Biological Evolution: What Makes it Good Science? Part 2

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April 16, 2013 Tags: Genetics, History of Life

Today's entry was written by Michael Buratovich. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Biological Evolution: What Makes it Good Science? Part 2

Note: This is a continuation of an essay posted yesterday. You can read the first part here.

The second piece of evidence is found in living creatures, which are littered with the remnants of their ancestors’ ways of life.  Bird and anteater embryos show tooth buds that are later absorbed and never erupt.  Baleen whale embryos even develop teeth that are later resorbed.  These are relics of their toothed ancestors.1 Flightless kiwi birds have diminutive wings underneath their feathers, which testify to the ability of their ancestors to fly.  Many cave-dwelling animals have rudimentary eyes that cannot see, even though eye development initiates in many of these species, but is later aborted.2  The same can be said for the hind limbs of snakes, which form limb buds during embryonic development, but die off later.3 All these are indications that they are descended from sighted and limbed ancestors, respectively. 

Such remnants are also found in our genomes.  Humans, unlike most mammals, cannot synthesize (make) our own vitamin C, but we carry the genes for synthesizing vitamin C.  One of these genes encodes the GLO (L-gulonolactone oxidase) enzyme, and this gene in humans contains inactivating mutations and is therefore a “pseudogene.”  This pseudogene and the genes that encode the enzymes of the vitamin C biosynthetic pathway are the remnants of our own evolutionary lineage from an ancestor that was able to synthesize its own vitamin C.4 Furthermore, the GLO pseudogene is just one of a graveyard of inactivated genes, transposons, retroviruses and other non-functional sequences that litter our genome.  While some of these sequences have been co-opted for particular functions, many of them have no known function.5 We share many of these non-functional sequences with chimpanzees.  The very presence of these genomic and anatomical flotsam and jetsam only makes sense if evolution has occurred.6

A third piece of evidence for evolution comes from biogeography.7 The flora and fauna of islands such as those of the Galápagos and Hawaii are radically unbalanced in that they lack many types of plants and animals but contain a profusion of clusters of similar species.  Hawaii, for example, has no native mammals, reptiles, or amphibians, but a profusion of fruit flies and silversword plants.8 One third of the 2,000 species of fruit flies are found on the Hawaiian Islands, which only covers 2 percent of the land on earth.  These islands were never connected to the continents and arose as a result of volcanic activity and were, at least initially, completely uncolonized.  The colonization of these islands occurred by means of occasional introduction of creatures from the mainland that then rapidly speciated on these islands to fill every available ecological niche.  Thus, the organisms most closely related to island species come from the closest mainland areas, and often include those creatures most likely to find their way to islands, such as birds and flying insects. 

The Galápagos Islands provide an excellent example of how biogeography provides evidence for evolution. The Galápagos have fourteen species of finch whose closest relative is probably the South American grassquit (Tiaris), yet only four of these finch species feed on seeds as finches normally do, while two others feed on cacti, seven eat insects, and another eats almost exclusively leaves.9 Darwin, while visiting the Galápagos, still thought that species only varied within a particular kind (though he would not have used that terminology) but could adapt to various local environments and become particular subspecies. Therefore, he originally listed the warbler finch (Certhidea olivacea) as a wren and listed the small cactus finch (Geospiza scandens) as a member of the Icteridae or the family of meadowlarks and orioles.  Only after Darwin had deposited his Galápagos specimens with the British ornithologist John Gould did Darwin discover (in a meeting with Gould that occurred during March, 1877), that his finch collection included thirteen or fourteen species of unusual finches that were all so closely related, Gould classified them in a single group all their own.  This meeting showed Darwin that the immutable barrier between kinds of species did not exist.  The Galápagos Islands were not a distinct “center of creation,” but a workshop for evolution in which an ancestral species made it to the yet uncolonized island and underwent a massive degree of speciation to adapt to the environment of the island.10 This is precisely what one would expect if the species of islands had arisen by evolution. 

