Posted tagged ‘genetics’

Do we need the Endangered Species Act?

April 30, 2012

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A complex story about trout and people

My first experience catching cutthroat trout was in 1989 while fishing in Grand Teton National Park.

Snake River Finespotted Cutthroat trout, Grand Teton National Park, Wyoming, 1989. Note the golden color, typical of cutthroats, along with the lack of spots in the middle (medial region), but increasing towards the tail (caudal region).

Since then, I’ve been blessed with opportunities to fish for trout as far away as Eastern Russia, and as close to home as our family’s pond.

Hatchery rainbow trout from Crystal Lake Fisheries in Ava Missouri, stocked in my pond in Texas for the winter of 2006-07. These are “Emerson strain” rainbow trout, registered with the National Trout Registry. Note the more concentrated spots in the caudal region, similar to the finespotted cutthroat pictured above.

Because trout are both fun to catch and good to eat, they are pursued with passion in the United States and elsewhere.  So much passion in fact, that over the last 150+ years, populations of native species, particularly  the so-called “subspecies” of cutthroat trout (referred to after this as “native” trout), suffered major declines and even extinction. The decline of cutthroats native to certain regions of the western and eastern slopes of the Rockies has been a classic example of the “tragedy of the commons”, where demand for a thing greatly exceeds what nature can supply.

In an effort to meet the demand for trout-filled streams and lakes at the turn of the 20th century, private, state, and federal agencies started building fish hatcheries. Today, virtually everywhere in the United States with trout habitat, you will find a hatchery nearby, ready to add more fish to streams and lakes on a “put and take” basis.

So native trout populations in the American West were first reduced primarily through overfishing, but also from habitat destruction. Today, the major threat to native trout populations comes from stocking nonnative trout, primarily brown trout and brook trout which tend to drive out the cutts, but also rainbow trout, with which cutts readily hybridize.

Brown trout from the Jemez River, New Mexico, 2012. The Jemez River is former habitat for Rio Grande cutthroat trout, which now occupy only about 10% of their historic range. Eastern Russia’s lenok trout (see photo below) lack the red spots of the brown trout, and brown trout lack the “cut”, but the two species do share similarities in color and shape with each other and with many other trout populations across Eurasia.

State and federal fisheries managers want to satisfy the great economic incentive of having trout-filled streams and lakes. For example, the value of trout stockings by the Leadville Fish Hatchery in Colorado is estimated at $2.75 million annually. And while many Rocky Mountain hatcheries are moving towards production of native trout, they also feel compelled to satisfy the desire of folks to just catch a trout, especially the highly esteemed (overesteemed?) rainbow. Originally from the McCloud River, a tributary of California’s Sacramento River, rainbow trout have probably been introduced to more places worldwide than any other fish species. They have misplaced and reduced native species time and again. And about the same time Hitler and his army of fools were applying social Darwinism, miles and miles of American streams were being poisoned to remove “inferior” species, replacing them with the “superior” rainbow. An excellent account of the history of rainbow trout stocking can be found in Anders Halverson’s An Entirely Synthetic Fish: How Rainbow Trout Beguiled America and Overran the World.

Greenback Cutthroat Trout, Leadville National Fish Hatchery, Colorado, 2010. Note the bright pink-red patch over the gill and along the side, similar to the Alaskan rainbows(see photos below). The Leadville Hatchery stocks rainbow trout, as well as Snake River and Greenback cutthroat trout.

So while native populations are making a comeback in places, their progress is stymied when government agencies set tight regulations and catch limits on nonnative trout, in effect protecting something that maybe doesn’t need so much protection. But in America, governments are designed to be run by the citizens, so if we want our government to change the regulations, we need to change our thinking about what we want. Do we want to simply catch a trout and have a successful trip and a tasty meal? Or do we want to have a fishing experience unique to a particular area’s natural history and culture? We should want both, but it is obvious enough that we could do more regarding the latter. Communities should work harder to patiently remove nonnative trout and reestablish native trout species. This can be done in a way that also satisfies the desire to simply catch and eat trout, regardless of species.

What is a species?

But what in the world is a “species” anyways? According to the1973 Endangered Species Act (ESA), the term ‘‘endangered species’’ means any species which is in danger of extinction throughout all or a significant portion of its range. And the term ‘‘species’’ includes any subspecies of fish or wildlife or plants, and any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature. All species classifications are ultimately based on human decisions, driven by our desire to group things using a system that organizes first by kingdoms, then phyla, classes, orders, families, genera, and species. Species are often broken down into subspecies, as is the case with cutthroats.

