Learning Log 7:
FIT - Ch 8
The Making and Evolution of Complexity

by Elleka Watts
Seminar E, Group 5
Professor Grymes

Synopsis:

(1) What are Microevolution and Macroevolution?

            Microevolution is the variation and evolution within species, whereas macroevolution is the formation of new species and the evolution of complex features above the species level. In a nutshell, microevolution is the process of evolution on a smaller scale – focusing on the mutations and variations of individuals within the same species. On the contrary, macroevolution is the process of evolution on a much grander scale, involving the development of new species through mutations over a longer period of time.

(2) What is "Evo Devo?"

            “Evo Devo” is a dubbed name for the study of evolution of development. The relationship between development and evolution is that all changes, mutations, variations, etc. of evolution in terms of physical form evolve through changes in development. This explains a lot about the evolution of complex bodies and body parts. Understanding development shows how complex structures are built, while comparing different developments within different species shows the evolution of complexity.

(3) Explain how discoveries about the Pax-6 gene show that all complex eyes evolved not from scratch each time but from a common ancestor having a very primitive eye.

            First of all, in a general sense it would seem less likely and more difficult to evolve a structure such as the eye from scratch rather than building upon parts that are already available. With the complex eye, scientists studied the fruit fly to examine what gene promoted eye formation and noticed that when the eyeless gene was isolated, it encoded similar proteins encoded by two genes in humans and mice (the Pax-6 protein). Swiss researchers proved the Pax-6 gene in different locations had the same capabilities by activating the gene on different locations of the fruit fly’s body causing eye tissue to form on legs, wings, etc. It has been further noted that Pax-6 is evident in other species such as squids, planaria, ribbon worms, and others that have various eye structures. Since Pax-6 is responsible for various types of eye development, it’s unlikely it happened from scratch or by accident, and instead a common ancestor used Pax-6 for developing a very primitive eye.

(4) Explain how studies of the ragworm show that the evolution of vertebrate eyes and other animal eyes were not independent events.

            The simplest eye according to Darwin, was supposed to be an optic nerve with pigment cells and a translucent skin covering – but not necessarily any lens or refractive structure. Such two-celled eyes were found in ragworm larvae, and they share common ingredients with more complex eyes. They have opsin proteins and utilize them for light detection, indicating opsin existed in the primitive eye in the common ancestor, too. The adult ragworm eye begins near the original two-celled larval eyes but has many more photoreceptors and pigment cells. The construction of larger primitive adult eyes and the use of the same genes as those in more complex eyes demonstrates how such complexity has evolved and indicated vertebrate eyes and other animal eyes were not independent events.

(5) What's the difference between proteins that are responsible for physiology (like opsins, globins, ribonucleases, and odorant receptors) and those responsible for form (like the Pax-6 gene) Use the phrase "tool kit" gene in your answer.

            Physiological proteins are responsible for vision, respiration, digestion, and olfaction. However, form proteins like Pax-6 and other tool-kit proteins control the number, size, shape of body parts, and identity of cell types in the body. Tool-kit proteins act directly or indirectly to control when and where different genes are used in the body, as well as take multiple roles in building the body and body parts. A major difference between the two kinds of proteins is the consequences that arise from mutations altering them. Mutations in opsins   may simply alter the light detected in the eye, whereas with a tool-kit protein, the eye could be abolished altogether. So, the gravity of mutation consequences are not so severe in a physiology protein, but very severe when speaking in terms of a tool-kit protein.

(6) What is the role of regulatory DNA sequences on how the tool-kit gene Pitx1 produces the two types of stickleback fish pelvic skeletons?  Make sure you explain just what regulatory DNA is and thus also explain its connection with genes that code for proteins.

            Pitx1 is a tool-kit gene that is responsible for the reduction of the pelvic reduction in stickleback fish. This gene controls other genes, has multiple roles in fish development, and has counterparts in other animals like the mouse. Though the sequences of the Pitx1 proteins of pelvic-reduced and full-pelvic forms of these fish are the same, their regulatory DNA is not. Regulatory DNA is noncoding DNA sequences in addition to the normal gene coding. This specific kind of DNA has switches that determine where and when a gene should or should not be used. Such switches are independent and do not affect switches elsewhere in the gene regulating DNA – which allows a tool-kit gene to be tuned without any side effects. When a gene has a certain switch on, it activates that gene and allows that gene to code for and as a result create a protein, but if the gene is inactivated by an off switch, that specific gene cannot code for that protein and thus not create one.

            In the pelvic-reduced stickleback fish, a particular section of the Pitx1 gene has been switched to an off position to make it so the pelvic is not extended like how it is in the fish’s other form. As a result, selective pressures are fulfilled by this section of its skeleton being thinner and more slender. For the full-pelvic version though, switches are on, allowing the Pitx1 gene to develop the pelvic fin area and thus extend the skeleton, making the fish bigger.

(7) Explain how one gene, the "paintbrush" gene, can create diversity in fruit-fly wing patterns (including a wing spot - how one evolves and how one disappears).

