Visualizing 11 Dimensions

The 11 dimensions predicted by string theory ( M-theory also) can sound like physics voodoo when you first hear about it, but it really isn't too hard to imagine as some physicist will have you believe. I will try and briefly explain where all of these extra dimensions come from...

We all know of the first 3 dimensions in space and the 4th through time (Yes classically the 4th dimension is time and not air being blown on to you like in a 4D experience ride). But where do the other 7 come from? Imagine some spheres, with there 3 dimension, all lined up together in the three dimension that you experience on a day to day basis. That is 3 sphere dimensions in each of the 3 classical dimensions, 3*3=9, giving 9 dimensions. But now you are thinking "A normal sphere has only three dimensions so no matter how many spheres you have it will still only be in three dimensions!?" Well yes this is 100% true. Mathematicians and physicist get around this by explaining these spheres' dimensions as "dimensions folded in on them selfs", so what we experience as 1 dimension is actually three! 

The last 2 dimensions are easier; the first being time, which we all come across daily but yet is arguably the hardest to visualise. The second though is slightly easier to imagine though sounds very impressive. Curved space. When it comes to this dimension just try to think of the little spheres lining up in a way such that they are simply curved if you were to look at them from a great distance away. This means that what we would experience as travelling along straight line with all of our best instruments telling us so is actually not truly straight. Almost like walking in a seemingly flat straight line around the Earth would be curved because the Earth is round.

To sum up, 11 dimensions aren't as hard to imagine as you would first think. You have the first 9 with three dimensions folded in on them selves in the three dimensions that we experience every day. The 10th is curved space, or just those spheres lined up around a curvy bend. And finally the 11th is time which I am running out of.

Ten (Fairly) Detailed Steps to Glycolysis

Glycolysis is a process that cells use to convert glucose, with the aid of two molecules of ATP (adenosine triphosphate) to two molecules of NDAH (reduced nicotinamide dinucleotide amine), four new molecules of ATP and two molecules of pyruvate.

Step 1: Glucose is phosphorylated by ATP and the enzyme hexokinase, to form the sugar phosphate; glucose 6-phosphate with a negative charge, preventing it from travelling through the plasma membrane of the cell, stopping it from escaping. This step also produces one molecule of ATP and a proton. 

Step 2: Isomerization of glucose 6-phosphate occurs; switching the ring form of glucose to its open chain form. This initial part of step two is very reversible, however equilibrium lies to open chain side due to the negative charge on the phosphate (on carbon 6) and the aldehyde on the first carbon. Phosphoglucose isomerase then changes the structure of the sugar phosphate, making a ketone group on carbon 2, thus meaning carbon 1 is left as a hydroxyl group (CH2OH). The resulting molecule being fructose 6-phosphate.

Step 3: The new hydroxyl group is phosphorylated by the second ATP molecule. Phosphofructokinase binds the phosphate group from ATP to the fructose 9-phosphate, creating fructose 1,6-bisphosphate and ADP. The entry of sugars into glycolysis is controlled in this step, through the regulation of the enzyme phosphofructokinase.

Step 4: Next the fructose 1,6-bisphosphate is split up by the aldolase enzyme, making dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate proceeds immediately through glycolysis.

Step 5: The other molecule made in step 4, dihydroxyacetone phosphate, is isomerized by triose phosphate isomerase in a reversible reaction to form another glyceraldehyde 3-phosphate molecule.

Step 6: A covalent bond is formed between glyceraldehyde 3-phosphate and the -SH side group of the enzyme  glyceraldehyde 3-phosphate dehydrogenase, which binds ionically to NAD+. Oxidation of  glyceraldehyde 3-phosphate occurs as a hydride ion transfers to bound NAD+ forming NADH. Part of the energy released during this process goes towards turning the bond between the enzyme and  glyceraldehyde 3-phosphate into a high energy thioester bond. A molecule of inorganic phosphate displaces the high-energy bond to create 1,3-bisphosphoglycerate containing a high-energy acyl-anhydride bond. 

