Human DNA and Evolution. A Carnival of Information. Nature is One Big Experiment, Always Mutating. Whole Genome Duplications, Human Genetic Diversity

Human DNA and Evolution

Young-Cosmos Creationists with higher degrees in the sciences admit that evolution is not a “theory in crisis,” and the evidence generally does favor an old-cosmos and evolution. They even add that less highly educated young-earth creationists are prone to speaking ignorantly on the topic.

Todd Wood is a young earth creationist with a Ph.D. in Biochemistry from the University of Virginia (Charlottesville, 1999). Toddʼs Ph.D. advisor was the famous Dr. William Pearson, the original developer of the widely popular FASTA suite of computer programs used for DNA analyses. When providing a reference for Todd in his subsequent academic position application, Dr. Pearson stated “he was the best graduate student I ever had.” Immediately following his Ph.D. work at Virginia, Dr. Wood accepted a position as the Director of Bioinformatics at the Clemson University Genomics Institute (Clemson, SC) which at that time, was directed by Dr. Rod Wing, a world famous scientist in the field of plant genomics. So Todd knows genes. He also does not think evolution is a theory about to collapse. In fact he wrote a paper pointing out the problem for creationism of the close genetic similarity between humans and chimps:

Wood admits that our genome is nearer to chimps than some species of cats are to one another, yet creationists accept that cats evolved from a common ancestor. So why not humans and chimps? In fact our genome is as near to chimps as sibling species of fruit flies are to one another. Yet creationists admit sibling species of fruit flies evolved from a common ancestor.

DENNIS VENEMA is an, Ph.D. biologist (and Christian), who often critiques I.D. arguments and explains how strong the evidence for evolution is in series of articles at the Christian website, BIOLOGOS. See his latest series!

Human Genetic Diversity, Nature Is One Big Experiment, Always Mutating

There is far more genetic diversity in the human genome than previously thought. Thereʼs tons of neutral mutations and also some interesting ones found among limited numbers of people today, like mutations that grant people the ability to recognize more colors, tastes or smells.

The mutation that led to the ability to digest milk sugar spread quickly after the domestication of cattle and the drinking of milk began, but has not yet spread to everyone on earth, especially some people in parts of Asia.

The fact of such genetic diversity is handy in that it refutes a recent global flood:

Speaking of genetic diversity, all the cells in your body are not uniquely your own. Your DNA and identity are not as entwined as once thought. In fact most people have multiple genomes floating around inside them! “DNA Double Take.”. I am sure this is as confusing for creationists as the fact that some people are born with stripes of both testicular and ovarian tissue in their gonads (are they males or females?) Nature is basically one big experiment, always mutating.

When the complete DNA of one human being was first sequenced in 2000, it was considered to be “the” human genome. Soon after, researchers began to explore the differences between individuals, launching the era of the “personal genome.” Now science is entering the age of the microgenome, in which research begins to explore the worlds within us, examining our inherent imperfections and contradictions, the multitudes we contain. Even though each of your cells supposedly contains a replica of the DNA in the fertilized egg that began your life, mutations, copying errors and editing mistakes began modifying that code as soon as your zygote self began to divide. In your adult body, your DNA is peppered by pinpoint mutations, riddled with repeated or rearranged or missing information, even lacking huge chromosome-sized chunks. This DNA diversity is called “somatic mutation” or “structural variation.” Yet it functions, as all jury-rigged evolutionary things do.

Nature Even Survives Mutations As Radical as Whole Genome Duplication Events. There Are Plenty We Know About in Both Plants and Animals, But The Interesting Thing is That…

The computerized comparison of genomes of many vertebrate species from fish to reptiles to mammals and humans, has uncovered evidence that the vertebrate genome leading from jawless fish to humans underwent at least two rounds of WGD (Whole Genome Duplication) events in the past. Thatʼs not just an extra chromosome or gene that is duplicated, but the entire genome is duplicated, with subsequent whittling down of the genome as the duplicated genes are either eliminated or mutate and find other uses. But wow, thatʼs a big mutation, duplicating the entire genome, and then that genome was slowly whittled down by further mutations and natural selection.

