THE SCIENTIFIC METHOD IS BASED UPON TESTING A FALSIFIABLE HYPOTHESIS:
This essay sets a case in favor of the scientific theory of universal common ancestry. One of the most dubious challenges to universal common descent I have reviewed is Takahiro Yonezawa and Masami Hasegawa, “Some Problems in Proving the Existence of the Universal Common Ancestor of Life on Earth,” The Scientific World Journal, 2011. While there is nothing wrong with the data and points raised in this article, it is not the objective of science to “prove” a theory. Also, the objective of identifying the universal common ancestor is not the the focus of the theory of universal common descent.
The scientific method is based upon testing a falsifiable hypothesis. In science, the researchers do not experiment to “prove” theories, they test an hypothesis in order to falsify the prediction. All we can do is continue to test gravity to determine if Einstein’s predictions were correct. We can never “prove” Einstein was right because his equations might not work everywhere in the universe, such as inside a black hole.
When an experiment fails to falsify the hypothesis, all we can conclude is that the theory is confirmed one more time. But, the theory is never ultimately proven. If it were possible to prove a theory to be ultimately true, like a law of physics, then it is not a scientific theory because a theory or hypothesis must be falsifiable.
The theory of UCD is challenged with formal research by multiple biology and biochemistry departments around the world. There is a substantial amount of scientific literature on this area of research. The fact that after all this time the proposition of UCD has not been falsified is a persuasive case supporting an argument the claim has merit. That’s all science can do.
I make this point because when we explore controversial topics far too often some individuals make erroneous objections, such as requiring empirical data to “prove” some conjecture. That is not how science works. All the scientific method can do is demonstrate a prediction is false, but science can never prove a theory to be absolutely true.
Having said that, there are scientists who nevertheless attempt to construct a complete Tree of Life. This is done in an ambitious attempt to “prove” the theory is true, even to the fanciful hopes of identifying the actual universal common ancestor. Much of the attacks on the theory of common descent are criticisms noting the incompleteness of the data. But, an incomplete tree does not falsify the theory.
This is important to understand because there is no attempt being made here to prove universal common descent (UCD). All that is going to be shown here is that the UCD as a scientific theory has not been falsified, and remains an entirely solid theory regardless as to whether UCD is actually true or not.
IS UNIVERSAL COMMON ANCESTRY FALSIFIABLE?
What would it take to prove universal common descent false?
Common ancestry would be falsified if we discovered a form of life that was not related to all other life forms. For example, finding a life form that does not have the nucleic acids (DNA and RNA) would falsify the theory. Other ways to falsify Univ. Common Descent would be:
• If someone found a unicorn, that would falsify universal common descent.
• If someone found a Precambrian rabbit would likely falsify universal common descent.
• If it could be shown mutations are not inherited by successive generations.
One common misunderstanding that people have about science is they have this idea that science somehow proves certain predictions to be correct.
All life forms fall within nested hierarchy. Of the hundreds of thousands of specimens that have been applied testing, every single one of them fall within nested hierarchy, or their evolution phylogenetic tree is still unknown and not sequenced yet.
SCIENCE PAPERS THAT SUPPORT UNIVERSAL COMMON DESCENT:
Here is just a tip of the iceberg of science papers that indicated the validity of the UCD:
• Steel, Mike; Penny, David (2010). “Origins of life: Common ancestry put to the test“. Nature 465 (7295): 168–9.
• A formal test of the theory of universal common ancestry (13 May 2010). “A formal test of the theory of universal common ancestry.” Nature 465 (7295): 219–222.
• Glansdorff, N; Xu, Y; Labedan, B (2008). “The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner.” Biology direct 3 (1): 29.
• Céline Brochier, Eric Bapteste, David Moreira and Hervé Philipp, “Eubacterial phylogeny based on translational apparatus proteins,” TRENDS in Genetics Vol.18 No.1 January 2002.
• Baldauf, S. L., Roger, A. J., Wenk-Siefert, I., and Doolittle, W. F. (2000) “A kingdom-level phylogeny of eukaryotes based on combined protein data.” Science 290: 972-7.
• Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E., and Stanhope, M. J. (2001) “Universal trees based on large combined protein sequence data sets.” Nature Genetics 28: 281-285.
The above are often cited in support of Univ. Common Descent. For anyone to suggest these papers have been overturned or outdated requires documentation.
NESTED HIERARCHIES AND BASIC PHYLOGENETICS:
A logical prediction that would be inspired by common descent is that all biological development will resemble a tree, which is called the Tree of Life. Evolution then will specifically generate unique, nested, hierarchical patterns of a branching scheme. Most existing species can be organized rather easily in a nested hierarchical classification.