Step 7:  Next the high energy bond to the phosphate is transferred to ADP to form ATP. Leaving 3-phosphoglycerate.

Step 8: The phosphor ester linkage on 3-phosphoglycerate is moved from carbon 3 to carbon 2 by the enzyme phosphoglycerate mutase, forming 2-phosphoglycerate. 

Step 9: Removal of water from 2-phosphoglycerate with aid of the enzyme enolase creates a high energy enol phosphate linkage, creating phosphoenolpyruvate.

Step 10: Finally the high energy enol phosphate linkage created in step 9 binds to ADP creating ATP and completing glycolysis, and leaving two molecules of pyruvate. 

The result being that 4 molecules of ATP are formed, however the net result is that +2 molecules of of ATP is produces because of the process using up two in steps 1 and 3. Notice that this form of glycolysis is a anaerobic procedure with no mention of molecular oxygen. This has its advantages and disadvantages. Anaerobic glycolysis is a fast procedure, used when cells need to create quick release energy. For example when an athlete jumps the energy will come from glycolysis, and if they continue to perform quick movements anaerobically NADH will not be able to be oxidised to NAD+ (as usually is completed in the citric acid cycle and oxidative phosphorylation). In this instance NADH donates it's electrons to the molecules of pyruvate formed, this creates lactic acid, due to lactic acid being produced by the reduction of pyruvate. This unfortunately leads to the achy feeling after exorcise.

 Conversely glycolysis can not compete with the citric acid cycle, driving oxidative phosphorylation, for producing  ATP. The citric acid cycle provides the respiratory chain with high energy electrons that create a proton gradient supplying ATPase with energy to bond inorganic phosphate to ADP. This, in turn, creates up to 30 molecules of  ATP from just 2 pyruvic acid molecules that are reduced in the citric acid cycle. Showing that aerobic rules the animal world! Sorry homolactic fermentation :( 

Why Cyanide Kills You...

Cyanides (-C≡N) are often found in fruit stones, seeds and bitter almonds in small amounts, but also can be produced by some bacteria and fungi. It is commonly known that most cyanides are highly toxic, but why?


Hydrogen cyanide is an inhibitor of the enzyme cytochrome c oxidase in the fourth complex of the respiratory chain, found in the inner membrane of mitochondria. The binding of a cyanide ion (CN−) and cytochrome c oxidase, stops this enzyme from being able to bind electrons to molecular oxygen, to then bind with protons to make water. Normally the enzyme would translocate H+ ions across the inner membrane in this process, creating a H+ gradient to drive ATP synthase, but this can not be completed because of the presence of the (CN−) on cytochrome c oxidase. As I have described before; ATP synthase catalyses the combination of ADP with inorganic phosphate (like a molecular ferris wheel), creating ATP for molecular energy. Thus now, all aerobic cellular tasks, such as those required in the central nervous system and heart, can not be completed.


When hydrogen cyanide is inhaled, in under 10 minutes, your body will no longer be able to produce the vital energy for life. This will result in death.


Thanks for reading.

H5N1 - 5 mutations to pandemic

The H5N1 virus is deadly to humans, but so far has not gone pandemic, as New Scientist's latest issue explains. H5N1 kills over 60% of the people it infects, the fact is not new, however the potentially leathal concept that 'Five easy steps to bird flu pandemic' coveys is expressed in the title. Research has shown that just 5 mutations in 2 genes has allowed H5N1 to spread between mammals in the lab. Ron Fouchier explained his work at a recent scientific meeting describing that the H5N1 once mutated can "spread as efficiently as the flew". Surely this fact combined with the 60% mortality should strike fear into the public's heart?

Fouchier's research was conducted on ferrets. They first gave H5N1 3 mutations know to adapt the virus to mammals, on giving this to the ferrets they inevitably died, but didn't transfer it on to others. By the tenth time the virus from previous ferrets was given to new ferrets it had mutated many times, and now could spread between them, thus it was air-born. Two further genes were identified as causing H5N1 to spread. 