Clumpers versus splitters

One problem with the ESA’s definition of species is that it pretty-much ignores the idea of Biblical kinds, while introducing the false concept of “fixity of species”, first introduced by Aristotle. The Biblical kinds, also known as “baramins”, are actually a better, yet still imperfect, way to think about living organisms. Populations that readily hybridize, especially naturally, suggest (but do not prove) common ancestry, while those that don’t readily hybridize may be from different baramins. Thinking of life’s diversity in terms of baramins allows us to account for unity while acknowledging that some genetic and epigentic changes are inevitable as time passes.

Taxonomists are usually either “clumpers” or “splitters”. Clumpers think more in terms of baramins, while splitters think more along the lines of how the ESA defines a species. Sometimes “clumpers rule”, while other times it’s the splitters. For example, at the turn of the 20th century, taxonomists had convinced themselves that over 80 sub-species of grizzly bear (Ursos arctos) existed. Today, there are only 2 subspecies, so as far as grizzly taxonomy is concerned, “clumpers rule” (NOTE: Grizzlies hybridize with polar bears, forming “pizzly” bears!)

It is unfortunate that, regarding the ESA, “splitters rule”. By defining a species as a “distinct population segment”, ESA listings slap a false fixity on populations.  But populations are not designed to stay “distinct” forever, so the ESA is actually promoting an impossible dream rather than anything that resembles reality. And for evolutionists who believe there are almost no limits to how much a thing can change, the logical conclusion for them is that all current populations are in danger of extinction!

Of course, neither the ESA’s “splitter” definition of species, or the evolutionist’s reasoning about life’s diversity, are helpful in describing reality. The reality is that organisms are designed to adapt and diversify, within limits, by naturally aquiring some genetic and epigenetic changes over time. This is what both Scripture and science confirm. 

Cutthroats are a prime example of how slight genetic and epigenetic changes over time can result in visibly distinct populations. Scientists have found that of the 16 so-called subspecies of cutts, their genetic diversity suggests they are virtually all identical, with westslope cutthroat populations sharing more in common with rainbow trout than with other cutts (Allendorf and Leary, 1988). In spite of their incredible similarities, 3 are currently listed as “threatened” under the ESA, one may make the list in 2014 (Rio Grande cutt), and the rest are either extinct (two subspecies) or considered to be of conservation concern (Pritchard et al, 2007).

How can this be? If genetics is the key to distinguishing between species, then it says these are all basically the same “kind”, with differences occurring at a few DNA base pairs here and there. To make matters even more confusing, Pritchard et al found that Rio Grande cutts in headwater streams above natural barriers were statistically less genetically diverse than their downstream cousins. So for “splitters”, not only do we have subspecies, we have sub-subspecies! Where will it end? The genetic tools we have for identifying differences in populations are truly amazing, but the information acquired can potentially make things much more complex than necessary, especially if you’re a “splitter” and feel compelled to classify cutthroats as sub-species, and then some.

Genetic drift happens

Salmonids are known to rapidly diversify, in less than 10 generations, into reproductively isolated populations. Applying this fact to the ESA’s species definition of “distinct population segments”, in 50 years or less, and assuming “splitters rule”, we could have dozens and dozens of new candidates for the ESA, possibly resulting in more and more restrictions on habitat use by humans. And then what will we do to maintain partitioning of these new and “distinct population segments”, create manmade barriers to prevent them from interbreeding with other segments? I would hope not! As far as trout diversity is concerned, it would be wise to get back to letting the “clumpers rule”, lest we end up overwhelming ourselves with more classifications, regulations, restrictions, and taxes to pay for the mess we’ve made.

No biologist, whether they are creationists or evolutionists, believe in fixity of species, but here we have the ESA anyways, trying desperately to prevent the natural fact that genetic drift happens.

Prior to the 1973 Endangered Species Act, fisheries managers across the West sacrificed diversity for the sake of unity, stocking the “superior” rainbow everywhere. But now with the ESA, we have a complete reversal, with unity (trout are one big family) sacrificed for diversity ( “subspecies” and “distinct population segments”). There has to be a better way.

Imagine no ESA

So do we need the ESA? No. What Americans need to do instead is stop waiting for handouts from the federal government via ESA listings, and instead encourage communities to responsibly restore and preserve the natural history in their region. And in the case of native trout, we need to work towards stocking them more and nonnative trout less.

