This week in AP bio, we took a turn for the worst and started talking about what seems to be chemistry. We have started taking about protons and electrons and bonds and everything else thats wrong with science. I’m not much of a science kid and more than that I’m not much of a chemistry kid. I have a very hard time grasping ideas and theories that I can physically see. I understand adaptation because I can see examples with my eyes but covalent bonds and why bonds even happen or why electrons are a thing, forget it. For the same reason, I hate space.

I couldn’t find a direct connect to any of the Big Ideas but Big Idea 4 talks about molecules a little bit and we are talking about molecules and compounds. The biggest part of the week, however, was pH. We talked a lot about acids and bases and what it means and how it changes or doesn’t change when buffers are introduced. PH is something you talk about in almost every science class ever so it felt good to have some back ground knowledge and feel a little more secure with a topic.

After spending the beginning of the week with pH if went back to chemistry and we started talking about organic molecules. We had to identify categories of biological molecules and look at amino acids, sugars and types of lipids. This is where I loose confidence. Working through this stuff in a group really helps and I feel a little better after class than I did going in to it. I’m still a little confused but to the point where I don’t know what my questions are.

Theories of Life

This week we spent a lot of time discussing  the origins of life as we know it. The two main theories are metabolism first and replication (RNA world). No one knows which theory is correct and there is a lot of proof to disprove both sides but no one really knows and new science is coming out all the time.

Metabolism first is the theory that electrons extracted from reduced organic molecules from hydrothermal vents. Then iron sulfide surrounds the organic molecules that are produced and electrons break off with temperature change. Over time tini life molecules collected and come together to form life. A major aspect of this theory is the Kreb cycle. The Kreb cycle is when electrons are extracted from reduced organic molecules. So pretty much hydrothermal vents = life. The arguments against metabolism first is that there hasn’t been enough testing because it’s a relatively new idea and also the big question that has yet to be answered is how can there be life with no DNA first?

The second and eldest theory is that there was first organic molecules and then it formed ribonucleotides which then replicated into long chain polymers then RNA and then the RNA got faster to form DNA. A DNA molecules primary function is replication and proteins carry out a variety of chemical reactions required for metabolism. Some theories predict that we came from space because these chemical reactions can happen on asteroids and comets which used to land on earth. SO the building blocks for life could have come from space. SOme arguments against this idea are that these molecules are unstable and may break down before they can form into nucleotides. It is, however, possible for nucleotides to form without first having sugar and a base. It is possible for nucleotides to link together to form RNA. But again, they are unstable.

Personally I don’t believe either. Both have been pretty much debunked. The only reason that metabolism first doesn’t have more evidence against it is because it’s the newest theory so there has been less time to disprove it. It would be pretty cool if we came from space though. 

Phylogeny Analysis

Looking at my sequence of animals, there are a few conclusions I can come to. One conclusion I can come to is that my protein, lipoxygenase, must be very common because a variety of animals are in the sequence you may not think of as “relatives”. Sense lipoxygenase is involved in the metabolism that shows that all the organisms in my sequence have metabolisms or some form of one, making this gene very common.

When initially searching this gene, many variations of humans and chimps came up. When I researched the protein it came up that it is mostly in plants. This surprised me because in the search for making the sequence, the front page was animals. There also wasn’t a huge variety in the animals until I dug a little deeper and found more animals on later pages.

I can not speak to question 3 because T-coffee has not generated an alignment for me. Its been processing for about 45 minutes and there seems to be no progress. I can, however, imagine that there will be a stand out in the alignment and I think it will be the zebrafish. On the tree it showed that arctic salmon and golden hamster are more closely related than arctic salmon and zebrafish. I’m not an expert on evolution but I feel like fish should be on the same branch and not closer to a hamster than another fish. That one stood out to me.

If I could add data to my tree I would add more species that I believe are closely related and see where they fall in the sequence. I would also compare organisms that I believed to be closely related that didn’t show up in the search of having this gene and see how their genes compare. Why do some organisms have it and others don’t? I am very surprised that some related organisms didn’t show up in the initial search. I am curious as to why. Is this gene not very important in relating organisms to one another?


Artificial Selection

A long experiment we started this week was our plant lab. It will take around 50 days but we get to selectively breed plants which is pretty cool. We watched a video on foxes that where selectively bred for the trait of kindness. After breeding the most friendly with the most friendly they noticed that the trait they selected wasn’t the only trait that was passed down. Other traits like floppy ears and elongated vertebrae where starting to become a trait that was passed down. The foxes had become domesticated. I think it’s pretty cool how this happened but I don’t know if I am morally for changing living animals to better enhance human lives. This experiment connects mostly to Big Idea 3. A lot of Big Idea 3 is about genotypes and patterns in traits. Also genotypes are the blue prints for phenotypes and what makes you look the way you do is proteins. There are different ways to get the same proteins from genotypes so there is more variation in genotypes from organism to organism than variation in proteins. Looking at the chart of the proteins that you get from the genes took me right back to freshman biology and I instantly remembered filling out sheets of proteins and the different ways to get to them. It felt good to remember something from freshman biology for once. I have forgotten most of it so its nice to know some information is still locked in my brain.

This week we also learned a lot more about Darwin and his theories. Even though Darwin didn’t understand genetics he believed favorable traits could be passed on to offspring. Darwin also had his theory of evolution, VISTA ( Variation, Inheritance, Selection, Time, Adaption). One thing I don’t understand is how he never knew about genetics if he believed traits could be passed on. What did he think was causing the continuation of traits? I don’t know if he had theories or not but it would be cool to know what he thought happened.

The main take away from this was that I might still know some biology but there is much more to learn. Also I’m waiting to use the dehydrated bees because I have no idea what they could be used for and I’m so curious/excited. If anyone knows please tell me.