I haven't been too active with reading or writing blogs lately - I've been traveling and trying to get some (publishable) analyses and writing done. But I just stumbled upon a blog I hadn't seen before by Ken Weiss and Anne Buchanan. Ken Weiss is an anthropologist at Penn State. He writes a lot about evolutionary concepts (some call it theory, but the math theorists don't like that). He had a published column for a while that I was a fan of - I even assign a few of them for my evolution class.
I am a fan because Professor Weiss is an ardent pluralist, comfortable with some ambiguity, and the fact that "dichotomies" are spectra, etc. This is a general philosophy I share, and use to make sense of the world and others' arguments.
So, I look forward to reading their blog, called the Mermaid's Tale (I'm not sure I'm fond of pun-ambiguity, but I guess it works in this case). It looks prolific, I don't think I'll be able to keep up.
Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts
Thursday, August 27, 2009
Saturday, January 24, 2009
Creationism and Evolution in our society
I was asked in an email to complete a survey about "creationism and evolution in our society". I came up with some answers, spur of the moment, and I thought I would paste them here. If it really is a student, I would like to help him out, and pasting it here gives me a little more incentive to complete it. (Anyone know what is a "Facharbeit"?)
Dear Reader.
I'm a german student who works on a "Facharbeit". We had to choose a subject and I think that the controversy between Evolutionists and Creationists is very interesting. Therefore I decided to learn more about it. I've created a survey and now I'm sending it around, hoping that many people are going to write something in the gaps. It would be very helpful if you answer me because here in my town I'm not able to talk to someone about this subject. If you are able to open the word file you can fill in the gaps there and send it back. This would make it very easy for me to evaluate the documents. Well, if this doesn't work, I've just copied the survey and you can fill in the gaps in this E-mail and send it back.
Hope hearing from you soon. Thank you.
Survey
Creationism and Evolution in our society
1) Do you support the evolution or the creationist theory?
I fully accept the enormous weight of scientific evidence that has accumulated for the theory of evolution. By "the theory of evolution", I mean the common ancestry of all living things, and descent of living things with modification.
I am not sure what "creationist theory" means. There are many stories of creation, many of which are not consistent with known facts and observations. I have not heard a creation myth that I support, and I know of no creation story that could be called a "theory" in the sense of a scientific theory.
2) Do you think that the other theory is non-sense? (Can you explain why you think that the other theory is non-sense?)
I would need more information about what is meant by "the other theory"; but many of the creation myths I've heard are non-sense in my opinion. For example, the Iriquois creationist story states that people once lived in the sky until a woman, pregnant with twins, was forced down to the Earth. At that time, the Earth was covered with water, there was no land. A giant turtle wanted to help the woman who had fallen to earth, so the turtle swam to the bottom of the sea and placed mud on its back to generate North America.
Yes, I think this creation theory is non-sense. There is no evidence of any turtle the size of North America, nor any evidence of any animal that could reach such a size. There is no evidence that this turtle is under North America today.
3) Are you sure that the theory you believe in is the right one? Why, why not?
Science should not be a matter of "belief". Given the enormous weight of evidence for common descent of all living things, and for descent with modification, I might say that I "believe" that this explanation will remain "the right" explanation for a very long period of time.
4) Do you think that there could be a danger if the world believed in the opposite theory?
Again, I am not certain what is meant by "the opposite theory". But, yes, I imagine that if belief in creation stories is a symptom of a potentially dangerous pattern of thought: When people believe what they are told without thinking critically about it for themselves, they are prone to dangerous manipulations.
5) Do you think that there’s a possibility that there’s an answer in between those two theories?
Again, I'd have to know which 2 theories. I don't think there is a true answer between the theory of evolution and the Iriquois creation story.
6) Maybe you’ve got an idea how that theory would look like?
7) If someone would find out that the theory you believe in is surly not the right one, would there be an effect on your life? Would you be frightened? Would you think that there’s something missing in our world?
Yes, if common descent and descent with modification were proven false, it would have an impact on my career. I would change the scientific questions I am studying. I do not think this would lead to something missing in the world, because the current scientific view of the history of life would simply be replaced with another scientific view of the history of life.
Friday, December 19, 2008
Opsins: An amazing evolutionary convergence
How predictable is evolution? If we could travel back in time 4 billion years and make a few changes, what would remain the same upon our return? This is an enduring topic of evolutionary inquiry (and movies and sci-fi shorts for that matter).
In his book Life's Solution, Conway-Morris made the case for a semblance of predictability in evolution. He argued that convergence - the independent origin of similar traits - represents an element of predictability in evolution. Octopus and humans have outwardly similar eye designs, so if we reply animal history over and over, these camera-type eyes would likely evolve in most replays.
Here I'll describe a truly amazing molecular convergence that was not discussed by Conway-Morris: the independent evolution of opsin proteins (a protein responsible for light perception) in two different groups of organisms. It turns out that a 7-transmembrane protein (opsin), bound to a light reactive chemical on the 7th transmembrane domain, has evolved twice to sense light!
If we could go back a few billion years and replay the evolution of life on earth a few times, chances are, opsins would evolve in many of our replicates.
[Disclaimer - the following is text from an encyclopedia article I've been asked to write on opsin evolution, so the writing style is a bit terse from here on out. I will add a little bit though, specially for the blog. But since many people I know think opsin originated only once, I feel it's my duty to spread the word of opsin convergence, starting here, at Evolutionary Novelties].