Gene and genome duplication have been thought to play an import part during evolution since the 1930s (Bridges 1936; Stephens 1951; Ohno 1970) . Ohno (1970) proposed that the increased complexity and genome size of vertebrates has resulted from two rounds (2R) of whole genome duplication (WGD) in early vertebrate evolution, which provided raw materials for the evolutionary diversification of vertebrates. Recent genomic sequence data provide substantial evidence for the abundance of duplicated genes in many organisms. Extensive comparative genomics studies have demonstrated that teleost fish experienced another round of genome duplication, the so-called fish-specific genome duplication (FSGD) (Amores et al. 1998; Taylor et al. 2003; Meyer and Van de Peer 2005). Because the timing of this WGD and the radiation of teleost species approximately coincided, it has been suggested that the large number (about 27,000 species—more than half of all vertebrate species (Nelson, 2006)) of teleosts and their tremendous morphological diversity might be causally related to the FSGD event (Amores et al. 1998; Taylor et al. 2001; Taylor et al. 2003; Christoffels et al. 2004; Hoegg et al. 2004; Vandepoele et al. 2004). Semon and Wolfe (2007) showed thousands of genes that remained duplicated When Tetraodon and zebrafish diverged underwent reciprocal loss subsequently in these two species may have been associated with reproductive isolation between teleosts and eventually contributed to teleost diversification. (See this PDF).

Gene duplication is a major force of evolution and plays a critical role in increasing complexity, and two rounds of whole genome duplication (WGD) have been proposed to occur during vertebrate evolution [1]… One whole genome duplication (WGD) event in the fish ancestor generated genome-wide duplicates in all modern species… Duplicated genes may adopt three major modes of evolutionary divergence: loss by deleterious mutations (nonfunctionalization), acquisition of a new adaptive function (neofunctionalization) or division of an ancestral function (subfunctionalization). The role of gene duplication in evolution is perhaps best illustrated by the growth hormone (GH)-prolactin (PRL) family. This family has arisen from a single ancestor by gene duplication followed by extensive functional divergence. Although GH retains the original role in growth control in all vertebrate species, the other members have distinctive functions between fish and mammals: PRL is important for the mammary gland in mammals but for osmoregulation in fish…They also exhibit differences in expression pattern… Fish models provide an ideal system to study the modes and mechanisms of duplicated genesʼ evolution in vertebrates. After split from the tetrapod lineage, fish has undergone a third WGD event in the common ancestor of all modern-day teleosts. Interestingly, the resultant genome-wide gene duplicates usually coexist, leading to more genes in fish…

Two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.

Scientists have suspected that spare parts in the genome — extra copies of functional genes that arise when genes or whole genomes get duplicated — might sometimes provide the raw materials for the evolution of new traits. Now, researchers report that they have discovered a prime example of this in fish.

Fish genomes provide an ideal context in which to examine the consequences of WGD.

Fugu Genome Analysis Provides Evidence for a Whole-Genome Duplication Early During the Evolution of Ray-Finned Fishes [with about 24,000 extant species, teleosts are the largest group of vertebrates. They constitute more than 99% of the ray-finned fishes (Actinopterygii) that diverged from the lobe-finned fish lineage (Sarcopterygii) about 450 MYA]

The rainbow trout (Oncorhynchus mykiss) is raised in aquaculture the world over and is among the most studied fish species. Scientists in France have now sequenced its genome, uncovering evidence of whole-genome duplications that were landmarks of vertebrate evolution and the divergence of teleost fish. The team uncovered and examined two copies of the ancestral salmonid genome within the rainbow trout genome, and used it to infer evolutionary relationships between the fish.

“Due to a relatively recent WGD [whole-genome duplication], the rainbow trout thus provides a unique opportunity to better understand the early steps of gene fractionation,” the rearrangement of the genome following duplication, the researchers wrote in Nature Communications this week (April 22). They added that their results challenge the hypothesis that whole-genome duplications are “followed by massive and rapid genomic reorganizations and gene deletions.”

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.

The Continuous Nature of Gene Duplications

Gene duplication has had a major impact on genome evolution. Localized (or tandem) duplication resulting from unequal crossing over and whole genome duplication are believed to be the two dominant mechanisms contributing to vertebrate genome evolution. While much scrutiny has been directed toward discerning patterns indicative of whole-genome duplication events in teleost species, less attention has been paid to the continuous nature of gene duplications and their impact on the size, gene content, functional diversity, and overall architecture of teleost genomes… Conclusions: We have analyzed gene duplication patterns and duplication types among the available teleost genomes and found that a large number of genes were tandemly and intrachromosomally duplicated, suggesting their origin of independent and continuous duplication. This is particularly true for the zebrafish genome. Further analysis of the duplicated gene sets indicated that a significant portion of duplicated genes in the zebrafish genome were of recent, lineage-specific duplication events. Most strikingly, a subset of duplicated genes is enriched among the recently duplicated genes involved in immune or sensory response pathways. Such findings demonstrated the significance of continuous gene duplication as well as that of whole genome duplication in the course of genome evolution.

