Scientists Document Complex Genomic Events Leading to the Birth of New Genes

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Article Date: 14 Feb 2005 - 18:00 PDT

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'Scientists Document Complex Genomic Events Leading to the Birth of New Genes'

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A team of scientists led by Peer Bork, Ph.D., Senior Bioinformatics Scientist at the European Molecular Biology Laboratory, report today in the journal Genome Research that they have identified a new primate-specific gene family that spans about 10% of human chromosome 2. Comprised of eight family members, the RGP gene cluster may help to explain what sets apart humans and other primates from the rest of the animal kingdom.

Human chromosome 2 has always intrigued primate biologists; it formed from the fusion of two mid-sized ape chromosomes and is the only cytogenetic distinction separating humans from apes. At the molecular level, however, the differences among the species are much more complex.

Bork's team systematically searched the complete genomic sequences from a broad range of taxa (mouse, rat, roundworm, fruit fly, mosquito, and pufferfish) for single-copy genes that had evolved more than one copy in humans. "Gene duplication is known to play a leading role in evolution for the creation of new genes," explained Francesca Ciccarelli, Ph.D., lead author on the study. The key to this, however, is that the duplicated copies of genes very quickly evolve functions that are significantly different than those of their progenitors.

Natural selection acts on gene duplications, most often by deleting them from the gene pool or by degrading them into non-functional pseudogenes. This is because fully functional duplicated genes, in combination with the corresponding parent gene, produce abnormally abundant quantities of transcripts. This overexpression often alters the fragile molecular balance of gene products on a cellular level, ultimately resulting in deleterious phenotypic consequences. If these duplicated genes acquire new functions, however, they may confer a selective advantage to an organism, leading to the rise of lineage-specific genes over evolutionary time.

Bork's team identified a total of 22 genes with more than one copy in humans but only a single copy in all other species tested. They then turned their attention to the gene that exhibited the most dramatic of these duplications: RanBP2. RanBP2 is the largest protein found at the nuclear pore complex, helping to regulate nucleic acid and protein traffic in and out of the nucleus. The corresponding gene is present in all sequenced animal genomes but not in other eukaryotes, such as plants or fungi.

The new gene family characterized by Dr. Bork and his colleagues was largely derived from RanPB2, but it had also acquired a domain from the neighboring GCC2 gene, whose protein product contains a GRIP domain that localizes intracellularly to the trans-Golgi network. The new gene family, spanning approximately 10% of human chromosome 2, was named RGP (for RanBP2-like, GRIP domain-containing proteins).

By analyzing the gene order around the RanBP2 and GCC2 genes, Bork's team was able to reconstruct the genomic rearrangements leading to the formation of the ancestral RGP locus. These events included a combination of duplication, inversion, partial deletion, and domain acquisition, and this was followed by a series of duplications that gave rise to each RGP family member. A total of eight RGP-family genes were identified, all of which are believed to be fully functional.

To demonstrate that RGP-family genes have functions that are significantly divergent from those of RanBP2, Bork and his co-workers examined the subcellular localization of one of the RGP-family isoforms. In contrast to RanBP2, which is found exclusively at the nuclear envelope, this RGP-family protein was detected in discrete cytoplasmic locations, thereby confirming its functional divergence from RanBP2.

Identifying and characterizing genes that are responsible for primate or human distinctiveness has been a major challenge to scientists. However, this work by Bork and his colleagues should further enable studies focused on the molecular basis for species specificity. "A thorough functional characterization of the other 21 new genes we've identified in this study would reveal the functionally most relevant areas for primate evolution," Bork says.

Dr. Francesca D. Ciccarelli (ciccarel@embl.de; Tel: +49 6221 387 456), first author on the manuscript, has agreed to be contacted for further information.

The article referenced here will be published online as a "Genome Research in Advance" paper on Monday, February 14, 2005, and will appear in the March print issue of Genome Research. The citation for the article is as follows: Ciccarelli, F.D., von Mering, C., Suyama, M., Harrington, E., Izaurralde, E., and Bork, P. Complex genomic rearrangements lead to novel primate gene function. Genome Res. 15: 343-351. For copies of this manuscript or questions about this news release, contact Maria Smit, Assistant Editor, Genome Research (+1-516-422-4013; smit@cshl.edu).

Genome Research (http://www.genome.org) is an international, monthly, peer-reviewed journal published by Cold Spring Harbor Laboratory Press. Launched in 1995, it is one of the five most highly cited primary research journals in genetics and genomics. The journal publishes novel genome-based studies and cutting-edge methodologies in comparative and functional genomics, bioinformatics, proteomics, evolutionary and population genetics, systems biology, epigenetics, and biotechnology.

Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit http://www.cshlpress.com.

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WHICH IS CORRECT?

posted by Kabriken on 15 Mar 2006 at 4:10 pm

The enclosed email was sent Dr.Francesca Ciccarelli of the European Molecular Biology Laboratory:-
Geneticists trace original organism

Ian Sample, science correspondent
Friday March 3, 2006
The Guardian

This article was brought to my attention by an evolutionist. However, I found information that seems to counter the entire basis for your conclusions. The information is reprinted below:-

KINGDOM OF THE PLANTS: DEFYING EVOLUTION
by Alexander Williams

One of the fundamental problems facing life scientists is the extraordinary variety and complexity of life on Earth—there is just too much to comprehend. Most biologists solve this problem by specializing, spending a whole career studying just one or a few areas. Occasionally someone will attempt a grand synthesis or overview to try to encompass the whole.

Such a one is Professor Lynn Margulis, of the University of Massachusetts, senior author of the book Five Kingdoms, now in its third edition.1 Margulis has spent most of her illustrious 40-year career researching the supposed evolution of the ‘higher’ forms of life from the ‘lower’ forms.

Until relatively recently, all living things were classified into just two great kingdoms—the Animal Kingdom and the Plant Kingdom. But in the last decade or so, as a result of studying gene sequences, a revolution has taken place in our understanding of the diversity of life.

As a botanist, I was particularly interested in Margulis’s view of plant classification. In her book, algae, fungi and bacteria have all been removed from the ‘old’ Plant Kingdom, with the ‘new’ Plant Kingdom consisting of just 12 phyla (a ‘phylum’ is a large grouping with certain features in common) of multicellular, green, mostly land-dwelling plants.

The ‘old’ Plant Kingdom was structured to reflect supposed evolutionary relationships between plant groupings. However, the alleged sequence of evolution of various plants contradicted their actual order of burial in the fossil record!2 (Not to mention the complete absence of any fossilized transitional forms.)

So, as I read Margulis’ revised descriptions, I was asking myself, ‘Does this revision improve the case for the evolutionary origin of plants?’ Well, the answer is ‘Not at all’. In fact it strengthens the case for special creation!

The plants are now divided into just two main groups, the Bryata (non-vascular plants—those which do not have specialized ‘plumbing’ for water transport) and the Tracheata (vascular plants—those which do have specialized ‘plumbing’ for water transport). My first observation was that the Bryata are the simplest and, if evolution were true, they should be the ancestors of the Tracheata.

Thus, according to evolutionary/long-age interpretations,3 they should be found ‘first’ in the fossil record, i.e. buried below the Tracheata. But no, the opposite is true; the Tracheata appear first!

The Bryata consist of three groups, the mosses, liverworts and hornworts. There is nothing that could logically be their ancestor among the multicellular algae or fungi. Their nearest supposed relatives are among the Chlorophyta, which are free-swimming, green, single-celled microbes (see inset, Figure 1).

Despite mosses being well represented in the fossil record,4 there is no joy for evolutionists. Margulis has to admit: ‘they do not seem to be the ancestors of the vascular plants [Tracheata] or of the hornworts or liverworts’.5 ‘Like hornworts and mosses, liverworts gave rise to no other plant lineages’.6 The hornworts appear before the mosses in the fossil record, but ‘the origin of hornworts cannot be deduced by examining the fossil record … . Hornworts, mosses and liverworts probably evolved independently of one another’.7

So here, supposedly at the base of the evolutionary tree, there is no evidence whatever of evolution. This is not merely a ‘missing link’, but a yawning chasm (between plants and the chlorophytes), and none of the simplest plants (Bryata) are ancestral either to one another or to any of the ‘higher’ plants (Tracheata)!

Climbing further up the supposed evolutionary tree, Margulis next deals with the Psilophyta, or whisk ferns. Once again, ‘no intermediate fossils have been found … . Chloroplast DNA comparisons suggest that psilophytes’ closest relatives are non-lycophyte vascular plants such as ferns … [but the] chemical evidence … fails to support a strong evolutionary relation between the psilophytes and the ferns … . Ancestral groups for psilophytes … are unknown at present’.8 So, more evidence that the Tracheata did not evolve from the Bryata!
Supposedly next to appear (in the alleged ‘Carboniferous coal forests’) were the tree-like 40 m (130 ft) lycopods. But lycopods ‘are related neither to pines and cedar … nor to mosses’.9 Although they have an excellent fossil record, it gives absolutely no clue as to where they came from.