A scientific theory also allows scientists to make predictions, and good theories provide accurate predictions.  Can the theory of evolution allow accurate predictions?  The answer, once again, is yes.  Darwin himself predicted that the earth must be very old for evolution to occur.  He did not know the age of the earth, but further research has shown that the earth is 4.55 billion years old, which is plenty of time for evolution to occur.  Darwin also predicted that since plants on islands were most closely related to certain mainland plant species, the seeds of these plants should be able to withstand immersion in sea water for long periods of time, and again, Darwin was shown to be right.11 Many decades after Darwin, we now know that variation in organisms is due to mutations in DNA and that these mutations are inherited, just as Darwin predicted.12 Also, Darwin’s principle of natural selection predicts that particular sequences of DNA should behave in a manner that benefits only themselves and not their carriers, which modern research has thoroughly confirmed with the discovery of transposons and other types of “selfish DNA.”13

Is evolutionary theory a good scientific theory?  It has been repeatedly tested for over 150 years since its inception, and it has passed those tests successfully.  The theory has been modified in response to new data, but the outlines of the theory have remained largely intact.  It has existed at risk from new data.  During the molecular biology revolution that began with the discovery of the structure of DNA by Franklin, Watson and Crick in 1953, the explosion of new data could have shown contemporary evolutionary theory to be wrong.  However, some of the most powerful evidence for the theory of evolution has come from a field of science that did not even exist during Darwin’s time.  The ability of a theory to withstand such intense scrutiny is a clear sign it is robust and enduring.  As shown, the theory of evolution has predictive power, and it also integrates and makes sense of data from several fields of science, including ecology, paleontology, genetics, historical geology, paleoclimatology, and comparative anatomy and biochemistry.  The highly integrative nature of evolutionary theory makes it a fine theory by any measure. 

In conclusion, when measured against the standards of a good scientific theory, modern evolutionary biology clearly qualifies as good science.  Ongoing debates within evolutionary biology exist about mechanism, rates, and causes, but not over whether evolution occurred.  Such a question has been largely settled by the last 150 years’ worth of research.  The future certainly looks bright for this field of science and I cannot imagine a more exciting topic to study. 

Notes

1. Davit-Béal, Tiphaine,Abigail S. Tucker, and Jean-Yves Sire. “Loss of Teeth and Enamel in Tetrapods: Fossil Record, Genetic Data and Morphological Adaptations.” Journal of Anatomy 214, no. 4 (2009): 477–501. 

2. Tian, Natasha M. M.-L., and David J. Price. “Why Cavefish are Blind.” BioEssays 27 (2005): 235–38; Yamamoto Y, Stock DW, and Jeffery WR (2004) Hedgehog Signalling Controls Eye Degeneration in Blind Cavefish. Nature 431:844–7; Jeffery, W. R. “Adaptive Evolution of Eye Degeneration in the Mexican Blind Cavefish.” Journal of Heredity 96, no. 3 (2005): 185–196. 

3. Bejder, L., and B. K. Hall. “Limbs in Whales and Limblessness in Other Vertebrates: Mechanisms of Evolutionary and Developmental Transformation and Loss.” Evolution and Development 4, no. 6 (2002): 445–58. 

4. Lachapelle, M. Y., and G. Drouin. “Inactivation Dates of the Human and Guinea Pig Vitamin C Genes.” Genetica 139, no. 2 (2011): 199–207.

5. Avise, John C. Inside the Human Genome: A Case for Non-Intelligent Design. New York: Oxford University Press, 2010.   Romano, C. M., F. L. Melo, M. A. Corsini, E. C. Homes, and P. M. Zanotto.  “Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys.” PLoS One 2, no. 10 (2007): e1026. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001026

6. Max, “Plagiarized Errors and Molecular Genetics,” http://www.talkorigins.org/faqs/molgen.

7. Coyne, Jerry A. “Intelligent Design: The Faith that Dare Not Peak Its Name.” In Intelligent Thought: Science Versus the Intelligent Design Movement, edited by John Brockman, 3–23. New York: Vintage, 2006. 

8. Kricher, John. Galápagos: A Natural History. Princeton, NJ:  Princeton University Press, 2006. 

9. Grant, Peter R., and Rosemary B. Grant. How and Why Species Multiply: The Radiation of Darwin’s Finches. Princeton, NJ: Princeton University Press, 2011. 

10. Sulloway, Frank J. “Why Darwin Rejected Intelligent Design.” In Intelligent Thought: Science Versus the Intelligent Design Movement, edited by John Brockman, 107–25. New York: Vintage, 2006. 

11. Darwin, Charles. “On the action of sea-water on the germination of seeds.” Journal of Proceedings of the Linnean Society of London (Botany). 1 (1857): 130–140.