Whole Genome Duplication and the Evolution of Flowering Plants

Scientists who sequenced the Amborella genome say that it provides conclusive evidence that the ancestor of all flowering plants, including Amborella, evolved following a “genome doubling event” that occurred about 200 million years ago. Some duplicated genes were lost over time but others took on new functions, including contributions to the development of floral organs. “Genome doubling may, therefore, offer an explanation to Darwinʼs ‘abominable mystery’—the apparently abrupt proliferation of new species of flowering plants in fossil records dating to the Cretaceous period,” said Claude dePamphilis of Penn State University. “Generations of scientists have worked to solve this puzzle,” he added. Comparative analyses of the Amborella genome are already providing scientists with a new perspective on the genetic origins of important traits in all flowering plants—including all major food crop species. “Because of Amborellaʼs pivotal phylogenetic position, it is an evolutionary reference genome that allows us to better understand genome changes in those flowering plants that evolved later, including genome evolution of our many crop plants—hence, it will be essential for crop improvement,” stressed Doug Soltis of the University of Florida…

Gene Duplication May Have Paved the Way For Human Evolution

Humans and Chimps, More To Consider About How Close We Are

Human and chimp genomes are Really close when you consider how many differences are simply due to gene duplications. Gene duplications are an important part of evolution. As for genes that are present in one species but not the other, they are not necessarily evidence of an unbridgable gap, especially not in the case of species as near as human and chimp. Thatʼs because both the intraspecies variation of the genome in a human population (overall human genetic diversity) and the intraspecies variation within chimpanzee populations (chimp genetic diversity) are comparable or greater in some cases than the variation between humans and chimps.

Furthermore, many genes have very little effect on phenotype. Even if they code for particular proteins, they donʼt have to be expressed. Much of the intraspecies variation consists of such genes.

Much of the difference between species is also relevant only to the histo-immune system profile of the individuals, i.e, a lot of the variation we see between genomes is simply comprised of genes that evolved to in resistance to pathogens, and many diseases are specific to a species. So there are variations in the genes for immunity based on the pathogens that each species encounters. Chimpanzees donʼt get all the diseases of humans, and vice versa. Neither should one want to define “human” in terms of the diseases one is prone to.


Speaking of Genetic Differences and the Almost Lego-Like Diversity of Various Mutations in Nature

Remarkable Diversity Of Viral Genome Structures as well as a previously unidentified evolutionary link between unsegmented and segmented viruses.

ORGANISMS CAN VARY A LOT VIA MUTATIONS—A trillion trillion microbes of cyanobacterium hover near the oceanʼs surface and produce half of the worldʼs oxygen. Given their abundance (results pub. in Science, 4/24/14) illustrate their astounding genomic diversity, which is not surprising… Remarkably, within the Prochlorococcus strain in her current study—the so-called high-light-adapted Prochlorococcus—individuals share only about 1,450 “core” genes among the 2,000 genes in each genome. The rest are Variable. (For comparison, humans share 95 percent of their genes with chimpanzees.)… And, “to get these single nucleotide polymorphisms [in the core genes], they need time.”

Evolution 101 For Creationists, I.D.ists, Etc.

DNA never duplicates itself perfectly. There are always mutations.

Most mutations probably are neutral, not necessarily deleterious, or they are deleterious and beneficial to only a limited extent.

The experiments that involved shooting xrays at fruit flies were like shooting buckshot at chickens, yes, they produce a lot of deleterious mutations. But in nature the mutations are not brought on by massive doses of x-rays, and the animals have many more generations to sort them out via natural selection.

Mutations do not have to be fully efficient in order to provide some added function. A famous recent example is the discovery of a simple frame shift mutation in a species of bacteria that allowed it to partially digest nylon, a recent man-made polymer. The bacteria did not receive a lot of energy partially digesting the nylon, but that is only the beginning of further mutations. Same with the recent experiment in which a bacterial colony in a lab evolved the ability to digest citrate. It did not happen all at once, but in stages (see Dennis Venemaʼs article, which also responds to I.D. assertions, Venema is a biologist and, and he also has an ongoing series on understanding evolution that goes into greater depth that youʼre liable to see elsewhere on the web.)

