Theory of Intelligent Design, the best explanation of Origins

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Theory of Intelligent Design, the best explanation of Origins » Theory of evolution » Newly Discovered 'Orphan Genes' Defy Evolution

Newly Discovered 'Orphan Genes' Defy Evolution

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Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome.

An important category of "rogue" genetic data that utterly defies evolutionary predictions is the common occurrence of taxonomically restricted genes, otherwise known as "orphan genes." These are now being discovered in the sequencing of all genomes.

Many multicellular animals share similar sets of genes that produce proteins that perform related biochemical functions. This is a common feature of purposefully engineered systems. In addition to these standard genes, all organisms thus far tested also have unique sets of genes specific to that type of creature.

The authors of a recent review paper, published in Trends in Genetics, on the subject of orphan genes stated, "Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs [similar counterparts] in other species" .

These orphan genes are also being found to be particularly important for specific biological adaptations that correspond with ecological niches in relation to the creature's interaction with its environment (2). The problem for the evolutionary model of animal origins is the fact that these DNA sequences appear suddenly and fully functional without any trace of evolutionary ancestry (DNA sequence precursors in other seemingly related organisms). And several new studies in both fish and insect genomes are now highlighting this important fact.

In the recent fish study, researchers sequenced the protein-coding genes in zebrafish and then compared the DNA sequences to other animal's gene sequences (3). The researchers classified the zebrafish genes into three different groups: 1) Genes commonly found in many types of animals, 2) genes that are only found in ray-finned fishes (the broad group of Teleost fishes), and 3) genes that are species-specific to only zebrafish. This third category refers to orphan genes. Thus there was a distinct group of genes found only associated with zebrafish and no other animal or type of fish.

In another study, researchers compared the genomes of seven different types of ants with other known insect genomes (4). When comparing the ant genes to other insects, researchers discovered 28,581 genes that were unique only to ants and not found in other insects. While the various ant species shared many groups of genes, only 64 genes were common to all seven ant species.

The researchers concluded that on average, each ant species contained 1,715 unique genes—orphan genes. Researchers not only found dramatic differences for protein-coding genes, but also for other types of regulatory DNA sequences that control how and when genes are turned off and on.

While these results clearly defy evolution, what do they mean within a biblical creation framework of origins? In the book of Genesis, created kinds of organism are defined as being able to reproduce and interbreed “after their kind.” These different ant species are not inter-fertile and they also inhabit different ecological niches, utilize different types of food sources, and have different types of social structures important to communal insects such as ants and bees. Combined with the fact that they also have unique gene sets, they possibly all descended from different created ant kinds.

While these orphan genes challenge evolution, they help creationists understand the patterns of genetic diversity related to created kinds. And ants may be a good example of animals that did not need to be saved from the Genesis flood by being sequestered on the ark, since they might have survived outside, on floating mats of vegetation. Ants would have, to some extent, also avoided a severe genetic bottleneck (5). If so, their present diversity would more closely represent the originally created array of ant genomes.

Clearly, the complexity and design of God's creation is astounding, vast, and incredibly amazing. Only an Omnipotent and Wise Creator could have been the source of these widely diverse, and yet complicated and precise genetic arrangements.

Last edited by Admin on Wed Jul 02, 2014 7:42 am; edited 2 times in total

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The tools of DNA sequencing are becoming cheaper to use and more productive than ever, and the deluge of DNA comparison results between organisms coming forth are becoming a quagmire for the evolutionary paradigm. To prop it up, biologists resort to ever more absurd explanations for discrepancies. A prime example of this trickery is in a recent DNA sequencing project performed in a microscopic aquatic multi-cellular animal called a rotifer (1).

In this effort, the researchers targeted those gene sequences that are expressed as proteins for DNA sequencing because the genome was too large and complex to sequence and assemble all of its DNA. They recorded over 61,000 gene sequences that were expressed from rotifers grown in stressed and non-stressed conditions. Of these, they could only find sequence similarities between rotifers and other creatures for 28,922 sequences (less than half). The researchers tossed the unknown DNA sequences out of their analysis since the non-similar genes were novel, apparently specific to rotifer, and essentially difficult for evolution to explain.

Of the 28,922 sequences for which they could obtain a match in a public database of other creature's DNA and protein sequences, a significant proportion (more than in any other creature sequenced) did not fit evolutionary expectations of common descent. Further complicating this picture, the rotifer gene sequences were found in a diverse number of non-rotifer creatures!

Some of the creatures that had gene matches to rotifers included a variety of plants, other multicellular animals, protists (complex single celled animals), archaea, bacteria, and fungi.

