The Demise of Evolution Objections: shared DNA changes between species

“Yes, evolution by descent from a common ancestor is clearly true. If there was any lingering doubt about the evidence from the fossil record, the study of DNA provides the strongest possible proof of our relatedness to all other living things”

~ Francis Collins, MD, PhD. 4/6/2007, CNN

"The new DNA evidence has a very important role beyond illuminating the process of evolution. It could be decisive in the ongoing struggle over the teaching of evolution in schools and the acceptance of evolution in society at large. It is beyond ironic to ask juries to rely on human genetic variation and DNA evidence in determining the life and liberty of suspects, but to neglect or to undermine the teaching of the basic principles upon which such evidence, and all of biology, is founded."

~ Sean B Carroll, PhD. "The Making Of The Fittest: DNA And

The Ultimate Forensic Record of Evolution".

Introduction

What if I told you that there have been some DNA discoveries that will end any further rational objections to evolution from evolution deniers or doubters? What if this DNA evidence is so sound and robust that it is just what people have wanted who have difficulty accepting evolution? That it involves human evolution and bypasses discussions and moves us to "macroevolution" since it involves humans and the other great apes?

What if I told you that when I have presented this to people they have in general failed to understand it because most get lost in the terminology and miss a very simple common theme that underlies all the major categories that address these DNA findings and observations? Once understood, evolution critics have been unable to discount this evidence supporting evolution. Objections are dismissed when examined closely.

Before the DNA findings are introduced by including links below to the blogs, I want to hammer home the central simple concept of all the DNA findings discussed. I will assume that people understand that evolution occurs in populations and not individuals and is change over time (what is evolution?). How this happens is through various mechanisms like natural selection, endosymbiosis, horizontal gene transfer and others and the how is not vital for knowing that evolution did happen due to fantastic DNA findings (see why "what" is first and "how" is often optional). What will be presented is DNA evidence that rises to the level of proof for "macroevolution", which in most cases is a forensic science and of course is accepted in courts of law to be definitive. DNA paternity testing for example. Yes, "proof" technically is reserved for areas of mathematics and philosophy but in science sometimes the evidence is so overwhelming and sound that to deny a conclusion is perverse. Though technically science deals only in provisional conclusions, some scientific theories like Gravity and Evolution are so well supported and tested with predictions that they can be revised but will never be overturned.

Origins: common design vs. common ancestry

You are a detective at a crime scene involving a shooting and there is a bullet recovered. If you want to connect it to another crime involving a shooting and think it's from someone using the same rifle you can compare the bullets side by side from different crime scenes. A rifle will scratch them exiting the rifle and if the scratches match you KNOW the origin is the same rifle. Forensic ballistics science tried and true. This one rifle thus must be a common source for the bullets found at different sites. Intel purposely puts error code in its chips (personal communication, B.D). If someone steals its design and claims it's just due to similar design restraints and functions they will loose in court to Intel because no one would find and use the same random errors. The competitor chip maker must have copied Intel's. They have a common origin - at Intel.

Textbook publishers purposely put errors in for the same reason Intel purposely puts error code in its chips. And in the case of textbooks there is case law that plagiarism took place and the competitor was found guilty. The identical wording in the two textbooks were not developed independently due to similar research and writing but rather due to plagiarism. If independent origins were true they would not contain the same errors. They both share the same origin because they both have the same errors. The copy is not original.

How good is DNA evidence?

Fantastically good! Paternity testing is nearly 100% accurate. It basically settles cases. We did not need to observe the conception. What about forensics? Same here also. DNA evidence is so important in the courts that they rely on it extensively if available. Even if a crime was not witnessed or recorded, if in context a person's DNA places them at the scene and they claim that they never met the person and was never there, they are usually in deep trouble in the investigation. DNA testing can tell us the genealogy of Egyptian mummies (were you there? - didn't need to be), the identity of crime victims, and of course DNA testing was definitive in solving the Russian Romanov Czar family death controversy. Many crime victims have been found guilty involving erroneous eyewitness testimony and are now having their sentences reversed based on DNA evidence. Chapters of the Innocence Project are widespread in the USA working to get innocent people out of prison.

It is disingenuous for evolution deniers to accept the DNA methods and evidence important for solving crimes and for accurate truth searching while rejecting the same source of evidence for species origins just because it disproves and exposes their presuppositions.

