’t post that, but if you say so........