The "dark matter" Carroll refers to in Chapter 5 are all of those sequences of DNA that we termed introns that are not translated to be a part of the final protein product, in fact they must be removed (in eukaryotes) before translation can begin.
I really liked the galaxy metaphor Carroll uses to describe "dark matter." As far as we know, Earth is the only place where organisms can live in the entire, huge galaxy. Only 5-10% of the millions and millions of DNA bases in our genomes actually code for the proteins that make us up. This was the clearest portion of this chapter.
Honestly, if we hadn't talked about introns and extrons in lecture before reading this chapter, I am not sure I would have any clue what Carroll was trying to get across. When he starts talking about all kinds of switches and what not, what I was reading started going over my head. All I really know about switches now is what is said on the last page of the chapter: "Switches enable the same tool kit genes to be used differently in different animals."
A much larger part of our DNA consists of sequences that are not part of the simple code for any gene and whose function cannot be deciphered simply by reading the sequence. This is the ‘dark matter” of the genome. The dark matter in our DNA controls where and when genes are used in development.
I found the gene switches interesting. The general function of a switch is to transform existing patterns of gene activity into a new pattern of gene activity. RNA interference, often called ''gene silencing," is like a genetic dimmer switch, a natural mechanism that allows a cell to regulate its genetic climate, turning one gene up during a crucial part of development, or turning another down, as a defense against mutations. Researchers are now harnessing the mechanism with the hope of crafting drugs that will turn off the genes essential for diseases like HIV, cancer, or influenza.
RNA carries instructions for making proteins from the DNA in the nucleus to the outer reaches of the cell. There the RNA churns out proteins that give rise to basic traits such as green eyes and blond hair, and lead to disease.
I'll have to admit this wasn't the most enjoyable chapter to read but parts of it were interesting. I understand the existence of switches and "dark" and "visible" parts of a DNA strand, but the slow reading made it difficult to follow along attentively. It is crazy to think that the "dark" matter of our genes are in control of where and when our genes develop and have a lot of power as to the composition of our bodies. I feel the word "dark" is not a positive word to use to describe such an important part of our development. Maybe a more enlightening word could be used, such as "foundation matter" or "pathway matter"..maybe "vital matter."
I really like your idea of using a different term, like "pathway matter", to replace the term "dark matter" b/c of possible negative connotations associated with the word dark.
Most of our DNA seemingly codes for nothing. Its just crap and noise. However, embeded in this crap and noise are things that control if and when a gene is expressed. This directly relates to what we're talking about in class right now. Sliencers are really just dimmers. Enhansers turn a gene on in certain situations. These all contribute to how and where spots, lines, and all sorts of patterns to making a body show up. It's amazing! Now, if only we could figure out what "switch" is thown for certain cancers and adverse, abnormal, crippeling genetic diseases.
The "dark matter" of genomes they are referring to in this chapter is the DNA that consist of sequences that don't code for any gene and whose function cannot be deciphered by reading the sequence. The dark matter controls where and when genes are used in development. The dark matter occupies much of the the animals genome and the part of the genes that we see only occupy a small portion of the DNA. I think how he compared the dark matter of genes to cosmologist helped in understanding how the dark matter works. It also talks about genetic switches that can turn genes on or off. These are things that we are discussioning in class right now.
In this chapter, the author try to explain where the operating instructions for the tool kit by using the analogy of cosmology. He also go over dark matter and the anology of switches, and i though that is very helpful and easy to understand when he explained that certain genes is control by a certain switch. The only part i found a little confussing is the figure on pg 121 about signatures added or removed for repressor.
In this chapter, Carroll talked about dark matter, which he said was the larger part of our DNA that have sequences that do not code for any gene and cannot be determined by reading that particular sequence. This dark matter is from our genome. Carroll said that only 3% of our dark matter actually contains switches that control what certain genes do. I found it interesting that these switches is that one gene is regulated by multiple switches, and are used frequently and in different places. This chapter overall I thought was very helpful in understanding switches and the dark matter of the genome.
The dark matter of genomics refers to the DNA that is not expressed. When looking at the picture on page 108 of EFMB, we can see the vast coverage of the dark material in comparison to the white spots of DNA that is expressed. It is comparable to the darkness of the universe and th bright stars that appear in it.
I found it pretty interesting that the dark matter actually controls what is expressed and not expressed, and it's pretty cool how biologists have determined that only 2-3 % of human dark matter contains genetic switches that control how the genes are used. That had to take a lot to determine.
In this chapter it defines "dark matter" in our DNA to control where and when genes are used in development. It contains instructions for making and patterning body parts. I liked how Carroll used the metaphor that the genetic switches were like a GPS (global positioning system) devices. Because just like a GPS locater in a car gets a positional fix by integration multiple inputs, switches integrate positional info. in the embryo with respect to longitude, latitude, altitude, and depth, and then dictate the places where gene are turned on and off.
I thought that Carroll's explanation of dark matter was very complex, and I would not have known what he was taking about if we didn't already talk about introns and extrons in class. Even now I still don't really get the whole concept, because it kind of made me more confused. I would have a say that this was not my favorite chapter to read. I hope it gets more interesting!
The "dark matter" of genetics refers to the massive amount of DNA that doesn't code for anything. The job of the dark matter is to determine exactly where and when genes should be expressed during development. I think Carroll did a good job of relating to the readers that the process of development is very intricate/complex. He goes into a little depth on the BMP5 genes and its surrounding switches. Then he tells us how this is just a single snapshot, one tiny frame in the huge and amazing 'movie' of development. Sometimes I find it irritating how Carroll talks about flies all the time, but then I remember that's what his research was on. I also didn't fully understand the combinatorial logic.