Relationships & Biodiversity

Original notes by: Lauren F.
Typed up by: Katelyn C.

Relationships and Biodiversity

Molecular Evidence

What are some markers of Biodiversity that have been identified in the Natural World?

Well, let’s look at a few:
Phylogenetic distance; Phylogeny- The study of the evolutionary history and relationships among individuals or groups of organisms
Fossil Record- imperfectness
*Genetic Analysis- Mathematical Sequencing- Technology*
Proteome (complete set of proteins expressed by an organism); Microbiome (The genetic material of all the microbes); Analysis (Current)

Questions about proteins?
-Proteins contain Carbon, Hydrogen, Oxygen, and Nitrogen. Some even contain Sulfur.
-Proteins are mainly used for the growth and repair of cells.
-Their building blocks are called amino acids, in which there are 20 different kinds
-Proteins are found in hemoglobin(carries oxygen), skin pigments(melanin), hormones, antibodies, enzymes, hair/nails, and cell membranes
-Proteins are composed of one or more polypeptide coiled or folded in a specific way. Polypeptides are chains of amino acids
What happens when the body takes in proteins (pick a type of amino acid) and digests it?
-When the body takes in a protein it sends it to the stomach, where through the process of mechanical and chemical digestion will proteins be broken down small enough to pass through cell membranes into the body tissues to be used as nutrients
Are there examples?
The digestive process takes, on average, 12-24 hours. Proteins begin their journey, as do all nutrients, and travel to the stomach. Here, hydrochloric acid and pepsin break down protein into peptide chains (A peptide bond is the bond between 2 amino acids, so a peptide chain would be a chain link of peptide bonds). Proteins finish their journey in the small intestine, where peptidases snip peptides into amino acids for absorption
How do proteins interact with other proteins?
As we’ve read from earlier, proteins are typically linked together, which helps us to see how they never act alone. These links are called, as previously mentioned, peptide bonds. These are formed by a biochemical reaction, called dehydration synthesis, where one water molecule is extracted as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid.
What could a mutation do in terms of its effect on a protein?
(This information came from help from the below link)
There are many different types of mutations that could affect protein function. A missense mutation changes an amino acid to another amino acid. This may not have a drastic effect on the protein, depending on what the amino acid actually does. A nonsense mutation changes an amino acid to a STOP codon, resulting in premature termination of translation. A silent mutation doesn’t change the amino acid, but can have a phenotypic effect by speeding up or slowing down protein synthesis. A frameshift mutation consists of a deletion or insertion of a number of bases that is not a multiple of 3. This will usually introduce premature STOP codons, as well as lots of amino acid change

What are plant proteins? Could they be interacting with our immune system? I.e allergies- food & environmental

Plant proteins are proteins that originate from plants. They will interact with our immune system, as the nutrients we obtain from these plant proteins from digestion will greatly help to make us feel stronger and better. These proteins could also trigger an allergic response, as they are a foreign entity that would enter our body. Antibodies can bind to the surface of mast cells, which contain histamine and can trigger an inflammatory response.

Biodiversity
Measure of type of organisms in a location

Eco-stability- When the different groups of organisms in an environment and the resources are in an equilibrium of each other

Darwinian Finches- Charles Darwin observed finches on the Galapagos Islands, and noticed how the finches on one island were different than those on another island. The differences were most notable in the beaks that the finches had. Some beaks were short and fatter, and some were longer and thinner. This was because finches on one island had more access to nuts and berries, while the others had better access to eating things like insects. He concluded that these species had adapted to the environment in which they were living in, and that not only the finches did this, but ALL species living on Earth arrived to their current form through centuries of Evolution and Adaptation.

Evolution by Natural Selection- 1. Some characteristic of trait (variation) must exist that is 2. at least partially hereditary. 3. Some variants must survive and reproduce in greater numbers

A population undergoes Evolution

We also see cool relationships between living systems. One modality of interconnection- symbiosis- shows the delicate balance and intricacies of the natural world at its finest

Think about the importance of balance and homeostasis in systems. A system must “calibrate” in order to work efficiently. Like a suspension bridge

In the case of a bridge, there is a range of weight/force it is built to withstand

Is it OK to think about our genetic code like this bridge? A system- a sequence of codes that allows for excess force, integration, and possibly even- dare I say it- expansion?

