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Showing posts from November, 2014

### How To - Variance & Standard Deviation

Hey Guys, today we do a quick intro on some basic terms and formulas that are used frequently in statistics

- Mode or Modal Value, Middle Value, Median, Variance and the Standard Deviation

We have a class of 8 Girls and 8 Boys, so a total of 16 kids. To get the Modal Value (m) and therefore represent the level of the whole class, we count how often each grade showed up - in our case 2 and 3

Next comes what probably everyone did at least once in school; calculate the class average or our Middle Value (a small X with a line over its top; sorry I can't write it out here .__. )

Using the Median is actually just being nit-picky, but good to know. In case your teacher breaks into your house in the middle of the night and wants to know... you will probably never use this one in your life
For uneven: look for the middle number
For even: look for the two middle numbers, sum them up and divide by 2 - that's your median

The formula for Variance may look difficult at first, but you just subtract…

### Metabolism - Biochemistry

Hey guys - although we entered into Biochemistry with the post about Glycolysis
I have a little summary here,
what metabolism in general is going to be for me, during this semester.

"Metabolism is the summed up lot of chemical reactions in our bodily cells, which we living organisms need to extract energy (in form of food and minerals) to perform actions, grow, heal or improve our physical self."

Because energy seldom comes in the form our cells can use it right away, we need processes to breakdown bigger chunks - catabolic processes - i.e. Glycolysis (greek for sugar-splitting), I mean this example is awesome, because stuff is literally being broken down.
And also energy is won from this reaction.

On the other hand side, we are not just a machine that consumes and spits out product 1:1
Our body has the possibility to store energy for later on
(yeah, shake that fat belly - don't worry it's potential energy is over 9000).
ANYWAY. So called anabolic processes release energy, or…

### How To -Glycolysis - Biochemistry

We are starting into a new semester and that means I am getting into Biochemistry II with you guys.
Main Topic this semester will be the metabolism and from experience I can say, the most difficult part is to remember all the different steps in the many metabolic cycles our body needs to stay functioning.

Glycolysis happens generally in 10 steps and is the process of breaking down glucose into smaller sugars

The reaction itself takes place in the cytosol and after investing 2 ATP you get 4 ATP and 2 NADH

First Step: Phosphorylation of Glucose
Enzymes: Hexokinase aka Glucokinase
Components: Glucose, ATP

Hexokinase catalyses under exclusion of water the two components glucose + ATP , the product is now negatively charged and therefor caught in the cytosol

Second Step: Isomerization
Enzymes: Glucosephosphate-Isomerase
Components: Glucose-6-Phosphate

This reaction is essential for step four, because only from fructose you can derive two C3-molecules.
Without isomerization, we would get a 2C-molecule …

### Problems fixed!

So I managed to save my pages, books and about are fixed now^-^
It was a compiling mistake, which I don't know how got into there ._. but it's gone, for now.

### The Evolution of Sex Part 1

First of all, we still don't really know why sex developed in the first place.
I mean for all the longtime singles out there, who desperately want a baby to give on their genes to the next generation (if you really just want to reproduce... uhm, maybe go and see a psychologist first?)  - things would be so much easier if they could just duplicate themselves.

VoilÃ¡ - perfect copy.
But you see, the problem here is - it's just a copy. There is nothing new about it. This might work for now for you, but we live in an ever-changing world. Technology changes and if you don't adapt, you will find yourselves as clueless about gadgets just like your grandma when you first tried to explain to her how CSGO Players talk to each other via teamspeak in-game.
But no innovation isn't the only problem. What if your genome suffers a deleterious mutation? You can't go to one of your other clones, that didn't have that mutation and say "Oi, give me that, mine broke" Because you …

### How To - ELISA - Methods in Biochemistry

That's a beautiful name, not the one of a young lady but rather stands for Enzyme Linked Immunosorbent Assay.
This is a method very commonly used in labs and the mandatory practical class for Biochemistry.

