bioorigins

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Decoding Snake-Venom Origins

The origin of snake venom has long been a mystery to both creationists and evolutionists. However, by stepping outside the standard research paradigm, scientists recently showed that snake venom proteins may have arisen from existing salivary proteins (1).

The Bible indicates that at the beginning of creation, God’s handiwork was not fraught with death, disease, and violence. Because of Adam and Eve’s rebellion, creation became subject to all of these negative factors, including snakes with toxic venom. The question then arises of how the curse on creation brought about these deadly changes. Were new genes of malicious intent added by the Creator, or was pre-existing genetic information corrupted or altered in some way? According to what we know about genomic decay and the character of God as revealed in the Bible, it is more likely that genomic modification, possibly associated with degradation (genetic entropy), was the cause (2,3).

On the other side of the scientific paradigm lies the evolutionary mindset which has traditionally believed that snake-venom proteins arose through the duplication of non-venomous genes that were then somehow reworked through random mutational processes to provide new functions combined with the expression of the new gene in just the right tissue. However, an enterprising group of secular scientists have acknowledged that gene duplication is itself an extremely rare event and that the mutational repurposing of a duplicated gene is even rarer. Thus, they began looking for other explanations for snake venom origins by carrying out a comparison of gene expression in venom glands and other body tissues for a wide variety of snakes (both venomous and non-venomous snakes, as well as a gecko).

The researchers started the discussion of their results by saying, “We find the hypothesis that snake venom evolves through the duplication of physiological or body genes and subsequent recruitment into the venom gland to be unsupported by the available data,” and, “Indeed for a large number of the gene families claimed to have undergone recruitment we find evidence of a diverse tissue expression pattern, including the salivary gland of nonvenomous reptiles.” In other words, venom genes are expressed in many other bodily tissues within both venomous and non-venomous snakes.

These results demonstrate that venom genes are serving other non-venomous purposes in reptile tissues, including a function in the salivary glands of both non venomous and venomous snakes. Interestingly, the authors state, “Our analysis in fact shows that the majority of snake venom toxins are likely derived from pre-existing salivary proteins,” and they admit that “snake venom should instead be considered to be simply a modified form of saliva.”

So, if these venom proteins are found in many different types of bodily tissues in both venomous and non-venomous snakes, then why the toxicity? The researchers state that their data “suggest that a possible route for pre-existing salivary proteins to become venom toxins may simply be an elevated expression level, where initial toxicity is dosage-dependent.” Therefore, more highly expressed venom genes would have been caused by possible alterations in their controlling regions. The authors state that this could occur by “the loss of transcription factor binding sites [gene control switches], which may occur by random mutation of single base pairs or larger insertions or deletions (indels) that may delete or disrupt the existing transcriptional regulatory sequences.”

Thus, the toxic levels of venom found in modern venomous snakes could be due to an alteration of genetic information that causes them to be over-expressed in venom glands. This type of genetic model is actually predicted by creationists who understand the concept that genomes are undergoing a process of information alteration largely associated with corruption, not upward evolutionary improvement—a process that was apparently kicked into high gear when the creation became cursed.

Perhaps the most amazing statement made by the authors of this secular research paper was a sound rebuke of the standard evolutionary reasoning. They state, “Our findings highlight the problem of ‘just-so stories’ in evolutionary biology, especially when they reach the point of being considered established fact.” It appears that some scientists are beginning to understand that the neo-Darwinian model actually limits the progress of research instead of advancing it. It also appears some secular scientists are brave enough to now seriously question long entrenched evolutionary explanations.

References

  1. Hargreaves, A. D. et al. 2014. Restriction and Recruitment—Gene Duplication and the Origin and Evolution of Snake Venom Toxins. Genome Biology and Evolution. 6 (8): 2088–2095.
  2. Sanford, J. C. 2008. Genetic Entropy and the Mystery of the Genome, 3rd ed. Waterloo, NY: FMS Publications.
  3. Sanford, J., J. Pamplin, and C. Rupe. 2014. Genetic Entropy Recorded in the Bible? FMS Foundation. PDF posted on kolbecenter.org July 2014, accessed July 25, 2014.