What is opsin and rhodopsin?
Opsins are a group of proteins that underlie the molecular basis of various light sensing systems including phototaxis, circadian (daily) rhythms, eye sight, and a type of photosynthesis. Opsins are sometimes called retinylidene proteins because they bind to a light-activated, non-protein chromophore called retinal (retinaldehyde). Opsins are also in some cases called “rhodopsins”, a name originally given to isolated visual pigments that contained both opsin protein and non-protein chromophore in a time before the two separate components were known. Today, the term “Rhodopsin” is used commonly to describe the opsin expressed in vertebrate rod (dim-light) photoreceptors, and the opsins of certain organismal groups, like bacteria. All opsin proteins are embedded in cell membranes, crossing the membrane seven times.
Type I and Type II opsins
Two major classes of opsins are defined and differentiated based on primary protein sequence, chromophore chemistry, and signal transduction mechanisms. Several lines of evidence indicate that the two opsin classes evolved separately, illustrating an amazing case of convergent evolution.
Type I opsins are present in bacteria and algae and are referred to by various names, including bacteriorhodopsin, bacterial sensory rhodopsins, channelrhodopsin, halorhodopsin, and proteorhodopsin. Type I opsins have varied function, including bacterial photosynthesis (bacteriorhodopsin), which is mediated by pumping protons into the cell, and phototaxis (channelrhodopsin), which is mediated by depolarizing the cell membrane. Type II opsins are present in eumetazoans (animals not including sponges), but are unknown from sponges or any non-animals. Because opsins are known from cnidarians and bilaterian animals (animals with bilateral symmetry, including humans, flies, and earthworms), Type II opsins are inferred to have been present in their common ancestor, which lived about 600 million years ago. Type II opsins have varied function, including phototransduction and vision, circadian rhythm entrainment, mediating papillary light reflex (pupil constriction), and photoisomerization (recycling the chromophore).
Despite their functional similarity and despite both being 7-transmembrane proteins, multiple lines of evidence indicate that Type I and Type II opsins evolved independently. First, the primary amino acid sequences of Type I and Type II opsins are no more similar than expected by chance. For example, try to align a Type I (say bacteriorhodopsin) and Type II opsin together. I just tried this with blastalign, with the following result:
Exhibit A. Blast search find "no significant similarity" of the amino acid sequences.
Sequence 1: gi|163443|rhodopsin
Length = 348
Sequence 2: gi|208055|bacteriorhodopsin >gi|208057|gb|AAA72603.1| bacteriorhodopsin
Length = 249
No significant similarity was found
CPU time: 0.04 user secs. 0.02 sys. secs 0.06 total secs.
Second, the orientation of the transmembrane domains differs between the major groups. We now have crystal structure data for both Type I and Type II opsins, and the arrangements of the parts of the protein that are stuck in the cell membrane are quite different, inconsistent with a single origin of opsins (unless this changed a lot during evolution, which is not impossible).
Exhibit B. Type I on the left, Type 2 on the right. Denser lines are positions of transmembrane domains. Figure is from Spudich et al (2000)
Third, the major opsin groups differ in chromophore chemistry. Prior to light activation, the chromophore of Type I opsins is an all-trans isomer. Light activation then involves isomerization of the chromophore to 13-cis retinal. In contrast, prior to light activation, the chromophore of type II opsins is 11-cis retinal. Light activation of Type II opsins involves isomerization to all-trans retinal.
Exhibit C. Type I on the left, Type 2 on the right. Chromophore chemistry differs. Figure is from Spudich et al (2000)
Fourth, Type II opsins belong to the larger protein family called G-protein coupled receptors (GPCRs), which transmit varied signals from outside to inside cells by activating GTPase proteins, which in turn signal to second messengers that affect the state of the cell in various ways. Type I opsins do not activate G-proteins. Furthermore, Type II opsins are more closely related to non-opsin, light insenstive GPCR’s than they are to Type I opsins. So even if there is some very, very distant and *undetectable* common origin of Type I and Type II opsins, chromophore binding likely evolved twice. Since chromophore binding is what allows photosensitivity, it is the crux of being an opsin (but see), and the realization that Type II opsins are closer to non-opsin GPCR's than Type I opsins is strong support for two separate origins.
Exhibit D. (Dashed lines mean no sequence similarity beyond random. Light bulbs mean origin of chromophore binding=light sensitivity=opsin.)
Finally, with two CS students, I tested the single origin hypothesis in a different way and found no support. Type I opsins show similarity of membrane domains 1-2-3 and 5-6-7, consistent with an origin by duplicating a 3-domain protein (and adding one). However, Type II opsins show no such similarity. If they Type I and Type II share a single origin, the duplication pattern of the domains should be shared too (unless there were drastically different rates of evolution in the 2 lineages, which is not impossible). This work is described here: Larusso et al (2008) J Mol Ev.
John L. Spudich, Chii-Shen Yang, Kwang-Hwan Jung, Elena N. Spudich (2000). RETINYLIDENE PROTEINS: Structures and Functions from Archaea to Humans Annual Review of Cell and Developmental Biology, 16 (1), 365-392 DOI: 10.1146/annurev.cellbio.16.1.365
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