Figure 1 displays the various parts of a phylogenetic tree. Nodes are where branches meet, and represent the common ancestor of all taxa beyond the node. Any life form that has reproduced has a node that will fit properly onto the phylogenetic tree. If two taxa share a closer node than either share with a third taxon, then they share a more recent ancestor.
Falsifying Common Descent:
It would be very problematic if many species were found that combined characteristics of different nested groupings. Some nonvascular plants could have seeds or flowers, like vascular plants, but they do not. Gymnosperms (e.g. conifers or pines) occasionally could be found with flowers, but they never are. Non-seed plants, like ferns, could be found with woody stems; however, only some angiosperms have woody stems.
Conceivably, some birds could have mammary glands or hair; some mammals could have feathers (they are an excellent means of insulation). Certain fish or amphibians could have differentiated or cusped teeth, but these are only characteristics of mammals.
A mix and match of characters would make it extremely difficult to objectively organize species into nested hierarchies. Unlike organisms, cars do have a mix and match of characters, and this is precisely why a nested hierarchy does not flow naturally from classification of cars.
In Figure 2, we see a sample phylogenetic tree. All a scientist has to do is find a life form that does not fit the hierarchical scheme in proper order. We can reasonably expect that yeasts will not secrete maple syrup. This model allows us the logical basis to predict that reptiles will not have mammary-like glands. Plants won’t grow eyes or other animal-like organs. Crocs won’t grow beaver-like teeth. Humans will not have gills or tails.
Reptiles will not have external skeletons. Monkeys will not have a marsupial-like pouch. Amphib legs will not grow octopus-like suction cups.Lizards will not produce apple-like seeds. Iguanas will not exhibit bird feathers, and on it goes.
The phylogenetic tree provides a basis to falsify common descent if, for example, rose bushes grow peach-like fuzz or sponges display millipede-like legs. We will not find any unicorns or “crockoducks.” There should never be found any genetic sequences in a starfish that would produce spider-like fangs. An event such as a whales developing shark-like fins would falsify common descent.
While these are all ludicrous examples in the sense that such phenomena would seemingly be impossible, the point is that any life form found with even the slightest cross-phylum, cross-family, cross-genus kind of body type would instantly falsify common descent. And, it doesn’t have to be a known physical characteristic I just listed. It could be a skeletal change in numbers of digits, ribs, or configurations. There is an infinite number of possibilities that if such a life form was unclassifiable, the theory of universal common descent would be falsified.
The falsification doesn’t have to be anything as dramatic as these examples. It could be something like when NASA thought it has discovered a new form of life when there was thought to be an arsenic-based bacteria at California’s Mono Lake. This would have been a good candidate to see if the life form had entirely changed its genetic code. Another example would be according to UCD none of the thousands of new and previously unknown insects that are constantly being discovered will have non-nucleic acid genomes.
Certainly, if UCD is invalid, there must be life forms that exist that acquire their characteristics aside from their parents, and if this is so, their DNA will expose the anomaly. It is very clear when reviewing phylogenies that there is an unmistakeable hierarchical structure indicating ancestral lineage. And all phylogenies are like this without exception. All I ask for was there to be simply one submitted that shows a life form does not have any parents, or it’s offspring did not inherit its traits. If such were the case, then there should be evidence of this.
METHODOLOGY OF FALSIFICATION:
For the methodology to determine nested hierarchies today, the math gets complicated in order to ensure that the results are accurate. In this next study, as a discipline, phylogenetics is becoming transformed by a flood of molecular data. This data allows broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.
As this discipline continues to be applied to molecular phylogenies, the prediction is continually confirmed, not falsified. All it would take is one occurrence for the mix and match issue to show a sequence out of order without a nested hierarchy and evolutionary theory would be falsified.
“ALL SCIENTIFIC THEORIES ARE SUPPOSED TO BE CHALLENGED”
Of course Charles Darwin’s hypothesis of UCD has been questioned. All scientific predictions are supposed to be challenged. There’s a name for it. It’s called an experiment. The object is to falsify the hypothesis by testing it. If the hypothesis hold ups, then it is confirmed, but never proven. The best science gives you is falsification. UCD has not been falsified, but instead is extremely reliable.
When an hypothesis is confirmed after repeated experimentation, the science community might upgrade the hypothesis to the status of a scientific theory. A scientific theory is when an hypothesis that is continuously affirmed after substantial repeated experiments has significant explanatory power to better understand phenomena.