Consider the Rio Grande cutthroat, for example. Organizations like the Center for Biological Diversity proudly exclaim that their work resulted in Rio Grande cutts being eligible for the Endangered Species list in 2014. But all this really means is more regulations, taxes, and “takings” of property by the federal government to protect a population that apparently already has many “distinct population segments”, and may have dozens more in 100 years. Instead of waiting around for an Endangered Species listing, what if instead local private and public groups made an effort to remove nonnative trout while also propagating Rio Grande cutts for reintroduction? This could be done slowly and patiently, one stream at a time, all without the help of the ESA.

We also know that all cutthroat subspecies will hybridize with each other, as well as with rainbow trout. And since rainbow trout are so genetically similar to cutts, we shouldn’t get too worked up about them interbreeding and waste tax dollars with over-hyped eradication programs. We just need to adjust the rules and get Rocky Mountain fishermen educated and involved in harvesting more rainbows, plus browns and brookies, while simultaneously restocking with native trout.  And for those interested in catching native rainbows, they should head to Alaska, Canada, or Russia’s Kamchatka Peninsula, where native ‘bows are plentiful.

Native Rainbow Trout from Lake Creek, Alaska, 2005. Note the reddish-pink patch on its gill cover, typical of lower Lake Creek Rainbows.

Native Rainbow Trout, American Creek, Alaska. 2007. Note the bright red-pink cheek and side, similar to the Lake Creek Rainbow, but also similar to the Greenback Cutthroat Trout. Sometimes, these rainbows have a faint “cut” under their lower jaw, similar to other cutthroat trout.

And speaking of Russia, all the way across the Pacific, near Vladivostok, I have caught lenok trout that display a distinctive “cut” on their throat, and in a way seem similar to both brown and cutthroat trout. It seems that trout really are just one big family, or baramin, containing both unity and diversity.

Closeup of the Lenok trout’s “cut”. Although not as bright as the cut found on many cutthroats, it is a cut nevertheless, and a key identifying trait of all cutthroats.

Lenok trout from stream near Vladivostok, Russia, 2010. Note the golden coloration and large spots, similar to patterns on many cutthroat sub-species.

What is a gene?

Trout were first classified based on phenotype (what they look like on the outside). But now that we also know their genotypes (what their genes look like), we can more readily discern whether a population of cutts has hybridized with rainbows, even if we cannot tell by phenotype alone. But for the people who are most interested in their preservation and restoration, namely fishermen, there is little interest in how much or how little they differ at a few microsatellites (small pieces of DNA a few base pairs in length that are used to distinguish between populations). So now that species and subspecies are being determined by genetic markers, the question of “what is a species?” should be followed with “what is a gene?”

Not surprisingly, scientists are having an equally hard time answering that question, as new information about cell complexity continues to gush forth like water over Yellowstone Falls. Long gone is the simplistic view of genes as neatly arranged beads on a string of DNA. So too is the “one gene makes one protein” idea, as we now know that one gene can code for tens, and in some cases hundreds of different proteins. Not only that, scientists are learning more about epigenetics and things like methyl tags that turn genes on and off. In The Mysterious Epigenome, Woodward and Gills provide a helpful analogy, describing the genes as ships and epigenetics as the captains. Without the captain’s direction, the ship does nothing. But the question remains, from where did the captain get his orders? The self-evident answer is that a Designer gave the orders (Romans 1:20).

And so it seems, the more we learn about cell complexity and epigenetics, the more difficult it becomes to truly define separate trout species based on genetic markers. Genetic markers alone do not tell the whole story of the unity and diversity we see in the trout family. Oncorhynchus mykiss (rainbow trout) and Oncorhynchus clarkii (cutthroat trout) are classified as different species based on pre-Civil War observations of phenotype alone. Today though, 21st Century genetics research and observations of natural hybridization tell us the two are nearly identical. With each passing day, the Biblical idea of a “trout baramin” becomes more appealing. While science can change with time, truth does not.

Trout live in worlds of extremes, of swift currents and lazy pools, flooding spring meltwaters and drought-like autumns, miniscule headwater streams and deep, wide rivers. It is obvious trout were designed to rapidly adapt, as opposed to the neo-Darwinian idea that they were sitting around for millions of years hoping for a gene with a novel function to randomly appear to advance them down the road of evolutionary progress. It seems instead that like other baramins, the trout baramin came pre-programmed with what they need to survive and adapt.

Trout come in many flavors

Yellowstone Cutthroat Trout from Cascade Creek in Yellowstone National Park, Wyoming, 2012.