Original post by author Tomkins – http://www.icr.org/article/8339/

For more information like this go to Designed-DNA.org

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Genome Scrambling and Encryption Befuddles Evolution

One-cell creatures called ciliates are expanding our knowledge of genome dynamics and complexity. Now a newly sequenced ciliate genome reveals unimaginable levels of programmed rearrangement combined with an ingenious system of encryption (1).

Contrary to the evolutionary prediction of simple-to-complex in the alleged tree of life, one-cell ciliates are exhibiting astonishing genetic complexity (2). The ciliate Oxytricha trifallax has two different genomes contained in separate nuclei. The micronucleus is dense and compact and used for reproduction while the macronucleus is dramatically rearranged, amplified, and used for the creature’s standard daily living.

After two Oxytricha perform sexual conjugation, the old macronucleus essentially disappears and a new one is formed from the contents of the micronucleus during development of the new ciliate. This involves an elaborate cascade of events in which about 90% of the germline DNA is deleted and the remaining fraction is dramatically reorganized and amplified into over 16,000 new chromosomes (called nanochromosomes) (3). While scientists previously understood that the genome of this creature underwent a dramatic reorganization, they did not understand the full significance of the phenomena, because only the macronucleus has been completely sequenced (3).

In this recent study, the researchers sequenced the micronucleus of Oxytricha trifallax and were surprised at the levels of complexity and rearranging they discovered. As it turns out, the germline genome of the micronucleus is fragmented into over 225,000 precursor DNA segments that are massively and precisely rearranged (unscrambled) during the construction of the new macronucleus and its nanochromosomes (most of which contain only one gene each). However, it gets more complicated. Many of the genes reconstructed in this process come from numerous individual fragments dispersed across the micronuclear genome—with some even being inverted in their orientation.

A complex system of genomic encryption was discovered that enable the decoding of these 225,000 plus fragments. This process uses specialized pointer sequences that flank the macronucleus-designated fragments as a type of encryption and addressing system. In addition, highly specialized RNA guides that are also encoded in the genome are used to mark the specific DNA sections that need to be moved as a type of decryption system. The authors state, “Most functional information is encrypted in the MIC [micronucleus], and macronuclear development is a process of decryption.” Because even the protein-coding regions of genes (called exons) are also fragmented, the authors state “Most IESs [internal eliminated sequences] interrupt exons (84.7%), making their removal a strict requirement for gene expression.” Thus, the whole process of slicing and splicing is not error-tolerant—on the contrary it is quite exacting and involves highly complex systems of encryption and decryption to function properly.

At this point you may be asking, “What’s the point of all this complexity?” Interestingly, the researchers also discovered that many of the precursor gene fragments were modular and could be rearranged in different ways to create more functional combinations—more “bang for the buck” as they say. The authors of the report state that a “notable feature arising from this radical genome architecture is that a single MDS [macronucleus destined sequence] in the MIC may contribute to multiple, distinct MAC [macronucleus] chromosomes.”

One of the most interesting features of the research paper was the overall lack of evolutionary verbiage it contained. Clearly the concepts of intricate genome rearrangements on a massive scale combined with complex encryption systems do not bode well for something allegedly derived by the random chance processes of evolution. From single-cell creatures to mankind, biocomplexity and extreme engineering speaks only of an omnipotent and all-wise Creator.

References

  1. Chen, X. et al. 2014. The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development. Cell. 158 (5): 1187–1198.
  2. Tomkins, J. 2014. Ciliate Genome Reveals Mind-Bending Complexity. Creation Science Update. Posted on icr.org September 10, 2014.
  3. Swart, E. S. et al. 2014. The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLoS Biology. 11 (1): e1001473.