The Concept

When the genomes of different species have been sequenced we can compare the letters that make up the DNA - the ATCG sequences - often billions of letters long. It turns out that most genomes are very active and have been changed often in the past. They end up having parts duplicated, some sections deleted, and some sections spliced out and then inverted when put back in. Breaks are frequent and quickly repaired. Viral parasitic infections in our ancestors repeatedly have inserted their viral DNA into ours (how often are you ill with "viruses" per year, although most of those don't insert into your DNA?). Some genes get mutated and no longer work and are called pseudogenes. These changes are by far random.

If we find the same random marks or changes to DNA that are SHARED between species we know that these random changes MUST have occurred before the species split. The odds of having the same random changes occur at thousands of the same homologous locations between species with the same DNA fingerprint

base changes independently is mathematically impossible.

There is no other rational explanation. Just like the same marks on two bullets means they came from the same rifle and must point to a common origin (rifle), the shared DNA changes must prove a common origin (ancestor) for our analysis. That's the basic observation and conclusion that must be reached. Notice this line of evidence is independent of how similar the bases are, how much DNA the species have in common, how complicated DNA is, where the DNA originally came from, or how the first cell evolved, etc. The DNA from two species or more are just compared for shared random DNA changes. These changes are not original to the DNA. We know this especially because this is how cancer develops starting with one random mutation (two people with the same leukemia type for example have different random mutations) after another producing a nested Russian doll type pattern we can follow backwards to tell accurately the history of the cancer. Two Christians cancer researchers are strong supporters of common ancestry because of their cancer work (Finlay and Swamidass; and of course Collins although his research was not directly in cancer).

Structure of the DNA blog entries

1. Discussion and unpacking of the issue

2. A few examples of the hundreds possible

3. Most often how these shared changes nest in evolutionary phylogenetic trees adding another level of proof of common ancestry and evolution

4. Most blogs also have a section on common evolution objections and why they fail and can be dismissed. This often makes the blog longer than it may need be if someone is just interested in how the DNA findings rise to the level of proof of macroevolution. But many reading this will be interested in finding answers to family or friends who are challenging evolution. I really have nearly all objections discussed and dismissed. Really! The advantage of reviewing objections and why they fail is because this will often produce a great window into how purposeful omissions and motivated reasoning reveals their presuppositional beliefs. Scientists in the hundreds of thousands in multiple independent scientific and medical fields accept and work successfully with evolution daily.

5. Multiple links or other embedded teaching items are important to understand the concepts and are included to help with the concepts and details. I have tried to keep them to a minimum. Links can also point the reader to original sources to fact check the blog. And of course those arguing against the DNA discoveries for evolution may wish to spend extra time on the information I provide.

We are in another Galileo Moment for anti-evolutionists when it comes to these amazing DNA discoveries supporting evolution. The blogs are best viewed on a computer and not on a cell phone.

Here they are; the major DNA findings that rise to proof of evolution

The easiest one to read is probably #1 DNA repairs. The most in depth because of the need to address many objections by evolution deniers is #4, ERVs. The blogs will also discuss how we know what we assert for evolution evidence is true.

1. Shared DNA breaks and repairs. DNA breaks frequently in random locations. The repair system grabs whatever DNA is nearby to patch them. This results in random breaks and unique patches/repairs producing a type of one-of-a-kind DNA "scar" by location and uniqueness. If you find hundreds of these exact same numerous scars between two species it must be common ancestry. In addition, comparing the "scar repairs" across many species that are closely related allows us to use DNA to confirm what the paleontologists have asserted. These patterns produce evolutionary trees adding yet another level of proof of evolution. Only a few of hundreds of examples detailed in Finlay's book are presented. 2. Shared segmental duplications. Whole chunks of chromosomes/DNA are often duplicated. This happens in plants where they have even duplicated their entire genomes. If we find these same random duplications of the DNA in the same homologous locations between two or more species we know it had to have happened before the species split. In addition, comparing these same shared duplicated DNA segments and genes across many species that are closely related allows us to use DNA to confirm and test what paleontologists have asserted. These patterns produce evolutionary trees adding yet another level of proof of evolution.

3. Pseudogenes and shared pseudogenes. Our genome contains thousands of disabled genes, knocked out by mutations. They are molecular fossils. When we find thousands of disabled genes that are shared between species and often have the identical mutations it is only rationally explained by the gene being mutated before the species split. In addition, comparing these same shared dead genes across many species often with the same disabling mutations that are closely related allow us to use DNA to confirm what paleontologists have asserted. These patterns produce evolutionary trees adding yet another level of proof of evolution.