So what is going on with trout? What scientists are finding is that very slight genetic and epigenetic changes in isolated populations have led to amazing and beautiful differences in phenotype, giving each region a particular “flavor” of trout. One conclusion is that the adaptive radiation we see in trout is partly a result of changes in climate and topography that occurred in the recent past. We’ve already discussed how rainbows readily hybridize with cutts, but by continuing the stocking of rainbows outside their normal range, we are, in essence, driving the formation of new breeds of trout. That is not necessarily a bad thing, but just because it is not inherently wrong, it doesn’t mean it is the best thing to do either. Restoring native trout to their historic ranges is a good idea, but we shouldn’t be “trout racists” either by overreacting to introduced populations. They’re all one big family anyways, right?

Preserving trout’s many flavors

Restoring historic ranges of native trout does not require the Endangered Species Act. In fact, the ESA could be repealed, or simply ignored, and reintroduction efforts could still move along beautifully. As mentioned earlier, the ESA is unhelpful because it promotes a false idea of species fixity, sacrificing unity for the sake of diversity. The best solution is one that seeks both unity (trout are one big family) and diversity (restoring native trout to their historic ranges). Instead of wasting time with the ESA, local communities should do the work needed to restore and preserve the natural history around them, while also managing it in a way that maximizes people’s enjoyment and use of available resources. Restoration can advance through level-headed efforts aimed at removing nonnative trout, while simultaneously restocking with native breeds.

We are learning more about how to maintain genetic diversity in hatchery brood stocks, and this information can be applied to propagate a breed that is unique to a given area, thereby preserving some of the natural history. In Appendix 51: Westslope Cutthroat Trout Hatchery Brood Stock Histories, a procedure is described where, in order to incorporate genetic diversity into the hatchery brood stock, fish are collected from a number of streams.

The native hatchery fish should probably be stocked in areas downstream of natural barriers.This would aid in preventing at least some intermingling with upstream populations, thereby encouraging genetic diversity. Fishing on stretches of headwater streams should be more restricted than on higher order streams, where primary productivity is usually greater and trout populations are naturally higher.

As we work toward better management of native American trout populations, we must realize that genetic drift is inevitable. And regardless of the level of human involvement, the so-called subspecies of cutthroats of 2112 may not look like the cutthroats of 2012, but that’s okay!

Managing natural resources

Human beings are not just part of nature, we are nature’s managers (Genesis 1:26-28). This also means we are part of  the story of natural history. And 100 years from now, I hope my great-great grandchildren will be able to look back and see that our efforts to manage nature paid off in a way that celebrates the unity and diversity He so obviously put into His creation. And I pray that future leaders will not try to discourage unity and diversity through the ESA and its adherence to the fallacy of species fixity, but will instead get local communities involved with restoring and preserving native trout to their historic ranges.

Perhaps in the future, instead of going to New Mexico to fish for rainbows and browns, Colorado to fish for rainbows and browns, Wyoming to fish for rainbows and browns, etc., future generations will live in a world filled with trout that are unique to each region, while understanding the native forms are part of a bigger trout family, just as the evidence from His word and works confirms.

21st Century Research Smashes Molecular Clock Myths

December 1, 2011

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Belief in evolutionism requires one to reject the authority of Scripture regarding special creation of humans, along with different created kinds, or baramins, of living organisms. Biblical history must also be rejected, because millions of years are apparently required for nature to perform its evolutionary magic. Belief in evolutionism forces one to cling to a number of 19th and 20th Century hypotheses that use artificial constructs like the geologic column and Thomas Malthus’ population data as evidence for bacteria-to-people evolution.

Fortunately, the more we learn about Earth and life in the 21st Century, the more they proclaim the glory of their Creator and the Truth of the incredible story revealed in Scripture. An example of 21st Century research is the mounting evidence against the idea of molecular clocks. Natural history researchers look at differences in genes along with fossil evidence to determine when two species diverged from a common ancestor. For the human species, researchers use molecular clocks to predict the date of “Mitochondrial Eve”, our Most Recent Common Ancestor (MRCA) that supposedly originated in Africa.

Molecular clocks came into use in the 1960s. In the 1990 edition of Biology by Neil Campbell, an age between 200,000 and 400,000 years is given for “Eve” (p. 669). Moving ahead to 2004, we find in the 10th edition of Biology by Starr and Taggart that Eve is now only 100,000 to 200,000 years old (p. 471). The fact that the estimates were cut in half, on top of the huge error involved (50%), would make any reasonable scientist question molecular clocks.