Every animal was something wrong with it in its chromosomes. No animals is perfectly healthy, only relatively healthy, and only the animals that live long and healthy enough to reproduce pass along their genes to the next generation and even among those who reach the point of mating donʼt all produce the same numbers of offspring. So a lot of animals along with their genes get whittled out of the process from fertilization until mating—and even those that mate produce different ratios of offspring.

Both animals and plants survive whole genome duplication events, which are the most massive forms of mutation one can imagine, they also survive whole chromosome mutations either the duplication of a whole chromosome, or a chromosome split into two, or a merging of two into a single chromosome. They also survive duplication of individual genes. In fact there are many groups of similar proteins as one might expect via the above mentioned duplication events. And there are plenty of pseudogenes as well, as one might expect via the duplication events mentioned above.

Viroids are fascinating. A single strand of their RNA alone can copy itself in a test tube. And some viroids appear to be as large as the smallest known bacteria. Bacteria also passively absorb DNA. Exactly how the earliest reproducing chemicals, reproducing cells and viroids co-evolved we donʼt know. But all life appears related as we look backwards from the present to the past in the fossil record (the Cambrian Explosion does not appear to be an exception judging by the way the earliest members of many phyla resemble worms, slugs, and/or little shellies, and diversify increasingly over time, i.e., the earliest vertebrate-like organisms have mere notochords, not bony vertebrae nor jaws, they are long like worms). Life also appears related in the genetic record. Though DNA exchanges grow increasingly less possible to trace as one looks further back since bacteria trade DNA all the time, as well as passively absorb it.

If organisms truly were designed intelligently they could continue to interact with their environment and change accordingly without having to compete to leave offspring, most of which die, or they reproduce in smaller numbers than others, or they never get to reproduce at all.

Mosquitoes resistant to DDT underwent a mutation that produced multiple copies of the esterase gene that helps detoxify DDT; But the cotton budworm underwent a mutation that altered the target of the DDT poison. And houseflies underwent a mutation that altered the proteins that transport the DDT poison. So a variety of POSSIBLE mutations could reduce the killing effects of DDT, and only one of those different mutations has to occur in order for the organism to develop resistance, and of course the organism that survives gets to continue passing that gene along. We donʼt know all the possible mutations that might allow Plasmodium to survive either. This increases the odds that such resistance could occur via random mutations. Also see this recent Take Down Of Beheʼs Argument That Malariaʼs Resistance To A Drug Could Not Have Evolved…

The Origin of Life, Abiogenesis

Experimental evidence concerning how life began and exactly how the earliest reproducing organisms evolved may be hypothetical but the cosmos does appear like one enormously old experiment continually mixing energies and atoms. The cosmos is quite an active laboratory.

How is I.D. going to prove that such an experiment on such a massive scale could never produce self-reproducing molecules and then living organism? And after self-reproduction begins, itʼs a matter of some molecules reproducing greater ratios than others.

The Inevitability of Lifeʼs Origin?

Snowflakes, sand dunes, tornadoes, stalactites, graded river beds, and lightning are just a few examples of order coming from disorder in nature; none require an intelligent program to achieve that order. In any nontrivial system with lots of energy flowing through it, you are almost certain to find order arising somewhere in the system. If order from disorder is supposed to violate the 2nd law of thermodynamics, why is it ubiquitous in nature?

From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.

  • “What is life-lecture: Jeremy England”

    Englandʼs theoretical results are generally considered valid. It is his interpretation — that his formula represents the driving force behind a class of phenomena in nature that includes life — that remains unproven. But already, there are ideas about how to test that interpretation in the lab. “Heʼs trying something radically different,” said Mara Prentiss, a professor of physics at Harvard who is contemplating such an experiment after learning about Englandʼs work. “As an organizing lens, I think he has a fabulous idea. Right or wrong, itʼs going to be very much worth the investigation.”

  • “God is on the ropes: The brilliant new science that has creationists and the Christian right terrified”

Yes, cells are complex, and thereʼs a natural reason for that. In fact, recent experiments indicate that replicating molecules that are more complex and that work in series can out-reproduce other replicating molecules that work alone. So complexity appears to be favored even on a biochemical level. See the new book, “What is Life?: How Chemistry becomes Biology” by Addy Pross and these other books on modern day biochemical research into the origin of life and rising complexity in the genome:

Bacteria as well as viruses, ruled the earth all by themselves for two billion years or more before larger more complex eukaryotic cells (of which we humans are composed) ever arose. Bacteria exchange DNA packets endlessly with other bacteria as well as absorb DNA passively when they encounter it. Sounds like a jury-rigged process of DNA exchange on a trial and error and on a massive scale, doing so for over a billion years. What might that NOT evolve into?