It is based on an enzymatic interaction between antibodies and the kind of substance you want to detect;
almost everything is possible - proteins like antigenes and viruses, hormones, and other organic material can be traced with this method.

Below with the green color, you see what a finished ELISA looks like. Some of the s.c. Eppendorf tubes are heavier on the green, while others don't show any kind of color reachtion at all:

In the following picture you can see how the process works as ELISA sandwhich method (the indirect identification of a substance):

In picture 1 you see the green 'Y's (representing protein-specific antibodies), they are fixed to a to a surface. Above them, the substance we are oh-so-interested in comes flying by.
Next you see that the proteins/subst…

### Current Projects

Hey there, coming week I have midterms for Methods of Biochemistry 2, simultaneously I'm reading "the search for the oldest stars" by Anna Frebel.
I reached page 92 today, and so far I can say this book easily communicates Astrophysics in an understandable form. It is very interesting and not dry-written at all; my only concern lies in how much emphasis the author put on the work of female scientists and assistants in her book. Don't get me wrong, there is still a huge gap of recognition between the same amount of work men and women do, and it is of grave importance to remember who contributed something truly and not only because they were more accepted at the time (not only female assistants and scientists, but also jewish, who were prosecuted before and during WW2 i.e.) Miss Frebel seems to fangirl during the chapters which already I read, about science and especially the women of science. But that's just something I noticed. After all she dedicates this book to &q…

### Bill Nye fights Creationists and Burnout

The day has 24 hours and although we never fill them, I feel tired in the morning. Even when I get to bed at 10pm (which is early - me grownup, me no need for sleep) or so, in the morning I feel fatigue already :/

Nonetheless, thinking about projects keeps me moving. For those who don't know me - I am currently doing some stuff:

I am taking my driving licence now (yeah I am 21, but fuck you if you laugh about that xD ),
Next month I am moving from my current student apartment into another place,
I got the first EvoGen exam coming up, as well as Methods of Biochemistry 1...,
And to top it all off... I need to remove my wisdom teeth.

of all this only the last point makes me worry though. But it is necessary... all my friends scare me that it is very painful to remove them under local anaesthesia >__< and truth be told, I hoped after my milk teeth and my braces that this was the last time I'd to go to a dentist for more than just a checkup.

But every cloud has their silver lining:

### Genetic Mutation

Mutation
The ultimate cause of all genetic variation is mutation. It occurs either during replication or under the action of a mutagenic agent, i.e. a chemical or radiation.
They can happen in somatic cells and in germ -line cells, but only mutation in germ-like cells have an evolutionary consequence.
There are a larger number of cell divisions involved in the male sperm line than in the female germ line, therefore more new mutations are transmitted through sperms than eggs.

The different types of mutation can be distinguished:

Gene mutations:
a) Point mutation: one base mutates to another
b) Frameshift mutation: insertion/deletion of a single base/short stretch of nucleotides, which shifts the whole reading frame

Chromosomal mutations
c) Duplications/deletions: “in-dels”, possible due to slippage or unequal crossing-over
d) Inversions: reversal of DNA order
e) Translocation: exchange of segments among non-homologous chromosomes
f) Fissions/Fusions: chromosomes merge or one becomes tw…

### How To - Hard-Weinberg Equilibrium - 3. Lecture

Okay, this one is not a complete summary, but rather a How-To for Population Equilibrium.
Should take about 5mins!

Hard-Weinberg Equilibrium

The Hard-Weinberg-Principle is mostly used to count and calculate population,
but with the side note, that the population we want to work with, is an ideal population.

There is no evolution, no natural selection, we just look at the state the group of animals is like, at this very moment.

