Archive for the ‘Conventional Theory’ Category

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An Educated Guess: 6 Strong Evidences for Evolution

May 16, 2007

I have been accused of being a creationist. That’s sort of like being accused of being a communist sympathizer or, (Bush-forbid), a terrorist. I’m really interested at looking at the full scope of evidence instead of putting blinders on and towing the party line. I have not spent any time covering conventional theories so far, because honestly these articles take a long time to write, and I don’t want to be simply repeating something that is widely known. I have spent two days writing this article. It’s a tip of the hat to conventional theory that has gotten us to where we are today. I think it is important to properly understand conventional theory before we propose alternatives. That is largely the purpose of education.

Evidence of Evolution
I often hear assertions such as “there is no proof of evolution” or “I don’t understand how scientists can believe in evolution”. To assert that a certain theory, especially a widely held theory, has absolutely no evidence is blatantly untrue. There are thousands, if not millions of scientists across the world who know that evolution is true and apply it to their respective scientific fields on a daily basis. In fact, evolution has been called the very foundation of scientific understanding. “Evolution is the cornerstone of modern biology” (TalkOrigins). Evolution extends beyond biology into other areas of science, including atmospherics, geology, astronomy, and even quantum physics. Today evolution has become a cultural icon as well, being incorporated into brand names or parodied in product ads. Evolution is the symbol of progress and modern scientific understanding. For this reason, I am going to summarize some of the strongest evidences for evolution that I have found as I have done my research.

Note: This is only a list of strong evidences. Most theories have numerous weak evidences that may be stretching or considered circumstantial. Many of these “evidences” actual weaken a theory if they are toppled. So here I will only cover the strongest evidences for evolution that I know of.

6 Reasons

marrus_orthocanna.jpg1) Common chemical basis for all life. Today it is generally taken for granted that all life uses the same chemical basis, but I would like you to stop for a second and truly appreciate that fact. All life on this planet uses DNA to code for amino acids. All life uses the exact same coding scheme to transcribe the same amino acids in the same way. All life forms use the same basic cellular structure: cell membrane containing the cell’s unique chemical environment, same basic organelles in varying degrees, and the presence of organized DNA. That means that your body runs on the same chemical process that keeps celery alive. This is not what I would call intuitively obvious, but it is what enables us to derive nutrition by eating plants and animals. We are literally subsuming the common amino acids and chemicals that they have pull from the environment. That’s right, we also have the same chemicals in use that exist in the dirt.

This is important to note when we consider all the other possibilities. There is plenty of discussion on what alien life might be like. We are carbon-based, but maybe you could have silicon based life, etc. There are also plenty of more mundane possibilities. Namely it would be just as easy to use a different amino acid encoding scheme for each type of life. The encoding in the DNA only needs to match the free codons attached to various amino acids floating in the cytoplasm. DNA can also exist in left-handed and right-handed varieties that would be unable to mix with each other but all DNA in all living creatures is the same orientation. This very trait of life is what makes genetic engineering possible. Jellyfish DNA is compatible with mouse DNA, which is compatible with humans. This most directly points to a common origin and common ancestor.

Retraction (Oct 31): At the time of writing I thought the “universal genetic code” was truly universal. Now I’ve found out that that is not the case. NCBI lists 16 different “alternative” genetic codes. Meaning that a certain codon codes for a different amino acid in that species. Multiple species have several codons that do not code for the same thing.  Including our very own Human Mitochondria, which contains six different codons! That means that genes from these species are NOT compatible. According to conventional theory, most of mitochondrial DNA migrated to the nucleus.  So how does that work?

The problem with changing the codon coding is that it represents a holistic change that affects the entire organism. It would alter the amino acid sequence of every single gene that the organism needs to survive. What’s harder to explain is that often times the stop codon is changed. That not only has the potential of changing an amino acid, it would randomly alter the length of every single gene. Most of the species studied so far are single cellular bacteria, but the list also includes highly complex multi-cellular invertebrates. Intuitively, this kind of drastic alteration would turn even a single celled organism into pureed protein soup. Most of the papers I have found focus on rationalizing how this could have happened. While explanations of how this could have happened can certainly be imagined, I think this no longer fits the criteria of “strong evidence”.

2) Morphological homologies in all forms of life: It was actually my mother who first pointed out that, while the historicity of exact lineages can be questioned, the usefulness of evolution in taxonomy cannot be questioned. Beyond a molecular basis, there is also a very obvious categorical hierarchy of “body plans” that animals seem to follow. These similarities have given rise to the modern taxonomic system. For example, almost all insects have six legs and two sets of wings. In beetles, one set of wings forms a hardened shell that protects the other wings. This is a good example of adaptation of one structure for another purpose. All vertebrate animals share the same four limb body plan (plus or minus a tail). That includes reptiles, amphibians, and mammals like bears and humans. This body plan extends to creatures that don’t look like they would need common features (hips in whales), as well as animals you would expect to have extra features. Giraffes have the same number of vertebrae as you and me. This commonality lends itself naturally to a common ancestry and a branching evolution of life on this planet. Why reinvent the wheel? Why reinvent the backbone? If it works, don’t fix it.