12. Futuyma, Douglas J. Evolution. 3rd ed. Sundbury, MA: Sinauer Associates, 2013. 

13. Dawkins, Richard. The Selfish Gene. New York: Oxford University Press, 2006.

 


Michael Buratovich is an assistant professor of biology at Spring Arbor University in Spring Arbor, Mich. He has taught biochemistry, cell biology, genetics, genes and speciation, human physiology, senior seminar and pharmacology. He has also directed student research projects in fruit fly development, antimicrobial agents, and fruit fly repellents and attractants. He has published articles in numerous encyclopedias, Developmental Biology, Drosophila Information Service, Reports of the National Center for Science Education, Genetics, Stem Cells and Development, Recent Patents on Anti-Cancer Discovery, and Perspectives on Science and the Christian Faith.

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Jose Loayza - #78955

April 23rd 2013

You are right that there is an ongoing debate as to the mechanism (s).... Stop and think: where would purposeful intelligent design fall? That’s right, it would be a mechanism. The ‘fact’ of evolution remains, no conflict there…


glsi - #79499

May 3rd 2013

Inexplicably, in his wordy and convoluted writing, Dr. Buratovich never mentions the basic fact that the Gallapagos finches are capable of interbreeding with each other, thus fitting the common definition of a single species. The Grants and others went back in the 70’s to check it out and, sure enough, they’re all still finches.  Not a finchokeet, a fincheagle, or a finchbeagle among them.  What’s so hard about adaptations within species for evolutionists to understand?


Michael Buratovich - #79736

May 8th 2013

Glsi

Since I referenced the Grant’s book, and since this book has an entire chapter in hybridization in Darwin’s finches, I was not unaware of this phenomenon. Ecologists speculated that hybridization occured among Darwin’s finches, but the Grants definitively demonstrated that hybridization does occur.  

You, however, overstate the degree of hybridization.  The finches are not all able to hybridize with each other.  Hybridization is rare and only between specific members of Darwin’s finches.  For a good reference, see Grant PR (1993) Hybridisation of Darwin’s finches on Isla Daphne Major, Gala´ pagos. Philosophical Transactions of the Royal Society of London B 340: 127–139.

For example, on Daphne island, about 1.8% of breeding Medium ground finch individuals and 0.8% of breeding Cactus finch individuals hybridize (see Grant BR and Grant PR (1989) Evolutionary Dynamics of a Natural Population. The Large Cactus Finch of the Galapagos. Chicago: Universityof Chicago Press).  It seems hybridization is more common among the Small ground finch individuals, and that is probably due to the scarcity of Small ground finch mates on this island.  The hybrids are fertile and viable.  According to Peter Grant, the relative fitness of hybrids depends on ecological conditions.   Therefore, ecological factors seem to be as important as genetic factors in determining the relative fitness of finch hybrids.  

Hybridization can also occur because of misimprinting of the mating songs of the fathers.  Since young make finches learn their father’s mating song, a crowded population where different species breed close together can cause some sons to learn songs from nonparental species.  Females will mistakenly mate with these confused males and a hybrid is born.  

Hybridization is a creative element of speciation that introduces new genetic information into the population.  

Incidentally, hybrids always backcross - mate with the parental species, which limits the ingression of the genes of the other species into the population.  

Darwin’s finches are extremely varied in their ecology, behavior and appearance, yet they descended from a common ancestor - genetic data makes this undeniable (see Petren K, Grant BR and Grant PR (1999) A phylogeny of Darwin’s finches based on microsatellite DNA length variation. Proceedings of the Royal Society of London B 266: 321–329).  This is not adaptations within a species or microevolution.,  This is speciation - the generation of a new species - or macroevolution and the evidence for it is extensive.  


glsi - #79752

May 9th 2013

species | ˈspēsēz; - sh ēz|noun ( pl. same)(abbr.sp., spp.) Biology a group of living organisms consisting of similar individuals capable of exchanging genes or interbreeding. 


“There is no evidence for an absolute genetic barrier between Darwin’s finch species, thus many species can potentially hybridize.  The reasons for hybridization include morphological similarity between individuals and biased sex ratios, that is the scarcity of conspecific mates.”(Grant, 1993)

Dr. Buratovich, it seems as though you are the one overstating your case.



