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Species and their classification

Taxonomy refers to the classification of living things by giving unique names to each species, and creating a hierarchy based on evolutionary descent. This is a challenging task, as most species that have ever lived on this planet are now extinct, and many more alive today have yet to be discovered and classified.

In order to achieve the above, though, we need a definition for both species and hierarchy. In the old days, a species was known as a collection of individuals similar enough in resemblance to be put in the same box. This was purely based on physical features. Today we know that similar physical characteristics on their own aren't enough to define a species.

species is defined in terms of observable physical features as well as the ability to produce fertile offspring.

This is Hercules, the liger. Hercules has a lion father and a tiger mother. Does that mean tigers and lions are really one species? This is one example of the issues surrounding both the definition of species, and taxonomy generally.

What is a hierarchy? A hierarchy, put simply, is a system of classification comprised of small groups contained within larger groups contained within larger groups, and so forth, where there is no overlap.

The above diagram is a phylogenetic tree. It is a representation of various species in terms of their genetic relatedness. Each "crossroads" is a different ancestor. From this diagram it is easy to see that humans are more closely related to whales than to birds, or indeed any other species represented.

The species with a red circle beneath are extinct. If a phylogenetic tree was made with all species that have ever lived up to today, the vast majority would be extinct. 

Aside from simple observable features and their similarity, advances in immunology and genome sequencing can add to the information required to create, maintain and update the tree of life according to new findings. Different organisms' genes, proteins and physiologies can be compared to see how closely related they are.

The names above are used for convenience, yet the scientifically correct way of classifying organisms is by giving them a two-word (binomial) name. These names are in Latin or Greek.

Let's take Homo sapiens for example (us!):

1. It's written in italics as all species names should be, by convention.

2. It's made up of two words: Homo and sapiens.

3. Homo denotes the genus to which the species belongs to. A genus is the group higher than species. For example, Homo erectus and Homo neanderthalensis are part of the same genus as Homo sapiens (both now extinct). That genus is called Homo... getting the hang of it?

4. Sapiens denotes the species itself, and is the smallest group in the hierarchy.

What does the rest of the hierarchy look like?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (fearing you can't possibly remember this sequence?)

Dazzling, Kinky, Policemen, Can, Often, Find, Gay, Sex. You're more than welcome.

Determining evolutionary relationships between species

In the era of molecular biology, we no longer have to rely on superficial visual cues only in order to classify species. We can look at and compare their DNA, proteins, etc. A common method of visualising these differences is gel electrophoresis which involves loading small volumes of samples on a gel and running a current across it in order to separate the samples by size.

Since the gel has a microscopic matrix inside that provides resistance against sample movement through it, the larger molecules move more slowly while the smaller fragments can move more quickly.

The positive charge is at the bottom of the tank, while the samples are loaded at the top. This way, they will move downwards towards the bottom of the gel because they have a negative charge as molecules. The current is run across the gel for around 30-60 minutes (ensuring the samples don't run too long and hence run off the gel into the buffer solution! if that happens they are lost) after which the sample's progression on the gel can be visualised by using a stain solution or pre-existing coloured label visible under UV light.

The protein or DNA samples for example can come from the different species' muscle or some other tissue source. DNA samples can be replicated in the lab using specific primers (in PCR) to make certain genes or sections of DNA that are to be compared and looked at on a gel. Alternatively, all present proteins in a sample can be investigated by running the whole sample on a gel and comparing the differences.

The bands on the gel might look something like this. Based on the height on the gel of the different bands (which represent different proteins in the sample), we can see that all species have the band at the top. This is a protein of the same size that they all share.

The second largest protein (the second highest band on the gel) belongs to Species Y and is unique to it, not being shared by the other species. Same for the third one down of Species Z. Looking at all the bands for each species, we can see that Species A and Species Z share the most bands in common (3), so we assume from this data that based on their proteins, Species A and Species Z are the most closely related compared to any other species combination here (A, X, Y, Z).

With advancing technology, scientists no longer have to rely on capturing animals or gathering data manually in the field. Bioinformatics enables the analysis of a whole genome from a computer. Once the initial DNA sequencing has taken place, a lot of research can be conducted just from that data. For example, the DNAmRNA or amino acid sequence between two individuals or species can be compared.