Think of the Prefrontal Cortex- and think neuroexpansion- think “junk” DNA as a seed that will emerge under the right circumstances as an aggregate of mutation and heredity- which is only plausible as genetic sequences are exponential functions.

Next, we must think about limits, and wonder if this is the sort of “critical density” in which the code mutates to the point that one mutation works with another to produce a “tertiary” effect- therefore, we observe neurological phenomena such as synesthesia. Synesthesia is a neurological condition in which stimulation of one sensory or cognitive pathway leads to automatic, involuntary experiences in a second sensory or cognitive pathway.

Introduction to Topics in Evolution

“Light will be thrown on the origin of man and his history” are the notable words of Charles Darwin in the introduction of The Descent of Man (1871).

Evolution arrose as a controversial topic, initially during the 19th Century. Much of the controversy derived from conflicts between religious or spiritual beleifs in creationism and naturalism and contentions were wagered against the ideas involved in the new theory that undermined those beliefs. Even those who accepted the theory as it applied to all living taxa, refused the idea that humans may have decended from ape-like ancestors.

Thomas Henry Huxley, a collegue and friend of Darwin, adressed the topic of the ancestral origins of man in Man’s Place in Nature (1863) while Darwin developed his ideas about the origin of humans in The Descent of Man (1871), shortly thereafter. He effectively predicted that our human ancestors would be found in Africa.

We should also know that Darwin was heavily influenced by the work of the Geologist, Charles Lyell. During Darwin’s time as a naturalist aboard the HMS Beagle, (when he made many notable observations that would lead to the development of his theory decades later) he kept volumes of Lyell’s, Principles of Geology (1830-1833). These works introduced Darwin to the topic of Uniformitarianism. Lyell’s ideas suggested that geological and biological forces were working the same way. This culminated in an old-earth theory, which suggested that the universe was billions of years old and therefore so was the earth. These theories worked as a framework in support of gradualism.

In time, the theory was accepted by the general population and the previously challenged notion of common descent or that we evolved from ape-like creatures, was thought plausible.

Intially, much of the evidence in support of the origin of man came from the clues offered by the fossil record.

Some fossil specimens seemed to have features that did not reflect as analogous to modern man. For instance, several specimens appeared to have smaller brains. (We compare the characteristic morphological features evidenced in the Fossil craniological record to make predictions about the brains of ancestoral humans.) While not as apparent in intermediate species, characteristics in the latter forms of fossil specimens bore more apparent similarities to those observed in modern man.

It would make sense that the newer forms came after the earlier forms- however -for the fossils that are dated to around similar timeframes, we can also make comparisons between their derived characterisitcs and observe how they link to another. This is how we come to understand which fossils specimens are our human relatives.

The incompleteness of the fossil record had possed challenges wherein intermediaty species are missing, and this is why, with new fossil discoveries, the human phylogeny is sometime redefined. The incompleteness of the fossil record basically means that there are missing and partial specimens. From this, we derive limited information about the progenitor forms. If we find a characteristic part of a fossil specimen such as teeth, we may be able to determine by looking at the characterisitcs of shape, size and thickness, how much the specimen relates to the other forms in the fossil record. Teeth and clues, to spur our scientific inquiry.

What we do see in the human family tree, is that most of the earliest forms appeared on the African continent.
Ardipithecus ramidus, the earliest known member of the human lineage was discovered in 1993 by Tim White, Gen Suwa, and Berhane Asfaw at Aramis, Ethiopia, and dated to 4.4 million years BP. The canine teeth are somewhat reduced from the primitive ape-like condition, but not so much as in Australopithecus (australopithecines); the enamel on the teeth is thin; the deciduous molars are intermediate between those of a human and a chimpanzee. The postcranial skeleton indicates that it was, at least to some degree, bipedal.

Another interesting specimen of the Australopithecine genera, specifically, Australopithecus afarensis, is one of the oldest intermediate specimens in the fossil record, to date-Establishing a fossil timeline of evidence for the age of man and his ancestors.