Chimp evolution into a Caucasian

3) Fossil Evidence of Early Man: I have grown up accustomed to scenes of archaeologists squabbling over tiny fragments of fossils they think might be a missing link. So I was a bit surprised to find that, while parts of the fossil record get pretty sketchy, there are a couple categories where there is tons of evidence. There are over 200 fossils which have been identified as Homo Erectus and around 300 fossils of Neanderthals. These fossils have been found with evidence of controlled fire as well as stone tools. This is more than the picking over a spare tooth or an unmatched skull fragment. There is good evidence that humans have undergone morphological changes in the past. Check out this video that does a pretty good job covering morphological similarities and fossils.

4) Evidence of Microevolution all around us: Examples of microevolution, or adaptation, are occurring in nature all the time. I feel I’d simply be repeating others to talk about the Peppered Moth, Mussels, bacterial resistance, new strains of influenza, etc. There a plenty of examples of the spread of a beneficial trait through a population. Feel free to dig up your own. I have a deep respect for the author of Things Creationists Hate, who has already stated this kind of day to day observation far more eloquently than I can:

“If anything, I have more daily-life experience to show me evolution happening than I have for those other things [gravity, bacteria, electrons]. I can see that offspring aren’t identical to their parents. I have seen new varieties of plants and animals developed within my own lifetime. I live in an area where boll weevils often win the evolutionary race to develop resistance to pesticides. I can easily catch a case of (newly evolved) resistant staphylococcus, which might very well kill me. I have seen and touched and personally found the fossils of the now-extinct ancestors of living creatures.”

dna.jpg5) Conservation Patterns in DNA: I think this is probably the strongest evidence for evolution I have ever seen and interestingly most people aren’t familiar with it because it is a bit technical. Through the use of gene sequencing we now have the opportunity to make direct comparison between DNA sequences of different species. There are many similarities in genes and pseudo-genes that would indicate a common ancestor. When a DNA sequence is the same in two animals it is described as being conserved and when it is different it is unconserved from the common ancestor. The pattern that we see in DNA conservation is exactly what you would expect from an evolution.

The parts of DNA that code for proteins, and hence the positions subject to natural selection are also the most conserved nucleotide positions. While regulatory regions vary more, and junk DNA is the least conserved. Junk DNA appears to be drifting randomly under no selection pressure. This variation matches taxonomic distance and has actually been used to judge how closely related species are. To top it off, inside protein coding sequences the third nucleotide position which can code for the same amino acid is less conserved than its neighbors. That’s quite a pattern. It appears that, despite the problems faced by natural selection, it is actually selecting for millions of nucleotide positions at the same time in spite of a high mutation rate.

Retraction: Well, we all do our best but we can only speak from what we know at the time. There is a major research initiative called ENCODE, on the same scale as the Human Genome Project, that released its results this summer. The ENCODE project upended many previously held notions that supported a classic view of Neo-Darwinian evolution, including conservation of functional elements across species. Here’s the summary from the ENCODE Press Release:

Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint – that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists.

According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction. As this pool turns over during evolutionary time, researchers speculate it may serve as a “warehouse for natural selection” by acting as a source of functional elements unique to each species and of elements that perform the similar functions among species despite having sequences that appear dissimilar.

The explanation given is that functional regions of DNA can somehow mutate freely and still maintain their same functionality over long stretches of time. As a computer programmer I have a hard time swallowing this explanation. While you can say the same thing multiple ways, there a big gaps between one functional design and the next that should hurt the organism, and thus create selection pressure.  Until this theory is really tested with the same rigor that uncovered the problem, I think I need to take “Conservation Patterns” (or lack thereof) off the Strong Evidences list.

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6) Evolution is commonly accepted in academic circles: More than anything else, this is the evidence that speaks loudly of the validity of evolution to the common person. We have thousands of trained scientists in specialized fields that all agree on the fact of evolution. Consider for a moment, the alternative or null hypothesis. If that many scientists can be wrong about something, it would call into question how one could even say that they were wrong. We have a highly structured education and peer-review process that is specifically designed to keep scientists honest. The only other regulatory systems like that I can think of are governmental checks and balances, and the banking system. Of course, if you can’t even trust scientists you could always try to get into the field yourself. I can almost guarantee you that if you went into a PhD educational process with the same philosophy, that after years of education, you would no doubt come to the same conclusions that they did.

(More references may be forthcoming. Here’s a funny moment I had while researching for this article. Gotta love text substitution.)