Hi Sam!

I believe my [family member] wanted me to talk you you about evolution. I shared an articles on Facebook a few days ago that I thought wrote irresponsibly on the subject. The website has since taken the article down so I'm not able to share it. Essentially though, the article was confused over the point of phyletic evolution vs. speciation. That is, evolution through radiation versus evolution along a lineage (i.e. across the entire species-- no splitting). This confusion led the writer to mistakenly assume that the finding that neanderthals were sister species to early humans, as opposed to being one of the earlier phyletic stages in human evolution, meant that neanderthals were unrelated to humans.

I guess in a broader sense though there are a lot of misconceptions about evolution. As someone who has been working in a lab studying evolution for the last three years, I want to try and dispel some of these misconceptions using even the cursory knowledge that I have of the subject, because I think understanding science is important. Further, understanding that science isn't a belief system that one can reject or accept is important, especially in an age where a scientific consensus on something like the existence of human-caused climate change is largely ignored as a real issue by politicians on both the left and the right. And I think a lot of this flippant treatment of science comes from people treating issues that are essentially resolved (i.e. the existence of evolution) as if they are still issues because pundits who disagree with the findings (largely because they contradict with religious sentiments) are louder than scientists and can rebrand these ideas as if they were still issues. And so then people feel like they can sort of pick and choose the science they want to believe because the scientists don't know what they're talking about, and anyone with a few minutes to spare watching videos from the guy that made the Creation Museum can be more knowledgable than a group of people that have spent decades studying a theory. In my view, that's a big problem.

This is not to say that there is no room for debate in science. Science is a constant debate and you'd be hard pressed to find scientists even from the same field that agree on all the specifics of a theory or an idea. And that's great! That's what makes science so exciting, and what, largely (hopefully), keeps it from being too politicized. But the points these scientists are arguing about aren't things like the existence of evolution or whether the earth is 8000 years old. Yet those still seem to be debates in the public, and I think that's sort of unfortunate for the future of our nation as an informed public on the cutting edge of scientific research.

That being said, I think some of the louder secular voices really don't help this by belittling people who disagree with them! I love talking about science with people-- for example I enjoy talking to my [family member], who is wary to accept some things that to me seem obvious. And I think healthy discussion of these things is the best way to learn about them.

My [family member] clearly respects the amount of time you have put into building your view on subjects like evolution. So I would like to know what you think about that subject! My views are pretty simple-- evolution is a well-supported biological phenomenon that has given rise to all the current diversity on earth from one or a few original forms of life. As far as where that original life came from, there are a number of hypotheses people have. Most biologists assume that some special combination of molecules and energy led to a very basic life form. Others hypothesize that some more advanced civilazation "seeded" life on earth, though this is not an actual origin-of-life theory because it just pushes the time scale further back. Another idea is that those more advanced civilizations were, in our understanding, supernatural. Now, science can't answer supernatural questions but you'd be hard-pressed to find a scientist that could empirically reject that a god or God or gods created life. That's not a question that science has or is ever able to address. And as of yet there's really not strong evidence for how life formed. But if you reject the supernatural hypotheses, you're pretty much left with molecules randomly falling into a configuration for life at some point.

Evolution after this original formation of life, however, does have strong support and rejecting it I find to be untenable. So, I am curious to know what your views are!

SAM

Sam,

I absolutely agree that science does not cover the entire range of human knowledge. As someone currently writing a book-length manuscript of poetry for my dissertation, I realize that the truths of human emotion are much better understood through creative work than through the scientific method. I would clarify though that this wandering into other realms (morality etc.) that you describe is not a product of science itself but is a product of misconstruing science (by scientists and otherwise). Blind adherence to a philosophy, even under a trusted name like science, is still blind adherence, and so without support it no longer really involves science. As I stated earlier, I'm not a proponent of most of the loud secular voices like Dawkins, if only for their condescending attitude.

To your points:

1. Let's ignore origin of life theories for now and focus on evolution, which is not a theory on the origin of life. Evolution can only occur once there are replicating, variable units.

2. Same as above. Evolution is not a theory on the origin of life.

3. As you yourself state, mutations that enable such things as antibiotic resistance occasionally do ​arise, therefore mutations are clearly not "uniformly deleterious." Most mutations have no effect on fitness, most of the remainder are deleterious, but a minority are beneficial, otherwise something like antibiotic resistance could never evolve. To your second point, yes. If you remove the inciting agent the original form will out-compete the adapted form. That is because the original form represents that species' best chance at dealing with the current environment (or at least the environment of the previous generation). If you then quickly change the environment back to what it was after a period of change, the original form will again be selected for. Nothing actually changed in the environment. The thing with natural environments is that these large-scale evolutionary changes that we observe are a result (in part) of permanent environmental changes (i.e. dramatic climate shifts, dispersal to a new environment, introduction of a competitor, etc.), not brief shifts in selection pressures.