One primary way in which we can date fossils is by dating the sedimentary layers they are found in, along with the more standard, carbon dating procedure. A. afarenis, also called informally, Lucy, likely originated in East Africa about 3.75 million years ago but it has also been claimed that fragments found in Kenya, of similar bones, appeared as early as 5 million years ago.
Australopithecus africanus was found in South Africa and is said to have lived 2-3 million years ago. Fossil skeletal remains of A. robustus/Paranthropus were also found in Kenya and are said to have lived 2 million years ago. A. robustus/Paranthropus is likely an intermidiate form linking Homo habilis and Homo erectus.
We know that the Australopithecine genera share the common feature of a small brain by studying cranial structures of fossils, as mentioned above. By comparison, we know based on the structure of their hip bones that they were bipedal and had the ability to walk upright similar to modern man.
Bipedal ability became the characteristic that linked certain fossils to a human lineage while the size of the brain was no longer emphasized as a requirement for phylogeny.

In March 2005, a partial skeleton from Ethiopia was claimed to be the world’s oldest bipedal hominid, dating from about 4 million years ago. It has not yet been classified or published in the scientific literature (2010) though it is said to fall between Ardipithecus ramidus and Australopithecus afarensis. It was found about 40 miles from the famous Australopithecus afarensis hominid, Lucy, who lived 3.2 million years ago and is thought to have given rise to the Homo line that ended in modern humans.

Lucy is the matron of our familial heirarchy of close fossil relatives and paradoxically one of the oldest fossils of the homo lineage found to date.
We have the example of a hominid fossil, Homo erectus, initially called Pithecanthropus erecturs and dubbed the nickname, Java man. It is beleived that homo erectus was the first hominid to appear outside of the African continent about 1.8 million years ago.
Notice that the oldest fossils of the homo lineage was discovered in… you guessed it, Africa! This evidence combined with the application of new molecular technologies to the study of archaic and present day genomes, led to the “Out of Africa Hypothesis.” When you consider and think about this hypothesis, think about what the earth may have looked like from a satellite, about 4million years ago. Consider that at one point, all of the continents were grouped into a supercontinent, called Pangaea. How may this have influenced our ancestors? Were they always in Africa? Did they migrate to there? Was it that the conditions in Africa existed in favor of creating fossils? Remember that anywhere fossils are found, there tends to be evidence of catastrophism. It is possible that the geological setting on other  Continents was quieter this part of the world? Think, Gradualism vs. Catastrophism.

Geneticist Luigi Luca Cavalli-Sforza had begun a new area of research by combining concrete findings from demography with a newly available analysis of blood groups in human populations to investigate the origin and diversity of human populations. Building on the work of Cavalli-Sforza, in 1987, Wilson with coworkers Rebecca Cahn and Mark Stoneking announced that they had evidence that the most recent maternal ancestor of all living humans was a woman living in Africa about 200,000 years ago. Based on analysis of mitochondrial DNA (mtDNA) taken from 147 individuals representing different races and geographic origins, this became known as the “Garden of Eden Hypothesis.”
Once again, a new scientific finding caused considerable controversy as well as a lot of misunderstanding of what Mitochondrial Eve represents.

When we study the out of Africa hypothesis, or the Eve hypothesis, named after the biblical Eve- (See, The Adam and Eve Creation Story in the Book of Genesis)-  we learn that mitochondrial DNA is being traced back to a common ancestor. It is important to note that mitochondrial DNA (mDNA)  is only inherited and passed on through the maternal line. (To study patrilineage, we look at haplogroups) Therefore, we must ask ourselves, how did our common female ancestor aquire mitochondrial DNA? It seems that here, the Endosymbiotic hypothesis becomes relevant in ways yet to be explored.  I hypothesize that Lucy is not necessarily our FIRST female common ancestor, insomuch as she is the first ancestor to have acquired mitochondrial DNA through an ancient Eubacterial proliferation leading to genomic integration. This  could have possibly changed the genetic code from that moment on, therefore leading us to believe that the last female ancestor was Lucy.  It seems to me that Lucy is more likely to be the most recent female specimen to have acquired mitochondrial DNA and there may have been progenitors before her.

 

As The fossil record becomes more complete, in-time, with new discoveries, we will continue to learn new things about our ancestors and perhaps more secrets hidden within our genetic code!

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