 

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Original post by author Tomkins – http://www.icr.org/article/8359/


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Gene Complexity Eludes a Simple Definition

In the early days of molecular genetics in the 1960s and ’70s, it was widely held that a gene could be defined as a single entity that encodes the information to make a protein. However, as genetic studies have progressed, our understanding of what defines a gene has become incredibly more complicated (1). We still hear evolutionists claim “this and that creature have the same genes and are therefore related through common descent in evolution,” but in light of recent genetic studies, this claim is grossly oversimplified.

First, the boundaries of what can be called a single gene are becoming increasingly hard to define, along with its complete set of functions. Entire chromosomes and genomes are a continuum of pervasive and overlapping transcription (copying DNA into RNA) (2,3). Recent discoveries have revealed that the genes of many plants and animals are not like single entities at all but are rather a mixture of genes within genes and even genes that overlap each other (3). The regulatory control regions of genes, called promoters, can be shared by two completely different genes running in opposite directions from each other. (Genes are found on both strands of the double-stranded DNA molecule.) Enhancer regions that also play an important role in regulating gene function can be up to a million bases away from the gene they regulate. As if this weren’t enough, many genes function both forward and backward at the same time—producing both sense and antisense transcripts (4). The regulatory sequences of genes can also be located inside other nearby genes, and researchers have determined that genes dynamically interact with each other in “gene neighborhoods” much more than previously believed, to the point of blurring the boundaries between them.

Secondly, the informational output provided by genes can change depending on different circumstances. These circumstances include cell type, tissue type, and other stimuli such as the external environments (5). In the genome, both the DNA molecule itself and the histone proteins that the DNA molecule is packaged around can be chemically altered or tagged. The study of these chemical tags is called epigenetics or chromatin remodeling (5). In addition to genes having overlapping boundaries and alternate functions, the information provided by the genes is epigenetically altered by the cellular machinery to provide just the right output for the situational need at hand.

When evolutionists talk about creatures sharing the same genes, they are typically referring to very small segments of DNA in the genome. And in most cases, they are only referring to the small pieces of protein-encoding genes called exons—not the whole segment of DNA that is actually responsible for producing the information to make the correct version of the protein at the right time and in the correct amount.

But what about all the other expressed DNA sequences in the genome besides protein-coding segments—can they be called genes too? Amazingly, there are actually more than twice as many long non-coding RNA genes in the human genome as there are protein-coding genes, and these are turning out to be the key factors in what controls and regulates protein-coding genes, and in what also makes different kinds of creatures genetically unique or distinct from each other (6).

Because of what we now know about the genome, you should be aware that when someone uses the term gene, the situation is a whole lot more complicated than it used to seem. To quote Dorothy from the classic movie The Wizard of Oz, “I’ve a feeling we’re not in Kansas anymore.” The biocomplexity of the genome is now reaching proportions beyond humankind’s wildest imaginations. An omnipotent Creator is the only possible explanation for such vast and elegant engineering.

References

  1. Portin, P. 2009. The elusive concept of the gene. Hereditas. 146 (3): 112-117.
  2. Djebali, S. et al. 2012. Landscape of transcription in human cells. Nature. 489 (7414): 101-108.
  3. Clark, M. B. et al. 2013. The dark matter rises: the expanding world of regulatory RNAs. Essays in Biochemistry. 54: 1-16.
  4. Antisense transcripts are believed to help regulate the genes from which they are copied in reverse—possibly by binding to the sense RNA transcripts directly or by facilitating the splicing and processing of the sense transcripts. See Pelechano, V. and L. M. Steinmetz. 2013. Gene regulation by antisense transcription. Nature Reviews Genetics. 14 (12): 880-893.
  5. Zhu, J. et al. 2013. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 152 (3): 642-654.
  6. Managadze, D. et al. 2013. The vast, conserved mammalian lincRNome. PLoS Computational Biology. 9 (2): e1002917.

See more at: Designed-DNA.org

Original post by author Tomkins – http://www.icr.org/article/8129/


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Chimp DNA Mutation Study—Selective Yet Surprising

Scientists just published a study describing chimp DNA mutation rates and compared a number of cherry-picked genomic regions to human—and this research doubled their evolutionary timeline (1). However, the selective data did not account for the vast chasm of documented genome differences that were not included in the analyses.