4. Again we're returning to the point of the evolution of life (this time couched in the evolution of DNA/RNA as an informational system). Such a birth of the biological language precedes the origin of life and therefore does not involve the theory of evolution.

5. Ok there are a number of different points here. One, yes mutations affect the developmental sequence. Some of these mutations are detrimental. Most do nothing. Some are beneficial. One example relevant to my own work that comes to my mind is the loss of limbs in ancestral snakes (which evolved from lizard-like ancestors). This loss of limbs was due to the expansion of thoracic Hox genes during development. This resulted in the entire body having a thoracic-like identity, where there were no limbs in the lizard. This loss of limbs is thought to have been selected for because ancestral snakes were fossorial and therefore serpentine movement through the dirt was more effective than active digging with the limbs.

Now to the question of "macro-evolution." You say we cannot see it. True, it takes a long time and we don't live long enough to document it happening in real time. We also cannot see any of the particles that make up everything in the universe, according to modern chemistry. We cannot see time as a variable as modern physics believes, we cannot see gravity or magnetism and we don't know why they perform in the same repeatable ways. But without directly seeing these things we still accept them because of the abundance of evidence for their existence. The same with evolution. We see its effect. We see it in the fossil record. --> http://chem.tufts.edu/science/evolution/horseevolution.htm

We see it in vestigial structures --> http://upload.wikimedia.org/wikipedia/commons/0/0c/Mystice_pelvis_%28whale%29.png​ (Why would whales have functionless bones that just happen to be in the same position and arrangement as the rear limbs of other mammals? To me this is clear evidence of evolution from a common vertebrate form).

We also see it in DNA. Similar species have similar DNA sequences and expressions. Which is what one would expect if more similar species share a more recent common ancestor than less similar species. In fact, evolutionary biologists can use the information in DNA sequences as a clock that can tell them how recently different species diverged from one another because we know the likelihood of mutations occurring in various regions of DNA. Chromosomes are also good evidence for evolution. Consider that all modern great apes have 24 pairs of chromosomes, except for humans who have 23. If you look at what regions make up these chromosomes, you can see that our second chromosome combined two previously separate chromosomes somewhere in our evolutionary lineage.

http://www.evolutionpages.com/chromosome_2.htm

You can also see evidence for evolution in island biogeography. Oceanic islands that have never been part of a continent always have high levels of endemic animals, totally unlike animals on the closest mainland (for example, marine iguanas, parasitic finches, flightless birds, and giant tortoises on the Galapagos Islands). One would expect these unique species if evolution were selecting species to fill empty niches (that exist because the islands in their early stages were largely uncolonized).

Thank you for your response and I look forward to hearing back!

Sam,

I will respond to each of your points.

1. Are there examples in nature that give us an idea of the actual power of mutation?

Yes! Here is an article http://blogs.scientificamerican.com/science-sushi/evolution-watching-speciation-occur-observations/​ that discusses that very issue in the first few paragraphs. There was a species of plant that gave rise to a new species of plant within a few generations, due to a polyploidy mutation. Clearly, mutation is very powerful! I also discussed the fusing of two chromosomes (a mutation) in a chimp ancestor that is thought to have contributed to the speciation of hominids in the previous email. Something important to keep in mind is that point mutations aren't the only form of mutation.

2. What are the actual mutation rates of different organisms and does this make a practical/ theoretical difference?

Here is an old but popular article that discusses differences in mutation rates among different taxa http://www.pnas.org/content/90/9/4087.short. So yes it does matter what species you're working with when making molecular clocks. It also matters what region of the DNA you're looking at, as some non-coding regions, or the "wobble position" in coding regions accumulate mutations more because they usually aren't deleterious. More recent research has found that some organisms are even capable of increasing their mutation rates in stressful environments. Presumably this increases the odds of evolving a beneficial mutation to better adapt in the presence of the stressor.

Do we know from nature how hard it is to get a two point mutation?