Here’s another paper in support of UCD, Schenk, MF; Szendro, IG; Krug, J; de Visser, JA (Jun 2012). “Quantifying the adaptive potential of an antibiotic resistance enzyme.” Many human diseases are not static phenomena, but are constantly evolving, such as viruses, bacteria, fungi and cancers. These pathogens evolve to be resistant to host immune defences, as well as pharmaceutical drugs. (A similar problem occurs in agriculture with pesticides).
This Schenk 2012 paper analyzes whether pathogens are evolving faster than available antibiotics, and attempts to make better predictions of the evolvability of human pathogens in order to devise strategy to slow or circumvent the destructive morphology at the molecular level. Success in this field of study is expected to save lives.
Antibiotics are an example of the necessity to apply phylogenetics in order to implement medical treatments and manufacture pharmaceutical products. Another application is demonstrating irreducible complexity. That is established by studying homologies of different phylogenies to determine whether two systems share a common ancestor. If one has no evolutionary pathway to a common ancestor, then it might be a case for irreducible complexity.
Another application is forensic science. DNA is used to solve crimes. One case involved a murder suspect being found guilty because he parked his truck under a tree. A witness saw the truck at the time of the crime took place. The suspect was linked to the crime scene because DNA from seeds that fell out of that tree into the bed of the truck positively identified the tree from no other tree in the world.
DNA allows us to positively determine ancestors, and the margin for error is infinitesimally small.
TWIN NESTED HIERARCHY:
The term “nested” refers to the confirmation of the specimen being examined as properly placed in hierarchy on both sides of reproduction, that is both in relation to its ancestors and progeny. The term “twin” refers to the fact that nested hierarchy can be determined by both (1) genotype (molecular and genome sequencing analysis) and (2) phenotype (visual morphological variations).
We can ask these four questions:
1. Does the specimen fit in a phenotype hierarchy on the ancestral side? Yes or no?
2. Does the specimen fit in a phenotype hierarchy relative to its offspring? Yes or no?
If both answers to 1 and 2 are yes, then nested hierarchy re phenotype is established.
3. Does the specimen fit in a genotype hierarchy on the ancestral side? Yes or no?
4. Does the specimen fit in a genotype hierarchy relative to its offspring? Yes or no?
If both answers to 3 and 4 are yes, then nested hierarchy re genotype is established.
All four (4) answers should always be yes every time without exception. But, the key is genotype (molecular) because the DNA doesn’t lie. We cannot be certain from visual morphological phenotype traits. But, once we sequence the genome, there is no uncertainty remaining.
CLADES AND TAXA:
A clade is essentially the line that begins at the trunk of the analogous tree, for common descent that would be the Tree of Life, and works it’s way from branches, limbs, to stems, and then a leaf or the extremity (representing a species) of the branching system. A taxon is a category or group. The trunk would be a taxon. The lower branches are a taxon. The higher limbs are a different taxon. It’s a rough analogy, but that’s the gist of it.
THE METHODOLOGY USED TO FALSIFY COMMON DESCENT IS BASED UPON NESTED HIERARCHY:
Remember that nucleic acids (DNA) are the same for all life forms, so that alone is a case for the fact that common descent goes all the way back to a single cell.
Mere similarity between organisms is not enough to support UCD. A nested classification pattern produced by a branching evolutionary tree process is much more specific than simple similarity. A friend of mine recently showed me her challenge against UCD using a picture of the phylogeny of sports equipment:
For example, it is impossible to objectively classify in nested hierarchies the elements in the Periodic Table, planets in our Solar System, books in a library, cars, boats, furniture, buildings, or any inanimate object. Non-life forms do not reproduce, and therefore do not pass forward inherited traits from ancestors.
The point in using the balls used in popular sports attempts to argue that it is trivial to classify anything subjectively in a hierarchical manner. The illustration of the sports balls showed that classification is entirely subjective. But, this is not true with biological heredity. We KNOW from DNA whether or not a life form is the parent of another life form!
With inanimate objects, like cars, they could be classified hierarchically, but it would be subjective, not objective classification. Perhaps the cars would be organized by color, and then by manufacturer. Or, another way would be to classify them by year of make or size, and then color. So, non-living items cannot be classified using a hierarchy because the system is entirely subjective. But, life forms and languages are different.
In contrast to being subjective like cars, human languages do have common ancestors and are derived by descent with modification. Nobody would reasonably argue that Spanish should be categorized with German instead of with Portuguese. Like life forms, languages fall into objective nested hierarchies. Because of these facts, a cladistic analysis of sports equipment will not produce a unique, consistent, well-supported tree that displays nested hierarchies.