And they do. As we entered the 21st century, we saw F.J. Ayala’s paper titled “Molecular Clock Mirages”. In 2006, world renowned evolutionary biologist Thomas Cavalier-Smith stated in a paper “Evolution is not evenly-paced and there are no real molecular clocks.” And then there’s F. Chang’s study using genealogy and statistics to predict an MRCA of less than 1,000 years ago. Chang began with an overly-simplified model, so over the next few years he added to it, and in 2003 colleague D. Rohde published research revealing an MRCA of between 2,000 and 5,000 years ago. And molecular clock skeptics Thorne and Wolpoff voiced their opinions in the 2003 Human Evolution Special Issue of Scientific American, flatly stating “putting aside the idea of a molecular clock, one can interpret the genetic data in a much more reasonable way.” (p. 52).

In 2004, Rohde, Chang, and Olson published their latest findings in Nature, and their computations shift the MRCA from Africa to somewhere in Asia. They also calculated that “all modern individuals have identical ancestors by about 3,000 BC.” Mentioning that their computer simulation was “far too conservative”, they used some more realistic numbers to come up with a “mean MRCA date is as recent as AD 55 and the mean IA date is 2,158 BC.”

The identical ancestors (IA) point differs from the MRCA. The MRCA is believed to have had many contemporaries of both sexes, and some of these also left unbroken chains of descendents down to today’s population. The IA differs in that it pushes further back in time to the point where populations can be divided into two groups: a group that left no descendents today, and a group from which all modern humans descended from. Such a scenario could arise from a population bottleneck, and the obvious example that comes to mind is the Flood described in the book of Genesis, which occurred around 2500 BC. The date of the Flood is within the range of IA dates computed by Rohde et al. During the Flood, a human population of 8 survived, and all others perished. While Rohde et al’s research does not “prove” the Genesis Flood, it definitely doesn’t rule it out.

In 2008, a paper by Matsen and Evans tried to tie genetics with the genealogy of Rohde et al, and they simply concluded genetic diversity is related to the number of descendants, confirming the ability of Rohde et al’s model to explain the human diversity we see today as resulting from a very recent ancestor.

21st Century research using genealogies instead of genetics may be a bit confusing, but the reason for that is not just the complex mathematics involved, but the basic fact that confusion exists over what happened in the past. To add to the confusion, in 2008 fossil collectors discovered a human footprint alongside that of a dinosaur. Fossil evidence like this is no problem for Christians who trust the historical accuracy of Scripture, but it is a huge contradiction to many others’ beliefs about the past. Is this fossil real?

The truth is, there will ALWAYS be confusion about what happened in the past because we cannot go back and verify it. Natural history research is not the same thing as testable, repeatable science, and should be approached as a “mixed question”, requiring inputs not just from science, but mainly history, followed by art, and philosophy. “Belief” in past events though is based on faith, either a God-given faith (Ephesians 2:8-9)in the story revealed in Scripture, or a blind faith in something else. Everybody believes in something, what do you believe?

Tiktaalik, a transitional fossil or just a fish?

November 10, 2010

This video presents some of the speculation and artwork that goes into describing fossils. Conclusions drawn about fossil finds are always subject to the interpreter’s bias. This video shows how a simple experiment can turn a round-headed fish into something resembling the flat-headed and supposed (by some) part-fish, part-amphibian known as Tiktaalik roseae.

There is evidence Tiktaalik was a “fishapod”, but there is also plenty of evidence it wasn’t.  Paleontologists (people who study fossils) should be more careful about explaining their findings, and they should set higher standards for themselves. They should not publish a “transitional fossil” until they have at least one fully intact specimen, as well as full or partial fossils of what it transitioned from and what it transitioned into. Paleontologists should also be very careful about passing their work off as “science”, because real science requires that conclusions be verified with direct observation, and we can’t do that with fossils. To prove what Tiktaalik really transitioned into, we would have to go back in a time machine and observe it over many generations, but we cannot do that. Interestingly, in all the real multigenerational studies, where scientists either have or currently are collecting data on what organisms transition from and into, not one of them shows evidence of transitioning from one kind of organism to another. Even multigenerational studies on bacteria, which can reproduce daily.

The Bible informs science, so it should be no surprise when scientists conclude over and over again that there are limits to genetic change. God said He created “each according to its kind” ( Genesis 1), and that “all flesh is not the same flesh” (I Corinthians 15:39) and man’s scientific endeavors with live organisms affirm this.

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