The HWE itself is simple, it looks like the binomic equation you probably got to know in high school.
Our population is a bunch of sheep, 1000 to be frank.
Of those sheep, 18 are black - black being recessive, the other 982 sheep are grey-ish.
Now I want to know how many of those are pure grey sheep and which are heterozygous grey-ish-black-ish sheeps .___.
Because we look at all possible constellations for 2 allele (p and q), there are 3 possible phenotypes:

(p + q) x (p + q) ==> p^2 (black) + q^2 (grey) + 2pq (grey-ish-black-ish BUT THEY LOOK FUCKING GREY)

Another th…

### Paleoevolution & Fossil Records - 2. Lecture

Paleoevolution & Fossil Records

Fossiles are defined as trace of past life - such as body parts, footprints and moulds, left as indents of organic matter or other kinds of thinkable traces.

Fossilisation can only occur if remains of animals are covered by sediments (sedimentation) before they decay (microbial action, scavengers).
The fossil must be preserved and eventually found. The change for any organism to leave a fossil is therefore generally very unlikely and depends on:
where organism lived
- within sediments better than elsewhere
- surface sediment > water column
- marine > terrestrialtype of organism
- large > small
- have skeletons/shell > soft bodied formsGeologists use relative and absolute techniques to date events.
Radiometric dating infers the absolute geological time:
It uses radioactive decay of isotopes (rubidium isotope 87Rb decay into strontium isotope 87Sr with a half-life(HL) of 48.6 x 10^9 years)

Radioactive decay proceeds exponentially constant and measura…

### Evidence for Evolution - 1. Lecture

This little series here covers the summaries I write for my EvoGen lectures, maybe somebody finds them helpful :)

Evidence for Evolution

Definition - the development from a simple to a complex formed organism (i.e. Procaryotes => Eucaryotes)

Lamarckism - theory of soft inheritance, inheriting traits that an organism acquired during its lifetime and passing it on to its offspring

Darwin

1) Final genetic process - Speciation; phylogenetic tree
2) The main mechanism of evolution is natural selection

Evolution is a phylogenetic process

In order to demonstrate Evolution in the sense of Darwin, there are 3 Points that need to be shown:
Species can go extinctSpecies can change over timeSpecies trace back to a common ancestorThree lines of evidence that can be used to prove these points are 1) Fossil record, 2) Embryology & Anatomy, and 3) Biogeography

Extinction of Species
The main source for the fact that species can go extinct, comes from the fossil record.
Aside from that scientific paleonto…

### Remember, remember the 5th of November

One of my favorite movies.

How often do I hear this sentence, every time when it is not us, ourselves saying it I cannot help but wonder. If it is true, truly something people fondly think of when remembering the short flicks on polaroid^^
V for Vendetta, I tend to like movies with an action filled plot, but mostly I like intriguing, charismatic and strong characters. Something we can identify with, i.e. Nothing pisses me personally off, like a whining, weak damsel in distress - weeping to be saved or at least spared.
People only intrest me if they grow in the face of struggle. That thought sometimes scares me of myself, what happens if I should stop growing? What will we become if we loose our drive?
Now that is something interesting to think of ;)

A happy 5th November to you - try and do something that interrupts the system in a POSITIVE way. For the greater good and stuff

### How To - Markov Models

Today in preparation for my upcoming exam I want to show you how to work with Markov Models.
This is one of the easiest parts of statistics, so bear with me and we get through this in no less then 5min ;)
Ok and I haven't yet figured out the HTML code to align my pictures correctly - so for all OCDs out there, I am so terribly sorry...

In a Markov Model, we work with states and their respective probability to transfer into a different state.
In our example you see the states written as z (z1, z2, z3) and their probabilities written in green (i.e. state z1 has a transition probability of 1 to transfer into state z2).
You can also see, that states can choose to stay in themselves, and not transfer into another state - with an arrow circling back to them.

We will create a matrix named M to store our transition values, this makes it easier to calculate with them.

Note: because we are working with probabilites, the values we work with can range  from 0 to 1 (it doesn't happen or it happens…