Heritable mutations are the rare changes that occur in DNA during the process of making egg cells in females and sperm in males, known as the germ line. Scientists believe that by determining the rate of mutations in the germ line, they can predict when evolutionary events occurred in the past. In this recent study, they sequenced the germ line genomes of nine different chimpanzees in a three-generation pedigree (family).

The researchers then compared selected DNA segments between chimpanzee and human that were highly similar, omitting the many non-similar regions. They state, “In the intersection of the autosomal genome accessible in this study and regions where human and chimpanzee genomes can be aligned with high confidence, the rate is slightly lower (0.45 × 10−9 bp−1 year−1) and the level of divergence is 1.2%…implying an average time to the most common ancestor of 13 million years [page 1274, emphasis added]”(1). There are basically two notable points from this summary statement that I will address.

The first important point is that the comparative data was clearly cherry-picked—the scientists only used the regions that were about 98% similar and essentially threw out everything else. These are the regions that the researchers stated “can be aligned with high confidence.” It appears that all the dissimilar DNA regions got tossed out because they didn’t fit the evolutionary paradigm and would have made the whole idea of chimps evolving into humans completely impossible.

It was initially noted by another group of evolutionary scientists that when comparing random chimp genomic sequence only “about two thirds could be unambiguously aligned to DNA sequences in humans”(2). In confirmation of this widely known, but seldom discussed, inconvenient fact among those evolutionists working in the field was a comprehensive study published in 2013 by this author (3). In that research, I compared each individual chimpanzee chromosome to human (piece-by-piece) and it was shown that the chimpanzee genome was only 70% similar on average to human, with only short regions being highly similar.

The second notable point is that even when these scientists used the cherry-picked, nearly-identical segments between humans and chimps, and then incorporated their newly discovered mutation rates, they had to double their hypothetical evolutionary timeline. One of the researchers on the project (Gil McVean) stated, “Our results add substance to the idea that the human-chimpanzee split was considerably older than has been recently thought ” (4). It was previously believed that humans and chimps shared a common ancestor only 2 to 6 million years ago. Now they are claiming that it is 11 to 17 million years ago with the average being about 13.

The reality of the situation is that simply adding more time doesn’t solve evolution’s immense problems. Giving evolution another 6 or 7 million years still does not explain why chimps and humans are so vastly different, not only in their anatomy and behavioral traits but also the glaring 30% difference in their genomes—some 900,000,000 DNA letter differences. Jesus Christ compared this type of philosophically flawed selective attitude to “straining out a gnat and swallowing a camel!” (5). When the entire genomes are compared between humans and chimps, it becomes clear that they were each engineered uniquely and separately by an Omnipotent Creator.

References

  1. Venn, O. et al. 2014. Strong male bias drives germline mutation in chimpanzees. Science. 344 (6189):1272-1275.
  2. Ebersberger, I. et al. 2002. Genomewide Comparison of DNA Sequences between Humans and Chimpanzees. American Journal of Human Genetics. 70 (6): 1490-1497.
  3. Tomkins, J. 2013. Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70%. Answers Research Journal. 6 (2013): 63-69.
  4. Choi, C. Q. 2014. Human & Chimp Genes May Have Diverged Twice As Long Ago As We Thought. Huffington Post. Posted on huffingtonpost.com June 13, 2014, accessed June 17, 2014.
  5. Matthew 23:24. ESV.

For more info like this go to Designed-DNA.org

Original post by author Tomkins – http://www.icr.org/article/8196/


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Comb Jelly Genome Gums Up Evolution

Comb jellies (ctenophores) look like disco balls with flashing lights that dance and spin as they float around the ocean. These creatures are so fascinating that one neuroscientist likened them to “aliens who’ve come to earth” (1,2). The genome of comb jellies has been sequenced, and it’s as alien as the creature looks—utterly defying all predictions about its evolutionary origins (3).