Michael Buratovich - #80060

May 14th 2013

No I don’t think so.  Look at Grant’s words:  “The reasons for hybridization include morphological similarity between individuals and biased sex ratios…”  In other words, the hybridization occurs between the more morphologically similar species.  Therefore Geospiza fortis hybridizes with Geospiza fuliginosa and Geospiza scandens, but they do not hybridize with Camarhynchus or Certhidea species. Hybridization occurs between some of the more closely related species and not the others. 

Furthermore, the lack of an absolute genetic barrier does not mean that there are not other reproductive isolation mechanisms (RIMs) between various species of Darwin’s finches.  Ecological RIMS, behavioral RIMS, or even habitat RIMs are barriers that prevent various members of Darwin’s finches from mating.  Furthermore, Grant says repeatedly that hybiridzation is not a common event. 

Thus we have a group of birds that are ecologically distinct, morphologically diverse, and clearly related to each other and descended from the mainland species Tiaris.  How is this not an example of evolution above the species level or macroevolution?  Just because some members of Darwin’s finches can exchange genes does not mean that all members do.  The fact that they do not says that they are distinct species and a remarkable example of macroevolution. 

Incidentally, you keep quoting Grant, but Peter and Rosemary Grant have repeatedly stated that Darwin’s finches are a robust example of macroevolution.  Therefore, how does quoting Grant support your case?


glsi - #80203

May 17th 2013

There’s a standard definition for the term species which I posted above.  If you don’t accept it, I don’t know what to say.  Then I posted a statement from your source which says there is no genetic barrier between the finches. There is a very remedial connection one can make between the two.  You do not need a PhD to understand it.

The only way to claim the finches are separate species is to either change the definition or change the research results.  You will need either a moving target or else employ some type of word game.

I’m curious why you would object to me using your source for this information.  The fact that they are evolutionary biologists only makes their results more potent doesn’t it?

The finch varieties are no different than dog breeds except that they are less varied than dogs. A toy poodle and a newfoundland would be quite an awkward morphological match which will rarely occur, but they are both dogs and nothing but dog. 


Michael Buratovich - #80326

May 19th 2013

The Oxford Dictionary definition for a species and the definition debated by ecologists, taxonomists, and evolutionary biologists are different.  The definition used by biologists is more expansive, nuanced, and data-driven. 

Species may not exchange genes with each because of prezygotic RIMs, which prevent the formation of hybrid zygotes, or postzygotic RIMs, which prevent hybrid zygotes from either developing properly or successfully competing in the wild.  The RIMs between species may be incomplete, allowing some hybridization in some locales, but the two organisms are distinct enough to merit being classified as distinct species.  Plethodontid salamanders, for example, live in Virginia, Tennessee, North Carolina and northern Georgia.  However, in southern Tennessee and northern Georgia, a distinct species of Plethodon lives, Plethodon teyahalee.  The other Plethodon species, Plethodon cylindraceus has a more northernmost distribution, but these two species overlap at the Tennessee/North Carolina border.  There, species hybridization occurs, but the two creatures are still distinct enough to be considered distinct species.  The whole Plethodon glutinosus group seems to be a collection of woodland salamander species that result from speciation events. 

For example, the hooded crow (Corvus cornix) lives in Northern, Eastern, and Southeastern Europe and the Middle East.  The carrion crow (Corvus corone) lives in Western Europe and Eastern Asia.  There is a hybrid zone that passes through the Saxon part of Germany and winds through Switzerland, all the way to the Mediterranean Sea.  In this hybrid zone, these two species interbreed.  However, the hybrids lack vigor and only live in this strip of land where the ranges of these two species overlaps.  Thus, there is no absolute genetic barrier between these two species, but they are nonetheless two distinct species with their own morphology, their ecological traits, their own mating rituals, their own nesting behaviors, and their own feeding habits.  Kind of reminds you of another group – like maybe Darwin’s finches?

As another example, the grey oak (Quercus grisea), which is also known as the scrub oak hybridizes with four other oak species where the ranges of each overlap:  The Arizona white oak or Quercus arizona, the Gambel oak, or Quercus gambelii, the Mohr oak or Quercus mohriana, and the sandpaper oak or Quercus pungens.  These hybrids only exist in the areas where the ranges of these tree species overlap and are not found outside the area of overlap.  Nevertheless, these four oaks are separate oak species, and represent an excellent example of sympatric speciation.  