​Yes. Getting two simultaneous point mutations in particular spots in the genome is extremely unlikely. Again though, there are other forms of mutation than point mutations. There are insertions, deletions, gene duplications, transposable elements, etc. in addition to epigenetic effects. It is also important to point out that some areas of the genome are much more prone to mutation than others. This article discusses this in relation to autism. http://sfari.org/news-and-opinion/news/2013/study-links-autism-to-genomic-hotspots-of-mutation. This is sort of obvious though, as some common (relatively speaking) genetic disorders are caused by very specific mutations (for example, cystic fibrosis is caused by a three-nucleotide deletion). 

Invisible Entities

​I agree with you! Those theories in those other fields are testable and supported by data, even though they are sometimes hard to wrap our minds around. For me, actually, it's easier to grasp the theory of evolution than it is to understand something like special relativity. It's a simple concept-- individuals within a species are different, those differences are heritable, some individuals survive and reproduce while others don't, allowing for the possibility for the average phenotype of the species to shift. Moving past the other requisities you listed (testability etc.) I think the true test of a scientific theory is its predictive value. If the theory is solid, you should be able to use it to to predict some event. You are able to do that with evolution. Evolution predicts that species will change through time due to chance events and selection pressures. This is what we observe in the fossil record, such as the fossil horses I sent in the previous email. A taxa changed through time. We can even predict how a species will evolve. In an environment with lots of mutagens, evolution should be faster. We see this in experiments with all model organisms--  mutagenizing individuals to produce more mutations is an essential tool to modern genetics. Island biogeography is another example of how evolution has a predictive value. Drawing on lessons from evolution one would expect that extremely large endotherms with their demanding caloric requirements would fair poorly on small islands. That is what we find in the fossil records. Hippo species the size of dogs, elephant species the size of horses, miniature rhino species are/were all found on islands, presumably because these smaller animals survived better with the limited food supply available on small islands.

Deficiencies in the fossil record

​There will always be gaps in the fossil record if you set out to find them. Even the most contentious of all lineages, the hominid lineage, has a very nice transition of skulls that move towards having a larger brain case, smaller sagittal crest, etc. There will always be gaps because we aren't going to dig up the skull of every tiny transition a species lineage has ever had. This http://www.talkorigins.org/faqs/comdesc/images/hominids2_big.jpg to me is quite convincing enough. 

Irreducible Complexity

​This has long been dismissed by the scientific community because of its mistaken assumptions. The mousetrap is the classic example, right? Take one thing away and it doesn't work. But this is looking at the organism/adaptation as a completed, unchanging whole. It assumes the mousetrap is not alive and reproducing. Imagine instead the mousetrap was originally just a piece of wood-- a simple form of life that waited around on top of rocks and fell on its prey to smother it. Then, assume some of these ancestral mousetraps evolved a small hook of metal that could be draped around the ancestral mousetrap's prey when it fell. This resulted in an increased chance of prey capture and this trait went on to fixation. Then, some of these mousetraps evolved some smelling pheromone (the comparison to cheese) that attracted more prey to the ancestral mousetrap's rock, increasing prey capture success. Then a predator comes and there's further pressure on a different structure... you see where I'm going. The "modern" mousetrap is not some final form of a finished product. It's a constantly changing species whose current prey killing aparatus would have come from small modifications, such as to existing structures co-opted from different ancestral uses.

DNA as a language system

I think language evolution is a great parallel to natural evolution! Consider British English and American English. In the terms of natural evolution, these are two recently separated species. We can still communicate with the British (the parallel to natural evolution: successful hybridization) but there are noticeable differences in the languages that have accumulated due to geographic separation. This is exactly how evolution works! Eastern king snakes and Florida king snakes are different breeds of the same species that, given enough time and separation, may become separate species because of geographic separation. Portuguese and Spanish are fully "speciated" languages because the geographic separation between Portugal and Spain has been in place for a long time, and led to two separate languages. The languages have similarities but native speakers of either language cannot understand speakers of the other. A similar comparison could be made between asian and african elephants. They look similar, belong to the same family, but cannot interbreed due to prolonged geographic isolation and the resulting differences in selection pressures, genetic drift, etc.

It can also be useful to think about language evolution in terms of the modes of speciation it describes. If one language is a species and all the words in the language are genes or nucleotides, it's very easy to see how evolution works. One mode of evolution is natural selection. Some genes/ words survive better and go to fixation in a population. Consider the word "dude." This word has spread to the vocabularies of most young people today because, for whatever reason, this word was selected for. This addition to the vocabulary constitutes a small change to the English language and makes it different from how English was spoken in the past. This is how natural evolution works. So yes, here is an example of a change being introduced to a complex (and importantly, dynamic) system and it not breaking the system. Just like in natural evolution. 

Let me know what you think about these things!