Even prior to recent advances in genome sequencing, comb jellies perplexed evolutionists. While they resemble a jelly fish in some ways, they have complex nervous systems that detect light, sense prey, flash a colorful spectrum of bioluminescence, and move with unique musculature and tentacles. Scientists first placed them as evolving from animals without nervous systems such as sea sponges and flattened pancake-like creatures called placozoans. Others placed them earlier in the evolutionary tree—claiming that their spectacular nervous systems were later “lost” during animal evolution and then magically reappeared again. Now with the new wealth of genomics data, scientists are placing them at the very earliest stage of animal life—branching off into their own evolutionary lineage.

The baffling story of the comb jelly genome of the species Pleurobrachia bachei (Pacific sea gooseberry) is two-fold. The first oddity is characterized by allegedly missing genes representing cellular systems normally found in other animal genomes that are considered both more primitive and more advanced. The second baffling scenario is depicted by the discovery of many new types of genes representing biological and biochemical systems never seen before in any other animal.

First, the story of the supposed missing genes. The genome sequencing data showed that comb jellies lack many genes found in allegedly evolution-related creatures. For example, the researchers were unable to find many of the normal types of genes that regulate and control the patterning and development of the organism. Also lacking were the identifiable presence of an important class of small regulatory molecules called micro RNAs that are commonly found in both animals that lack a nervous system and those with more complicated nervous systems. Finally, the basic proteins that initiate many types of immunity responses in other more simple and complex creatures were entirely missing.

In contrast to the story of the many allegedly missing genes is the amazing presence of many novel and unique genes. This oddity was highlighted by the fact that for the 19,523 predicted protein-coding genes the scientists were able to identify in the comb jelly, only 44% had any similarity to known genes in other animals. Many of the new genes that were discovered are related to the unique development of the comb jelly during its life cycle, including the organization and function of its incredibly bizarre nervous system—a system biochemically unlike any other known creature.

Another interesting aspect of genetic novelty is the presence of many types of genes representing highly complex information processing systems. For example, the comb jelly genome was found to contain the highest number of RNA editing enzyme-encoding genes reported so far in animals. RNA editing is the process whereby specialized cellular machines literally change the code of gene sequences encoded in RNA molecules after they are copied (transcribed) from DNA. In line with this incredible level of post-transcriptional processing, scientists also discovered dozens of novel RNA-binding protein genes that produce specialized machines that participate in other aspects of the complex informational processing of RNA molecules.

These profound discoveries led the researchers to absurdly proclaim “ctenophores, despite being active predators, underwent massive loss of neuronal and signaling toolkits and then replaced them with novel neurogenic and signaling molecules and receptors.” How and why could the random and mindless naturalistic process of evolution eject a fully functioning set of complex cellular systems consisting of hundreds of interlocking/interacting genes and then replace them with something else that is completely different? Why can’t researchers state the obvious—that these marvelous and fascinating examples of extreme biocomplexity are the handiwork of an Omnipotent Creator?

References

  1. Callaway, E. 2014. Jelly Genome Mystery. Nature. 509 (7501): 411.
  2. See brief video clip of a ctenophore (Pleurobrachia bachei), posted on youtube.com on May 21, 2014.
  3. Moroz, L. et al. 2014. The Ctenophore Genome and the Evolutionary Origins of Neural Systems. Nature. 510: 411.

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Original post by author Tomkins – http://www.icr.org/article/8190/


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GULO Pseudogene Evolution Debunked

A technical journal paper was just published that for all practical purposes, gets to the bottom of the controversial human GULO pseudogene argument for human evolution – debunking it’s status as evidence for humans having evolved from apes. The abstract is below along with a link to the PDF download of the full paper.