The Discovery Instituteʼ Negligence in Acknowledging the Age of the Earth. If They Canʼt Fully Acknowledge That, Then What Do They Really Know or Care About Genuine Science?

The evidence for an OLD earth presently includes:

  1. Individually (C-14)dated tree-rings in two or three separate tree-ring series, stretch back 12,000 years. (Even Young-earthers like Aardsma, formerly with the Institute for Creation Research, have admitted that the evidence from individually dated tree-rings in two totally separate tree-ring series on two different continents, demonstrates the reliability of C-14-dating stretching back 12,000 years in time).

  2. Individually (C-14)dated varves in a lake in Japan, stretch back 40,000+ layers. (Green River varves have not been individually C-14 dated, but that would be an interesting experiment to perform since there are over 2 million layers per ancient fossil lake in that region, and all toll, when you count the layers of all the fossilized lakes in the Green River region, noting the lowest and highest layers in each lake and how the time overlaps in each lake, there are over 6 million layers.)

  3. Deep ice cores feature 100,000 layers of ice — each layer having its own distinctive isotopic signature (and other types of layer-distinctive signatures as well), stretching back over 100,000+ layers. Latest core drilled was two miles deep and contained 700,000 layers of ice.

  4. Evidence of extremely slow sea-floor spreading over 100,000,000 years. New sea floor is seen forming today from molten rock that emerges from a ridge that runs right down the middle of the Atlantic ocean. On each side of that mid-Atlantic ridge, new molten rock continues to emerge, then it cools and hardens, and the date of cooling (as well as the direction and strength of the earthʼs magnetic field at the time it cooled) is sealed inside the rock in the iron crystals that harden there. Then the next strip of molten rock emerges from the mid-Atlantic ridge, cools, and hardens, as the continents on either side of the Atlantic ocean continue to drift slowly apart from each other. This forms distinctive strips of sea-floor rock that run all the way from the middle of the Atlantic ocean (where the youngest radiometrically-dated strips are found) to the shoreline (where the oldest radiometrically-dated strips are found). Such strips of rock along both sides of the mid-Atlantic ridge reflect over a hundred million years of sea floor spreading that occurred as the continents of North and South American slowly drifted away from Europe and Africa.

    Moreover, the radiometric dates that stretch from the middle of the Atlantic to the shoreline, agree with independent measurements (both land based and satellite based) of the present rate of movement of North and South America away from Europe and Africa. And such direct measurements of the slow current rate of continental drift are cumulative and more accurate over time, leaving little doubt as to the known average rate. In both cases, the expected time it would take for the continents to move apart at their known present rates of speed equal the data based on radiometric dating of the strips of rock from the middle of the Atlantic to its opposite shores.

    Even Young Eartherʼs agree that if you try, as they have, to explain the evidence for extremely slow sea-floor spreading simply by speeding up the process and imagining that the continents zipped into their present positions in a mere “year,” that hypothesis would require a MIRACLE to cool the molten rocks down instantly and in distinctive stages — because if the continents “zipped” along, then the rocks and their radioactive isotopes would have run together like soft butter spread on microwaved bread, neither would the sea floor rocks exhibit the crystallization patterns that rocks exhibit that have cooled under conditions of much lower temperatures and pressures, which is what the sea floor rocks presently exhibit. Moreover, after the continents had ceased “zipping” along but slowed to their present extremely slow speeds, what odds would there be of achieving the same Match between the known range of radiometric dates of sea-floor rocks from the middle of the Atlantic to the shoreline, And the present speed of the continentʼs moving apart from one another today? What a coincidence! The strictly scientific odds look far better that the “continental zip” hypothesis is wrong, and the continents took over a hundred million years to separate, and at the same rate they are presently separating.

    The evidence of an old-earth is enormous and defies the “odds.” There are thousands of individually dated tree rings — tens of thousands of individually dated lake varves — a hundred thousand distinctive layers of ice — and, endless numbers of sea-floor rocks formed in succession, having hardened over successive periods stretching back over a hundred million years.

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