Evolutionists have two options in which to categorize these unusual gene matches based on their naturalistic presuppositions. First, they can say that these genes evolved independently in separate creatures in a hypothetical process called "convergent evolution." However, in cases where there are literally hundreds of these DNA sequences popping up in multiple organisms, this scenario becomes so unlikely that even evolutionists have too much difficulty imagining it. The second option is called "horizontal gene transfer," or HGT. This involves the transfer of genes, perhaps via some sort of microbial host vector such as a bacterium (2).

In the present report, the rotifer under study was asexual, limiting heredity as an option for aiding in gene transfer. So the researchers concluded that it stole hundreds of genes via HGT from a plethora of other creatures.

HGT is considered somewhat common among bacteria because they form connective tubes (called pili) and exchange little bits of DNA, like sharing software. Also, HGT can occur rarely between a bacterium and a multicellular host that it interacts with during its life cycle (3).

How will rotifer researchers account for the massive transfer of hundreds of genes from a broad range of hosts that they believe includes 533 supposed source genomes for which no biological host-based relationships exists? Some sort of causal host relationship must occur for the transfer of one gene, let alone hundreds of genes from hundreds of sources (1).

Another problem is that the researchers showed that the so-called "stolen genes" were well-integrated into the rotifer cell biochemistry and its environmental adaptation mechanisms. A separate 2012 study showed that highly expressed native genes could not be shared via HGT, even among bacteria, because they would severely disrupt essential cell biochemistry (4). And these are exactly the types of genes that were surveyed in the rotifer.

In this case, evolutionary biologists have resorted to fictional stories cloaked in technical terminology to escape the straightforward conclusion that rotifer DNA was purposefully crafted. If a large bunch of newly discovered genes don't make evolutionary sense, then evolution proponents ascribe their origin to HGT despite the fact that HGT is not known to operate without any host-based relationship. HGT is also not known to occur en masse, and HGT of essential genes is in theory impossible (4).

The unique mix of rotifer genes along with their flawless biochemical integration into the rotifer's cell system, clearly and abundantly supports the special creation described in the Bible.

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A recently discovered organism found in “a little lake 30 kilometer south of Oslo in Norway” has caused a stir. An analysis of its genome has found that it has almost, if not completely, nothing in common with any known organisms. It is seen as a new ‘branch’ on the putative “Tree of Life.”

Quoting from the article:

   When researchers from the University of Oslo, Norway compared its genes with all other known species in the world, they saw that the protozoan did not fit on any of the main branches of the tree of life. The protozoan is not a fungus, alga, parasite, plant or animal.

   “We have found an unknown branch of the tree of life that lives in this lake. It is unique! So far we know of no other group of organisms that descend from closer to the roots of the tree of life than this species. It can be used as a telescope into the primordial micro-cosmos,” says an enthusiastic associate professor, Kamran Shalchian-Tabrizi, head of the Microbial Evolution Research Group (MERG) at the University of Oslo.

Nevertheless, we’re told in the Science Daily article that:

   The protozoan from Ås has four flagella. The family it belongs to is somewhere between excavates, the oldest group with two flagella, and some amoebae, which is the oldest group with only one flagellum.

Now, although scientists have chosen (why?) to call this organism “The Protozoa,” it actually belongs at the base of all eukaryotes, which means that it is not really a “protozoa”, and hence likely does not share so-called “common descent” with bacteria.

   The family tree of the protozoan from the lake near Ås starts at the root of the eukaryote species.

   “The micro-organism is among the oldest, currently living eukaryote organisms we know of. It evolved around one billion years ago, plus or minus a few hundred million years. It gives us a better understanding of what early life on Earth looked like.,” Kamran says to the research magazine Apollon.

Remembering that this organism is: (1) not a protozoa (despite the name it’s been given—again, why this name?), (2) has four flagella, and (3) has no known genetic sequences that match up with any already known organisms(!!), then we have an instance of existing flagellum that can in no way–at least right now—be explained on the usual bases of “exaptation” and “cooption.” So, is this really “Irreducible Complexity”?

Last edited by Admin on Tue Jul 15, 2014 6:26 am; edited 1 time in total

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As scientists sequence more genomes from different organisms, they are discovering that roughly 10-20% of each genome's protein-coding sequence is new, that is, unlike any other known protein-coding sequence. This was a one of the biggest surprises to come out of the whole genome-sequencing project, though by no means the biggest.

given common descent and the fact that most housekeeping genes are shared among living things, and the assumption hitherto that evolution occurs by incremental small changes, orphan genes (protein-coding sequences without known protein-coding antecedents) should be rare if not non-existent.

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