Carl Linnaeus, the famous Swedish botanist, physician, and zoologist, is known for being the man who laid the foundations for the modern biological naming scheme of binomial nomenclature. When Linnaeus invented the classification system for biology, he discovered the objective hierarchical classification of living organisms. He is often called the father of taxonomy. Linnaeus also tried to classify rocks and minerals hierarchically, but his efforts failed because the nested hierarchy of non-biological items was entirely subjective.
“DNA doesn’t lie.”
Hierarchical classifications for inanimate objects don’t work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors. It is this inheritance of traits that provides an objective way to classify life forms, and it is nearly impossible for the results to be corrupted by humans because DNA doesn’t lie.
Caveat: Testing nested hierarchy for life forms works, and it confirms common descent. There is a ton of scientific literature on this topic, and it all supports common descent and Darwin’s predictions. Again, there is no such thing as a design-inspired prediction for why life forms all conform to nested hierarchy. There is only one reason why they do: Universal Common Ancestry.
The point with languages is that they can be classified objectively to fall within nested hierarchies because they are inherited and passed on by descent with modification. No one is claiming that languages have a universal common ancestor, even if it they do, because its beside the point.
In this paper, Kiyotaka Takishita et al (2011), “Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen,” published in Biology Direct, the phylogenies of unicellular eukaryotes are examined to ascertain how they acquire sterols from bacteria in low oxygen environments. In order to answer the question, the researchers had to construct a detailed cladogram for their analysis. My point here is that DNA doesn’t lie. All life forms fall within a nested hierarchy, and there is no paper that exists in scientific literature that found a life form that does not conform to a nested hierarchy.
The prediction in this instance is that if evolution (as first observed by Charles Darwin) occurs, then all life might have descended from a common ancestor. This is not only a hypothesis, but is the basis for the Scientific Theory of Universal Common Descent (UCD).
There is only one way I know of to falsify the theory of UCD, and that is to produce a life form that does not conform to nested hierarchy. All it takes is one.
DOES A COMB JELLY FALSIFY COMMON DESCENT?
One person I recently spoke to regarding this issue suggested that a comb jelly appears to defy common descent. He presented me this paper published in Nature in support of his view. The paper is entitled, “The ctenophore genome and the evolutionary origins of neural systems” (Leonid L. Moroz, et al, 2014). Comb jellies might appear to be misclassified and not conform to a hierarchy, but phylogenetically they fit just fine.
There does seem to be an illusion going back to the early Cambrian period that the phenotype of life forms do not fall within a nested hierarchy. But, their genotypes still do. The fact that extremely different body types emerge in the Cambrian might visually suggest they do not conform to a nested hierarchy, the molecular analysis tells a much different story and confirms that they do.
To oppose my position, all that is necessary is for someone to produce one solitary paper published in a science journal that shows the claim for UCD to be false. Once a molecular analysis and the phylogenies are charted on a cladogram, all life forms, I repeat all life forms conform to nested hierarchies, and there is not one single exception. If there is, I am not aware of the paper.
In regarding the comb jelly discussed in Moroz (2014), if someone desires to submit the comb jelly does not fit within a nested hierarchy, there is no content in this paper that supports this view.
For example, From Figure 3 in the article,
“Predicted scope of gene loss (blue numbers; for example, −4,952 in Placozoa) from the common metazoan ancestor. Red and green numbers indicate genes shared between bilaterians and ctenophores (7,771), as well as between ctenophores and other eukaryotic lineages sister to animals, respectively. Text on tree indicates emergence of complex animal traits and gene families.”
The authors concluded common ancestry and ascribe their surprise regarding the comb jelly to convergence, which has nothing to do with common ancestry.
The article refers to and assumes common metazoan ancestry. The common ancestry of the comb jelly is never once questioned in the paper. The article only ascribes the new so-called genetic blueprint to convergence. The paper both refers to and assumes common ancestry several times, and even draws up a cladogram for our convenience to more readily understand it’s phylogeny, which is based upon common descent.
The paper repeatedly affirms the common ancestry of the comb jelly, and only promotes a case for convergent evolution. It is an excellent study of phylogeny of the comb jelly. There is nothing about the comb jelly that defies nested hierarchy. If there was, common descent would be falsified.