However Doubts have been expressed towards the validity of these results. It is questionable that we can immediately generalise results conducted on ferrets straight to humans, lessening the worry about the 5 mutation rule 'New Scientist' commits to. On the other hand, ferrets have been proven to have a similar reactions  to virus's that humans  may experience. Still this leaves the statement of 5 mutations unfalsifiable to humans, as the exact mutations needed for the virus to spread between humans would be different. The bottom line is; we have to stay vigilant to the very real threat posed, even if it can not be directly proved that only 5 mutations are needed to start a pandemic in humans, we have to do everything we can not to lose that 60% of the people infected.

Eukaryotic Development - "The Hydrogen Hypothesis"

As promised here is an explanation of the how of the development of eukaryotic cells.  As proposed by Martin and Muller the hydrogen hypothesis goes initially against logic by arguing that it is hydrogen that forced eukaryotes to develop and not oxygen (the bottle neck most commonly thought of as pushing for aerobic respiration and thus mitochondria). However the theory is broken down into very logical evolutionary steps that make a lot of sense.

The hypothesis starts with a methanogen (as discuses in previous posts) which thrives of carbon dioxide and hydrogen gas producing methane as its only form of energy. Now it is evident that the methanogen living in anaerobic conditions could not survive for too long in an oxygen rich environment, as oxygen would react with the hydrogen forming water, meaning the cell could not form glucose in its normal way. Now at the same time a bacterium is living in close proximity with the methanogen, benefiting the methanogen by releasing the carbon dioxide and hydrogen the methanogen loves. The bacterium has special genes to absorb glucose that the methanogen can only dream about at this point.

As the relationship between the methanogen and the bacterium is so beneficial to the methanogen, it is not surprising when the larger methanogen engulfs the bacterium and now becomes a part of the newly formed cell. Now this may appear to be irrelevant to how eukaryotes develop as we all know the modern mitochondria are aerobic and use oxygen. Additionally this seems strange because eukaryotes can also use phagocytosis to 'absorb' food stuff. The likeliest explanation of all is that some horizontal gene transfer occurred from bacterium to what now cant really be considered to be a methanogen, but eukaryote.

 Now the eukaryote has all of the full sections of coding genes to absorb glucose, just as the bacterium once did. The mitochondria (most likely to have once been alpha-proteobacteria) produce energy much more efficiently than the methanogen ever did by it's self (mentioned in previous posts). this combined with the abundance of oxygen in the new world. The eukaryotic cell is born. 

Abundant Evidence For Evolution

I recently took part in a scientific debate at a local college where, as usual, the casual conversation turned to over-zealous debate directed towards stem cell research. And then evolution Vs creation.

I am not one to argue that creation isn't true, because who am I to control what people believe. The only thing I can do is present facts and address floored counter arguments, that are always omitting a vital factor, or based on anti-truth.

The first argument the pro-creationist in this debate used was "Their are gaps in the fossil record therefore their is no proof for evolution". Firstly of course there are gaps, it is obvious that we do not posses every fossil on earth. But more importantly we do have intermediary species as examples in fossil records. Take for example the abundant examples of the creatures thought to be ancestors of the whale, with there ever obvious hind limbs at a almost totally fin-like stage of mutation, whereas there front legs are as any land mammals (especially similar to the joints of a cow or sheep). Additionally we can see there nostrils that are usually positioned at the front of a mammals snout, but it has shifted via mutation to a position we would expect to find a blow hole in. And these aren't the only example. There are hundreds. Take also the famous rapter/bird fossil: http://eternian.wordpress.com/2010/11/18/the-enotes-hoax/ The link I have used is not coincidental, It leads me onto my second point...