From this short sequence of amino acids in the haemoglobin of these different species we can infer several things. Let's do humans and chimps first! How many differences are there? Lys, Glu, His, Iso and... Lys, Glu, His, Iso. Right. Absolutely no difference. Humans and gorillas have one difference, zebras and horses have one difference and zebras and humans have 3 differences!

We can infer a lot of different information from this table, and it's just a very small sequence in just one protein looking at just five different species. The potential of investigating diversity with molecular biology tools is astounding.

DNA can be studied similarly, and a lot of creativity can be employed to come up with ways to twist and turn heaps of genetic data in such a way that interesting information can be pulled out. In this example, it's a fairly straightforward, run of the mill comparison between the DNA sequence itself of a mouse gene versus a fly gene.

We can see that the sequence itself is 76.66% identical, while the protein product resulting from the exons only, is actually identical in its entirety at 100% between the two sequences (highlighted in green). 

Evidence and the scientific process

As you can see, data comes in many different forms and from many different sources obtained in many different ways, so curating it all together in a specific field or to answer one question is a big task.

Humans are still happy to attempt this task, even though it is clearly one for the machines to tackle. Soon enough this will be the case, however for background or at least a history lesson, here is how things run with humans involved.

Scientists strive to publish their work in scientific journals which are ranked based on the popularity of their content in terms of how many new scientists refer back to older work by previous scientists (or sometimes their own previous work!), and carry out the peer review process which attempts to act as quality control on the work submitted for publishing.

Peer review means that scientists in a relevant field to the work submitted comment on the submission. This informs the journal editor in their decision to accept or reject the submission, sometimes subject to new work being added onto the submission, or changes to be made.

This process is very poor and has fallen victim to many fundamental issues: personal issues between scientists, peer reviewers and editors, as they can often be working together or competing; personal-political issues between scientists, institutions and private companies, as vast funding, reputations and relationships can rely on certain work being published in a certain journal at a certain time; human error, as the process often relies on as few as one or two peers judging one submission.

The publishing process itself can take as long as months or years to complete, and the top journal which is Nature is a for-profit organisation which fuels this broken system and routinely rejects most of its submissions, even though they are perfectly valid and often end up being published anyway in a "lower" journal. Hence, an artificial hierarchy is established where amazing and groundbreaking work simply does not have space in the limited space of the overly glorified and undeservedly attained top spot that just one journal has, of hundreds of others.

Quite literally scientists are forced to make it their career goal to publish in Nature or Science, and one can see the level of corruption this type of mania can entail. There are cases of withdrawn submissions, outright data fabrication and exaggeration and this type of outrageous outcomes that do nothing but hinder science and scientists.

Another sphere of scientist communication (what is one to do with months between publishing and not being allowed to disclose anything prior to publishing to prevent someone else "stealing" the idea?) is conferences. These are meetings, some generic and some very specialised, where scientists in the field deliver presentations and exhibit posters of their latest work, and network with others to catch up with what everyone is up to. This is where one might find out what someone is working on before their work is actually published.

Three domains or five kingdoms?

An example of the role of the scientific community in validating evidence is the classification of life into 3 domains versus 5 kingdoms. Archaea, Bacteria and Eukarya or perhaps Monera, Protista, Plantae, Fungi and Animalia

Domains are higher up than kingdoms, so refer to the very earliest differences between living things. Originally, the kingdoms were established based on superficial analysis of different organisms, and an even earlier classification called Linnean classification simply split everything into animals and plants, based on whether they moved!

Monera (or Prokaryotae) kingdom was split into bacteria and archaea because very fundamental differences between these organisms were found as a result of better comparisons such as molecular biology techniques such as those outlined above. The remaining 4 kingdoms could then be grouped under Eukarya.

The response of scientists to this evidence follows that older evidence was treated differently in light of newer, more insightful evidence. Evidence can always build up, break down or change in other ways to change our understanding of life. At first, archaea and bacteria looked similar, so they were treated as closely related. As their inner workings were investigated with the use of more sophisticated tools, it became apparent that their characteristics beyond appearance were very different.

Ok byeeeeee

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