Margulis next deals with the horsetails, surviving today only as the single herbaceous genus, Equisetum. Once again there is an excellent fossil record. Abundant fossil specimens of tree-like 15 m (50 ft) horsetails are buried in layers labelled ‘Devonian’ and ‘Carboniferous’. But ‘Ancestral groups for … horsetails … are unknown at present’.10
And what about the ferns? ‘Fossilized ferns abound in the fossil record from the Carboniferous through the present’, with some tree-ferns up to 25 m (82 ft) tall.11 But again, not a single clue here to their origin.
Climbing the evolutionary ladder further, we come to the gymnosperms, or naked seed plants. They include four living phyla: the cycads, gingko, conifers (pines) and gnetophytes.

The cycads are well known as garden plants and the group includes the sago palm. Cycads were once considered to be the closest living relatives of flowering plants, related through their common ancestor, the extinct seed ferns. ‘However, seed ferns and living cycads are no longer believed to be direct ancestors of flowering plants’.12 And there is no hint as to their supposed evolutionary origin!

The gingko tree is represented by a single living species, Gingko biloba, in a single genus, in a single family, in a single class, in a single phylum. Its fossil history extends down to ‘Permian’ rocks, and it appears there were once many more species. But here again they appear suddenly and fully formed, leaving evolutionists with no clue as to their origin.13
The conifers or pine trees range from ground-creeping shrubs to the Sequoia redwoods of California—probably the largest living things on the planet, reaching up to 115 m (380 ft) in height and 8 m (26 ft) in diameter. ‘Conifers likely descended from the progymnosperms’.14 And what are the ‘progymnosperms’? Imaginary evolutionary ancestors—there is no evidence that they ever existed! And are the conifers the ancestors of anything? ‘Conifers gave rise to no other plant phyla’.14

Last of the gymnosperms is the curious group, the gnetophytes, consisting of three ‘vastly different’ genera, Ephedra, Gnetum and Welwitschia. They share some characteristics with other gymnosperms and some characteristics with flowering plants. Unfortunately for evolutionists, they appear fully formed in the fossil record, just as ‘vastly different’ as they are today. So there is no fossil evidence of their evolutionary lineage before they appeared, nor after, for ‘Gnetophytes are believed not to have given rise to any other plant lineage’.15

Finally, supposedly at the top of the plant evolutionary tree, we come to the flowering plants, the Anthophyta (or angiosperms), with their unique flowers and fruits. They are ‘the superstars of diversity and abundance’, with possibly as many as a million species, occurring all over the globe. They have an abundant fossil record but, once again, they appear fully formed, with no sign of any evolutionary lineage.

The only suggestion from Margulis and her co-author is the gnetophytes. But since ‘Gnetophytes are believed not to have given rise to any other plant lineage’15 they have to imagine what an ancestor of flowering plants might have looked like. In a blind leap of (evolutionary) faith, they surmise that the incredibly intricate flower structures we see today, complete with ovary (female) and pollen (male), exist because evolution has modified leaves into ‘a shoot specialized for reproduction.’16 Yet there is not even a fragment of fossil evidence for this.

Well, there we have it. The plant fossil record is now more clearly defined than ever before, and it testifies more clearly than ever before that not one of the phyla is either the ancestor or the descendant of any other!

Once more the evidence of the real world is seen to be consistent with the truth of Genesis; plants reproduce ‘according to their kind’. That is, gingkos have consistently produced gingkos, pines have consistently produced pines, and magnolias have consistently produced magnolias ever since the Creator spoke them into existence to reproduce ‘after their kind’.17

References and notes
Margulis L. and Schwartz K.V., Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth, 3rd ed., Freeman, New York, 1998. Return to text.
Williams A., Did plants evolve? Creation 19(4):10–12, 1997.

While Darwin acknowledged that the lack of transitional forms in the fossil record was the most serious objection to his theory, he was confident that, in time, further fossil discoveries would provide support. In reality, over 140 years later, the ‘missing links’ are still missing.

END

MY COMMENT:-

The geneticists didn't try working on plants to see if one type can or did evolve from another, which would have had to be the case if evoloution is true.

Another thing - If plants evolved as is supposed, would there not be traces of fruit trees or other vegetation that were transitional, that is, some that would produce part-orange, part-apple, part-grape, part pinecone, etc, etc, etc or have they all been converted into coal and oil?

ALSO, there MUST have been a time when the flora of the entire earth was composed of only one type of plant! What thought processes on earth could have seen, and been behind, the need for diversity? Did diversity come gradually or all at once?

Kabriken.

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