The theory of evolution is built on elegant observations such as these – species splitting into new species.  Speciation, of which Darwin’s finches are an example, builds small changes that split species into new species.  Over time, these changes can eventually generate organisms that are completely novel.  This is the reason why Darwin’s finches and examples like it are important evidences for evolution. 


glsi - #80364

May 20th 2013

So you are changing the definition to suit your need.   As I indicated above, there’s really no way of having a conversation then because nothing means anything.  I’m sticking with Oxford American and the many other sources which are overwhelmingly accepted as authoritative by the majority of people.  You can write your own definitions and then talk to others in your field like they do at Esperanto conventions.

 

It’s painful to say, but I think its a serious credibility problem.  If you want to understand why so many people in the church and in society at large don’t believe in this theory, this would be one place to start.



Michael Buratovich - #80387

May 21st 2013

I am not changing the definition of species.  I am trying to convey the difficulty with applying a one-size-fits-all definition to living organisms that do not seem to care about our definitions and have a variety of borderline cases and so on.  I am also trying to communicate that speciation occurs in steps and stages and organisms at various stages of speciation can really mess with our neat little definitions of species and so on.  Remember glsi, the language we use is meant to serve our understanding and communicate it as accurately as possible.  Language should never dictate our understanding.  

Say, are you familiar with Francisco Ayala’s work on speciation in South American and Central and Carribean fruit flies?  That is a great example of the various stages of speciation and various species “frozen” in intermediate forms that defy neat classification as one species or another.  We can talk (or type) more about it if you want in future comments.  

One penny for your thoughts - since dandelions are spouting all over my lawn this time of year, I will use them as an example.  Dandelions (Taraxacum officinale Weber) make lots of pollen and cause horrible allergies for some people.  However, these flowers reproduce without the benefit of pollination - they reproduce asexually by means of apomixis.  How would you classify the different dandelions into species?  The Japanese white flower, Japanese, Russian, Red seeded, and California dandelion all look distinctly different and have robust ecological differences.  You can’t mate them to see if they are distinct species.  So how do you classify them?  You see, the species definition in the Oxford dictionary starts to become rather unhelpful.  Do you see what I mean?


glsi - #80398

May 22nd 2013

Thanks for your gracious and thoughtful responses.

About 10 yrs ago I went to an Evolution conference at the U of Georgia.  I questioned the panel whether any of them could cite any clear example of fossil evidence showing the evolution of one species into a new species.  There was a bit of silence and then one of the panelists gave the scientific name for some extinct flower and claimed it evolved into a different extinct flower which he also named.

To this, I thought:

a.  They are certainly not coming forth with many examples, in fact, only one.

and 

b.  He’s claiming these two extinct flowers are separate species, but I’m well aware that botanists studying living flowers don’t even necessarily agree when one particular flower species is deliniated from some other flower species.  So why would I have confidence that the panelist at UGA wasn’t simply wanting to see two separate species of  flowers when possibly they are simply variants of each other?  

It seems not at all clear cut regarding your dandelions, but whether they are one species or multiple in no way lends credulity to the idea that your weeds could ever evolve into an animal.


Michael Buratovich - #80460

May 24th 2013

Take a look at MJ Benton and PN Pearson, Speciation in the Fossil Record. Trends in Ecology and Evolution 16, no 7 (2001): 405-411.  

No one, to the best of my knowledge, argues that any animals are descended from weeds.  


glsi - #80464

May 25th 2013

Well I’m glad no one’s saying we’re descended from weeds.  But you do think we’re descended from sea sponges, right?  How is that any less preposterous?  What exactly is the genetic barrier in place inside dandelions that prevents them from taking a randomly selected and mutated turn back to the sea and then taking the animal kingdom route one day back to land?

 

I can only see the abstract of the source you suggested for examples of speciation in the fossil record.  Here’s the final 2 sentences:

 

“Marine plankton appear to show gradual speciation, with subsequent morphological differentiation of lineages taking up to 500000 years to occur. Marine invertebrates and vertebrates more commonly show punctuated patterns, with periods of rapid speciation followed by long-term stasis of species lineages.” (Benton and Pearson)

So that says to me that they’re seeing gradual fossil changes in plankton and not much else.  Which sounds like a probable case of adaptation in plankton.  Do these plankton differentiate more that the Galapagos finches?  Any plankton shown changing into anything that’s not a plankton?  I seriously doubt it.



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