CHAPTER 11: THE MEANING OF IT ALL

- When taken over millions and billions of years it is quite easy to see how new, novel features appear in populations. There are thousands of examples of this. These are novel traits that appeared in the human population. Due to selection over time, those traits will become more and more prevalent in the population.

- Shubin makes it very clear in this chapter that Tiktaalik is a wonderful intermediate between fish and their land living descendants, but the odds of it being our exact ancestor are very remote. It is more of a cousin than an ancestor. No sane paleontologist would ever claim that he or she had discovered “The Ancestor.”

- Another interesting point that Shubin makes is that much of the relationships and knowledge about basic evolution are so strong, that for all intents and purposes, they are facts. This is why you don’t find recent works talking about common descent or natural selection. There are hundreds to thousands of papers, reports, and experiments that support these claims. Many of them are a hundred years old or more.

- Humans are unique forms of hominids. We are in the larger group of primates, sharing many of the characters of primates, including some mistakes in our genes. We are mammals. There is no fundamental difference between our hair and the hair on dogs or whales. We are chordates. Again, this is a fundamental feature of our anatomy. We are animals. We are multicellular, without cell walls, and cannot manufacture our own food. We are a living thing, and like every other living thing on the planet, we respire, we use chemical energy, we respond to our environment, we are made of cells, we have information stored in nucleic acids, etc.

- Shubin ends with a large list of the faults of the human body, from swollen knees to hernias. There are many, many more besides what he lists in the book to. These are all things that are easily explained by common descent.

CHAPTER 10:: EARS

- Reichert discovered that two of the bones in our middle ear are the same bones that are parts of the jaw in reptiles. He learned this by tracing the resulting structures during development of embryos. He tracked what happened to those gill arches from the earliest development all the way through a completed organism. There was no mistake, what becomes a jawbone in a reptile becomes the middle ear bones in a mammal. They were the same. But without an evolutionary framework, how can two bones in two widely different organisms be ‘the same’.

- When paleontologists got involved with this line of research (1910-1913) they provided additional evidence. When you look at the very earliest of the mammal-like reptiles, you find one middle ear bone and a jaw composed of several different bones. But as you move upward through time, following the line that started with the mammal-like reptiles and subsequently as you move towards the more mammal-like organisms, you can actually watch the bones that become the middle ear reduce in size and change position. The jawbones had become middle ear bones.

- One of the effects of having a high blood alcohol level is that the inner ear system goes off balance and you stagger around for a day or so. This is because the alcohol from your blood stream goes into your inner ear canals and displaces the fluid that is used in your balance system. That movement of the fluid as it is displaced is sensed by the nerve cells and is reported to the brain as movement when you aren’t moving. The reverse happens the next morning. Your liver has removed most of the alcohol from the blood, and the alcohol in your inner ear slowly diffuses back into the blood stream. The inner ear fluid moves back to where it’s supposed to be and your ear reports that as movement too.

- This inner ear system is directly descended from sharks. A neuromast organ is a tiny little system that sharks use to detect movement of the water around them. Those neruomast organs are similar to the system in your inner ear. The same jelly-like substance in a sac with sensory hairs stuck into it. As the sac is compressed or moves from side to side by ocean currents (or you bending over), the fluid moves the sensory hairs and the shark can sense a fish and you can sense the change in your orientation.

- All this goes back to the genes. This time Pax2 controls the development of the inner ear. A mutation here results in a badly formed or missing inner ear.

CHAPTER 9:: VISION

Q. How can a common organ such as the eye be used to trace evolution?

 

-The main function of our eyes is to gather light and focus the light onto a retina. The retina consists of special cells called rods and cones. These rods and cones are specialized light absorbing cells, that respond to a certain form of light and send nerve impulses to the brain. The brain in turn interprets the pattern of nerve signals into we an image.

- One can trace the evolutionary history of an eye from simple light gathering cells on the surface of a planaria to the highly intricate eyes of an octopus. However the molecules that actually absorb the light energy and covert it in to an electrical impulse, which can start a nerve transmission are called opsins. Opsins are found in majority of the organisms; humans, insects, clams, and scallops all use opsins.

- Evolutionary principles can be used to make predictions. One would predict that organisms that are more closely related to humans would have similar vision systems. Which in fact is true. Humans have three genes producing opsin, thus giving us a a large spectrum of color vision. This is indeed the case, with the majority of mammals have two genes for color vision and the higher primates  having three.

- There is an intricate relationship among eyes in the animal kingdom. There is a noticeable difference between vertebrate ‘camera-style’ eyes and invertebrate ‘compound’ eyes. Until 2001, this might have been considered an unbridgeable gap and many prominent biologists assumed that eyes developed twice in the history of multi-celled life on the Earth.

- But in 2001, Detlev Arendt found that a polychaete worm had the basics both kinds of vision systems. The worm has a ‘normal’ invertebrate eye with connections to the neurons and opsins but, underneath the skin, were tiny photoreceptors with vertebrate opsins and tiny bristle like projections that matches basic rods and cones. This animal has the precursors to both vision systems in use by the animal kingdom.

- Research on fruit flies produced the discovery of a mutated gene that causes a reduction or the elimination of eyes in fruit flies. The eyeless gene was unique. By turning on this gene in cells in various places in the fruit fly, research could grown an eye there. Whole generations of fruit flies were born with eyes on their legs and abdomen and mouths and wings. Some of these eyes, could even respond to light and considering they aren’t actually connected to the nervous system.