The Human GULO Pseudogene—Evidence for Evolutionary Discontinuity and Genetic Entropy

Abstract
Modern genomics provides the ability to screen the DNA of a wide variety of organisms to scrutinize broken metabolic pathways. This wealth of data has revealed wide-spread genetic entropy in human and other genomes. Loss of the vitamin C pathway due to deletions in the GULO (L-gulonolactone oxidase) gene has been detected in humans, apes, guinea pigs, bats, mice, rats, pigs, and passerine birds. Contrary to the popularized claims of some evolutionists and neo-creationists, patterns of GULO degradation are taxonomically restricted and fail to support macroevolution. Current research and data reported here show that multiple GULO exon losses in human, chimpanzee, and gorilla occurred independently in each taxon and are associated with regions containing a wide variety of transposable element fragments. Thus, they are another example of sequence deletions occurring via unequal recombination associated with transposable element repeats. The 28,800 base human GULO region is only 84% and 87% identical compared to chimpanzee and gorilla, respectively. The 13,000 bases preceding the human GULO gene, which corresponds to the putative area of loss for at least two major exons, is only 68% and 73% identical to chimpanzee and gorilla, respectively. These DNA similarities are inconsistent with predictions of the common ancestry paradigm. Further, gorilla is considerably more similar to human in this region than chimpanzee—negating the inferred order of phylogeny. Taxonomically restricted gene degradation events are emerging as a common theme associated with genetic entropy and systematic discontinuity, not macroevolution.

Link to full research paper (PDF)

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DNA Proof That Neandertals Are Just Humans

The study of ancient DNA (aDNA) is currently all the rage in the field of genomics, with more and more researchers jumping into the fray. Despite the fact that many problems still plague the field, several new research papers are claiming that scientists can now detect and study Neandertal genome sequence in modern human DNA databases using only electronic tools (1,2).

The consensus among secular researchers in the field of human origins is that Neandertals represent an ancient group of humans who—despite a few early controversies to the contrary—are now believed to have widely interbred with other humans across Europe and parts of Asia. The acceptance of this idea is what led several different research groups to develop electronic methodologies that would allegedly ferret out the many different introgressed Neandertal DNA regions in modern human genomes.

In two recent studies, both research groups took slightly different approaches. One group used a two-stage strategy. In the first step they attempted to map out the areas of the human genome sensitive to variation among different modern global people groups. They then compared those regions to the Neandertal reference genome and determined whether any matches occurred more significantly than by chance alone. In their conclusion, they state that “35-70% of the Neandertal genome persists in the DNA of present-day humans” (1).

The second group combined three different sources of genetic variation to identify patterns of alleged Neandertal ancestry. Like the previous study, they also utilized Neandertal DNA genomic sequence as a reference. If all three sources of variability came back positive and also matched Neandertal, then the segment was demarcated as being Neandertal in origin. As in the other study, they did this for the many modern human genome variants represented across the globe. This group was less committal about the extent of the Neandertal genome persisting in modern humans but did say that “we identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology” (2).

Although these studies demonstrate the widespread mixture of Neandertal DNA at varying levels among modern humans, there are several problems with these studies. The first is that our knowledge of the Neandertal genome is based on only a few individuals—only one of which has a complete and well-developed genomic sequence (3). How can you use the DNA sequence of just one or a few individuals to make such broad-ranging statistical assertions about the modern genomes of humans across the globe? The second problem is that the researchers had to use multiple statistical models and then apply a “majority rule” approach to deciding which outcome was valid and which wasn’t. Clearly, there were many cases where the decision of the DNA segment could have gone either way—essentially meaning that it is all human DNA anyway.

From a creationist perspective, these studies really add very little to the already clear genetic evidence showing that the Neandertals are nothing but another variant in the human lineage derived from the eight individuals who survived the global Flood as recorded in the book of Genesis. Because the remains of these archaic humans are found in burial sites in caves rather than in flood sediments, we can therefore infer that their age is no more than about 4,000 years—not the 40,000-plus years typically given by evolutionists.

References

  1. Vernot, B. and J. M. Akey. Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science Express. Published on sciencemag.org January 29, 2014.
  2. Sankararaman, S. et al. The genomic landscape of Neanderthal ancestry in present-day humans. Nature. Published on nature.com January 29, 2014.
  3. Prüfer, K. et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature. 505 (7481): 43-49.

Original article post: http://www.icr.org/article/8006/

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