4. Shared ERVs between species. This is probably the most in-depth discussion, primarily because so much has been written by evolution deniers to try and dismiss it. Therefore there is more discussion supplied to show why these objections are negated. Basically, there is a group of viruses that insert their DNA into host DNA and use the host machinery to make new parasitic viruses. The most recognizable example is HIV, the cause of AIDS if not treated. We know this retrovirus well and all retroviruses have the same gene types, life cycle, and footprint. They insert randomly to locus. After a retrovirus collects mutations it becomes unable to reproduce and is called an endogenous retrovirus (ERV) because it's inert and fixed in the host population. Most of the ERVs are so degraded only a part is left, called an LTR. These LTRs are still functional however and the host uses them to promote replication of it's own DNA products. Sort of like using old wood from a barn to decorate in a new home. We find many ERVs in the same locations between closely related species and many even have the same mutations that disabled them. Between chimps and humans alone there are 200,000 shared ERVs. They originally came from parasitic retroviruses; we know this for many reasons discussed in the blog. The only rational explanation since they insert randomly and are found in the same locations between species is they had to have inserted before the species split and thus shared a common ancestor between the species. In addition, comparing these same shared ERVs across many species at the same locations that are related allows us to use DNA to confirm what the paleontologists have asserted through fossil evidence. These patterns produce evolutionary trees adding yet another level of proof of evolution.

5. Shared transposable elements between species. Our genome and those of many other species contain thousands of genes that are mobile. These are called transposons or jumping genes. One type, the retrotransposon Alu element is only found in primates. TEs have jumped around genomes for millions of years and insert randomly into genomes. Thus, we can compare genomes from different species and if we find hundreds of the same TEs that match not only in location but also in length and mutations we can be certain that they must have inserted into a common ancestor before the species split. There is no other rational conclusion. In addition, like other DNA findings that rise to the level of evolutionary proof, these also can be nested into phylogenetic evolutionary trees confirming common ancestry, often going into the deep past.

Other DNA findings for evolution

These are not as strong evolution evidence because they technically can still be accommodated by anti-evolutionists, although they are better explained by evolution.

1. Human Chromosome 2 Fusion. Humans have 46 chromosomes (DNA condensed into small packets like luggage so they can be moved around easily when the cell divides). The other great apes have 48. Since we evolved from shared ancestors with them where did the "extra" DNA go? It wasn't lost, it just got repackaged. Turns out we shared an ancestor with chimps about 6 - 7 million years ago and after breaking off from them what were ancestral chromosomes 12 and 13 got stuck end to end to form our longer #2 chromosome. This is called a Robertsonian Translocation and is not uncommon. Even now 1:1,000 people have 45 instead of 46 chromosomes because of fusions of other chromosomes. All the DNA is there; the only problem is when they want to have children. The 45 and 46 chromosomes can't line up properly. We have fantastic evidence that this fusion happened and it's not the first time in our history that there were chromosomal fissions and fusions. One could still argue that a Great Designer after making chimps, gorillas and orangutans created humans that way for some reason. Possible, but that does not fit well with all the other DNA findings. It's definitely a fusion.

2. Junk DNA. This is controversial even with evolutionary biologists and molecular biochemists. Although a minority position currently, the evidence that most of our genome is junk DNA is so strong that it can't be ignored. To many scientists and especially creationists there is predicted to be little or no junk DNA. But we find 50% - 90% is junk, consistent with millions of years of evolution involving mutations that knock out genes, parasitic viral infections and DNA that jumps around and makes copies of itself (ALUs for example). Also important will be to address and understand why an influential study called ENCODE has conclusions that are wrong or misleading.

Conclusion

This blog introduces the reader to the major categories of comparative DNA findings between closely related species showing shared changes that rises to the level of proof of evolution, "macroevolution." Several examples are discussed as analogies for how common origins can be determined and common design ruled out. This is how the DNA findings can be viewed also. They are shared random changes to the DNA of species, and different types are discussed including shared ERVs, pseudogenes, segmental duplications, and DNA emergency repairs with unique patches. In all cases the DNA marks are random. Since we find thousands shared DNA marks between certain species the only rational explanation is that these random shared changes must have occurred in a common ancestor before the species split. Equally important, the various shared DNA changes can be nested in hundreds of evolutionary phylogenetic trees confirming paleontology. If evolution were not true, this could not be constructed. In addition to discussing the major categories of DNA evidence for evolution, much discussion in most of the blogs involves addressing potential objections and why they are disproven. This also can be very revealing to establish motivated reasoning and omission of important facts possibly by intent that would falsify the objections.