Universal Common Descent (UCD) is a scientific theory that all life forms descended from a single common ancestor. The theory is falsified by demonstrating the node (Figure 1) of any life form upon examination of its phylogeny does not fit within an objective nested hierarchy based upon inheritance of traits from one generation to the next via successive modifications. If someone desires to falsify UCD all they need to do is just present the paper that identifies such a life form. Of course, if such a paper existed the author would be famous.
Any other evidence regardless of how much merit it might have to indicate serious issues with UCD does nothing to falsify UCD. If this claim is challenged, please (a) explain to me why, and (b) show me the scientific literature that confirms the assertion.
OTHER CHALLENGES TO THE ISSUES AND PROBLEMS WITH UCD DO NOT FALSIFY DARWIN’S PREDICTION AS A SCIENTIFIC THEORY:
One paper that is often cited to W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science 25 June 1999. This is Doolittle (1999). I already cited Baldauf, S. L., Roger, A. J., Wenk-Siefert, I., and Doolittle, W. F. (2000) above. Doolittle is very optimistic about Common Descent, and does nothing to discourage its falsification. In fact, the whole point of Doolittle’s work is to improve on the methodology so that future experimentation increases the reliability of the results.
In figure 3 of the paper, Doolittle presents a drawing as to what the problems are during the early stages of the emergence of life:
In Doolittle 1999, there are arguments fully discussed as to what the problems are regarding lateral gene transfer (LGT), and how it distorts the earlier history of life. But, once solving for the LGT, the rest of the tree branches off as would be expected.
Thanks to lateral gene transfer, taxonomists have identified 25 genetic codes all of which have their own operating systems, so to speak, for the major phyla and higher taxa classifications of life. They’re also called mitochondrial codes, and are non-standard to other clades in the phylogenetic tree of life.
The question is, do any of these 25 non-standard codes weaken the claim for a common ancestor for all life on earth? The answer would be no because the existence of non-standard codes offers no support for a ‘multiple origins’ view of life on earth.
Lineages that exhibit these 25 “variants” as they are also often called are clearly and unambiguously related to organisms that use the original universal code that reverts back to the hypothetical LUCA. The 25 variant branches of life are distributed as small ‘twigs’ super early at the very dawn of life within the evolutionary tree of life. There is a diagram of this in my essay. I will provide it below for your convenience.
Anyone is welcome to disagree, but to do so requires the inference that, for example, certain groups of ciliates evolved entirely separately from the rest of life, including other types of ciliates. The hypothesis that the 25 mitochondrial codes are originally unique and independent to a LUCA is simply hypothetical, and there is no paper I am aware of that supports this conjecture. There are common descent denying creationists who argue this is so, but the claim is untenable and absent in the scientific literature.
Although correct, the criticism that the data breaks down the tree does nothing to falsify universal common descent. In order to falsify UCD one must show that a life form exists that does not conform to a nested hierarchy.
The fact that there are gaps in the tree, or that the tree is incomplete, or that there is missing phylogenetic information, or that there are other methodological problems that must be solved does not change the fact that the theory remains falsifiable. And, I already submitted the simple criteria for falsification, and it has nothing to do with seeing how complete one can construct the Tree of Life.
The abstract provides an optimistic summary of the findings in Doolittle 1999:
“Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.”
There many challenges to universal common descent, but to date there is no life form that has been found that defies conforming to nested hierarchy. Some of challenges to common descent relate to early when life emerged, such as this 2006 paper published in Genome Biology, authored by Tal Dagan and William Martin, entitled, “The Tree of One Percent.”
Similar problems are addressed in Doolittle 2006, The paper reads,
“However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true”
That paper does discuss hierarchy at length, but there’s nothing in it that indicates its findings falsify common descent. The article essentially makes the same points I made above when I explained the difference between an subjective nested hierarchy and an objective nested hierarchy in reference to the hierarchy of sports equipment. This paper actually supports common descent.
As a scientific theory, UCD is tested because that is what we’re supposed to do in science. We’re supposed to test theories. Of course UCD is going to be tested. Of course UCD is going to be challenged. Of course UCD is going to have some serious issues that are researched, analyzed, and discussed in the scientific literature. But, that doesn’t mean that UCD was falsified.
This information should not alarm anyone who favors the scientific theory of intelligent design (ID). ID scientists like Michael Behe accept common descent. I have no problem with it, and it really doesn’t have much bearing on ID one way or the other. Since the paleontologists, taxonomists, and molecular biologists who specialize in studying phylogenies accept univ. common descent as being confirmed, and not falsified, I have very little difficulty concurring. That doesn’t mean I am not aware of some of the weaknesses with the conjecture of common descent.