- Another gene was discovered in mice, Pax6. It’s the mouse equivalent of eyeless. With some creative genetic engineering, they found that Pax6 could be used to grow an eye in fruit flies (again, anywhere the researchers wanted), but it was still a fruit fly eye. These two genes, one in a fly and one in a mouse, were so similar that either of them can trigger the complex developmental cascade that results in the formation of an eye.

CHAPTER 8:: MAKING SCENTS

Q. Explain how mutating a gene which codes for receptor proteins, eventually lead to the loss od certain scents.

 

 

-          So far we have discussed how limbs and body structures and even teeth portray common descent. However it is interesting to know that the study of scent can also be used to root back to common ancestry. Each chemical responds to two different sets of proteins; some respond in air and some in water. These chemicals attach to their respective protein which in turn passes a signal to the brain there by inducing various different actions. One such action might retrieve a memory in the brain, like the smell of a brownie, or maybe even gasoline.

-          The human nose can identify around 10,000 different odors as the 3% of our genome is constituted by receptor proteins. However over the years due to mutations humans have lost the ability to identify over 300 scents. The slightest change to gene can affect its ability to sense an odor.  Humans only possess air sensing proteins and fish only have water sensing proteins. Amphibians however possess both. Cetaceans on the other hand present another interesting effect. Of all the thousands of scent genes, not a single one is functional in dolphins and whales. Losing them does not affect the fitness of the organisms.

CHAPTER 7:: ADVENTURES IN BODY BUILDING

Q Elaborate on the polymorphic characteristic characteristics portrayed by cells.

- Organisms are classified as single celled organisms and multi-celled organisms based on their size. Fossils prove that single celled organisms have evolved before multicellular organisms, as they are less complex and utilize a lesser amount of energy. Multicellular organisms require large amounts of energy, in order to supply energy to a numerous cells. A cell that uses oxygen produces 20 times more useful energy than a cell that does not. 

- Martin Borass performed an experiment in which he grew algal cells for a thousand generations, after which a predator was introduced.  Masses of algal cells were held together by proteins and other cellular produced compounds between the 10^th and 20^th generations.  Within another few tens of generations, the size of the proto-bodies became stable at 8 cells per body.  This size was large enough to prevent the predators from eating  the cell mass and small enough to ensure that all the 8 cells would get sufficient nutrients.  The cells had formed the first proto-body, for the first time.

- Volvox is a colony of green algal cells, which have begun specialize, thereby showing traits of polymorphism (when two things doing the same thing, one can change/evolve and the other can continue the original task). When a volvox cell is split in half, two smaller cells are produced. However when a human cell has been split in half the cell can no longer survive without the presence of other organelles.

CHAPTER 6:: THE BEST- LAID (BODY) PLANS

-All tetrapods have the same body plan, one head and four limb arrangements. This chapter also introduces a new term atavism, which is the reappearance of traits that had disappeared generations ago.

-The sixth day after conception, the zygote which has been duplication eventually forms a blastocyst which is embedded into the lining of the uterus wall. After implantation the cells begin individualizing. Within each organism a hollow tube, consisting of three layers is formed. One end of the tube becomes the mouth , the middle section becomes the digestive track and the other end becomes the anus. The three layers of the tube then constitute the various organs of the organism.

- The specific differentiation of the tube into these three major regions is due to the presence/ absence of a certain set of chemicals which are produced by the cells themselves. The region with a high concentration of these chemicals turns into the head; subsequently the region with a low concentration becomes the anus.

- The same genes in every organism result in the formation of these chemicals and thus in the formation of such tubes.  Sea anemones have sides, a front and a back.  Even though they are radially symmetrical (humans and most other animals are bilaterally symmetrical), they still have a head region and a tail region.  Those same genes that form the head and tail ends are in other animals, including humans.

CHAPTER 5:: GETTING AHEAD

Q: How can the branchial arches provide evidence to common ancestry?

 

- The head is one of the most substantial parts of the human body, as it houses the brain. It might be astonishing to realize that the human's head and a shark's gill originate from the same pieces of an embryo. Every vertebrate animal starts with these four arches known branchial arches, having the same shape. They are labeled as 1, 2, 3 and 4.

- In humans, the first arch develops into the upper and lower jaw, the malleus and incus bones in the inner ear, and the blood vessels and muscle that attach to them.  The second arch turns into the third ear bone (stapes), a bone in the throat, and the muscles that control facial expressions.  The third arch forms the muscles, bones, and nerves of the throat (swallowing).  The fourth arch forms the larynx and other parts deep in the throat.

- Whereas in sharks the branchial arches develop into the different features. The first arch becomes the jaw, same as us.  The second arch in sharks becomes a bar of cartilage and muscle.  In humans that bar breaks up to become the stapes and some small structures of the throat.  In the shark, the bar becomes the structure that allows sharks to extend their jaw slightly out of their mouth while feeding.  The bone that allows this in sharks, if you carefully trace its evolutionary history becomes our stapes.

- Humans sometimes get ruptured disks in our spines.  Those disks are a holdover from Amphioxus, a worm.  A non-vertebrate that does have a notocord and gill slits, the precursors of our own spine and allowing to speak