            Melanin-producing enzymes are the paintbrushes in tool-kit genes. These enzymes are responsible for producing the black spots commonly found at the tip of male fruit fly wings and are an example of how new patterns evolve when old genes learn new tricks. Species with black patterns on their wings these enzymes (or paintbrushes) foreshadow the black pigment areas. Such patterns are controlled by switches surrounding the coding of each paintbrush gene. Several changes within paintbrush genes explain the evolution of wing spots. Rather than a spot all of a sudden appearing, it actually went through a series of steps in which the spot had switches change in its intensity and shape to make it appear. Wing spots are an example of adding up variations to develop a physical trait. Just as the wing spot had appeared in a fruit fly’s wings, it also has recently disappeared. The loss of this trait could have been due to female flies not choosing spotted mates – relieving the pressure to maintain it in the male population. Also, the switch that made the spot appear previously had accumulated mutations that caused the switch to be changed again – thus inactivating the spot’s presence. Having such paintbrush genes and switches to regulate them based off of the gene’s noncoding DNA allows for a variety of fruit flies with different wing patterns.

 

Take Away Idea:

            The idea I’d like to take away from this chapter is the fact that there is noncoding DNA that determines gene regulation within a gene’s whole coding sequence, Since scientists have been learning more and more about how gene regulation works, they can alter the appearance of animals and maybe even apply it to humans, too. Learning how gene regulation works in humans can allow us to focus on turning on or off specific switches in genes that make us more susceptible to certain diseases and unattractive traits.

 

Most Challenging Concepts:

            I think the most challenging concept was trying to understand in detail exactly what a paintbrush gene is and how it works. Through reading that section a few times over and trying to look at the diagrams and envision it in my head, it helped me understand the concept a bit better – but I still think some clarification is in order. Specifically, I don’t quite understand how the switches function to create the color, like what exactly is happening during the process of the wing spot forming to be completely visible and apparent on the fruit fly’s wing. Secondly, I don’t quite understand what would change within the female fruit flies to all of a sudden make a wing spot not as necessary or as attractive to finding a mate with a male.

 

A Seminar Question:

            Do you think we have switches in our melanin-producing genes similar to that of the fruit fly? What impact do you think these switches have on us – such as hair color, eye color, skin color, etc.? Do these switches have anything to do with why some people have lighter skin and darker skin? Could it be possible there are inactivated switches which could give unusual colors of skin and hair such as blue, purple, green, etc. provided they were activated?

 

Competency:

            Aesthetic Awareness is probably the most evident competency exhibited in this chapter. In order to see the complexity of evolution, one has to be aesthetically aware of the physical characteristics that have developed among different species to make them look as they are now. Aesthetic awareness depends on the eye and what the eye observes and understands in this case – and which would not be possible if it had not been for the evolution of complexity. Evo Devo gave us the complex eyes we have today in order to observe and appreciate the wonders of evolution around us in the natural world. Not to mention being aesthetically aware like how the scientists who studied the fruit flies were, allows you to see the intricate differences of wing spots on male flies and appreciate the diversity that complexity brings.

            Communication is another prominent competency in this chapter, but it isn’t with humans, instead it’s within a piece of DNA. Regulatory DNA has its own form of communication within a gene’s coding to tell that gene how to work and whether or not certain traits should or should not be expressed. Although it is seemingly simple communication, it is what it is regardless. Regulatory DNA gives the “yay” or “nay” in terms of what switches are supposed to be turned on or off within a gene and communicates that order effectively enough to give a fruitfly its spots, a human a pair of eyes, etc.

            The connection I find with this chapter and my NCC learning is with the gene regulation. Professor Grymes was talking to the class in seminar about how there are new findings about the “junk” DNA scientists had previously ignored in human DNA and now they’re finding it is a bunch of sequencing that codes for gene regulation. Also, the concept of switches within genes for the purpose of gene regulation connects with previous learning I’ve had outside of NCC. In high school biology, we learned in depth more about how gene regulation works, too.

 

Vocabulary:

1. Physiology - the branch of biology dealing with the functions and activities of living organisms and their parts, including all physical and chemical processes.

2. Rhabdomeric - consisting of rhabdoms which are any of various rod-shaped structures

3. Ciliary - noting or pertaining to various anatomical structures in or about the eye.

Key Concepts:

1. Tool-kit genes

            These are genes that determine the number, size, shape of body parts, and cell types in the body and also are responsible for developing the body and body parts. Mutations in tool-kit genes are very severe (for example a mutation could result in not having an eye if in the Pax-6 gene). Examples of tool-kit genes are the Pax-6 and Pitx1 genes (though the latter is also an example of a paintbrush gene). When switches are changed in a tool-kit gene, they do not affect the status of other switches within the same gene.

2. Noncoding regulatory DNA

            Regulatory DNA is found after a gene’s encoding DNA which basically tells a gene when, where, and how it will work (or express itself). Regulatory DNA is responsible for determining what switches should be on, and which ones should be off, as well as just regulating how the gene works overall. Most of the coding sequence in a DNA molecule is regulatory.

3. Evo Devo

            This is a shortened term for the evolution of development. Evo Devo is a main concept of this chapter in that evolution generally happens through the gradual development of characteristics, especially physical. Evo Devo is the theory behind explaining how the primitive eye developed into more various and complex versions from building on top of a simple foundation using the same materials. (An example of this is with the larvae having two celled eyes, but the adult form developing a more complex eye with more cells and photoreceptors – such is the case with all different eye developments in various species).