Creationist often say they conduct there own "creationism research". This immediately lacks objective intentions, as they are researching souly to prove evolution wrong. Thus making this "research" consist of only "research" into evolution and counter-statement's against it, with no evidence at all. A common counter-statement used in child-like arrogance and with the mentality that if I cant have cake no one can: is that evolution isn't a science at all. "What?" I hear Darwin say as he turns in his grave. This argument is based on the falsely assumed factor that evolution can not be empirically tested or seen (invented as this is true for creation). I have already shown the example of the intermediary fossils, but what about mutation it's self.

Pseudo-genes.
Or fossil genes if you like. By looking at the genome for any eukaryote we can see old, decaying genes that are no longer used or coded for. Genes with similar functions in other ancestor species, that were used before in the species but the function is no longer needed. Along with many other factors that I will add to this blog soon, this certainly proves micro-evolution to be true. But what about macro-evolution, the theory that huge changes occur in the genome, meaning that say the human species could have once been chimps or at least a common ancestor with them. As hard as it is to believe for real scientist this is what all the facts point to. The fossil of "ape-man" discovered, then "man-apes" to Neanderthals, are all a big pointer towards macro-evolution. Additionally the more scientific detail I will go into with my next post will display the mechanisms for mutation, and I will combine this with natural selection to show with more evidence that macro-evolution is very likely.

Finally I will finish with the quite offensive argument that evolutionists are atheists. And that all evolutionist are out to prove creationist wrong. This is ironic because I am sure this is exactly the motive of the "creationism researchers". Scientists try to understand the world using testable theories and facts, there is no conspiracy that all scientists are "out to get" creationists, and many scientists are religious and believe in God. We scientists just want the truth. We don't want to argue. I will end with a quote from a letter signed by 188 pastors from various religious denominations and churches, since agreed with by over 10,000 religious preachers from across the world and USA. "We believe that the theory of evolution is a foundational scientific truth, one that has stood up to rigorous scrutiny and upon which much of human achievement rest. To reject this truth or to treat is as 'one theory among others' is to deliberately embrace scientific ignorance and to transmit such ignorance to our children."
In the words of Sean Carroll:
Amen.

The Evolution of Cells

The evolution of cells is a hot topic amongst biochemists as it answers the most fundamental question a biochemist can ask: How can a 'random' collisions of molecules bind together in such a way to create life?

Biochemists and biologists commonly believe that mitochondria (the little 'power houses' of cells that produce ATP through oxidative phosphorylation and the citric acid cycle) were once bacteria that lived independently of the eukaryotic cell. A cell is thought to have eaten the bacterial mitochondria through phagocytosis, a process on which a cell takes on an external body as shown in the YouTube animation http://www.youtube.com/watch?v=a1xPpsxvhVA. After the mitochondria was taken on to the eukaryotic cell biologist conceive the cell and bacteria to have existed ever since in symbiosis.

Evidence shows that all know eukaryotes have or once have had mitochondria, suggesting that perhaps this symbiotic relationship and the uptake of mitochondria occurred several times in the evolution of eukaryotic cells. Yet the evidence for mitochondria once being bacteria is not certain. Mitochondria are the right size to be seen as bacteria and this may explain the initial assumption. However we would expect if mitochondria were once independent bacteria they would have an independent genome coding for all the proteins the mitochondria needs for its self. In fact the mitochondria only has 20 genes that code for proteins and the nucleus of the eukaryote coding for the masses. This may or may not support that the eukaryote may have constructed these little organelles its self, due to the paradoxical notion of when we look at the mutations in the mitochondria's genome compared to the cells. Research has proved that mitochondria have evolved far further than the cell, making growing mitochondria in a culture like we could easily with bacteria now, not impossible, but very hard.

The evidence is inconclusive to the 'how' of the evolution of mitochondria in eukaryote cells but the 'why' is apparent; giving cells energy and intern fuelling life. And the answer the the question of how cells developed in the first place is not a mystery when we consider the time frame they evolved from atoms to molecules to life in: 1000's of millions of years. Long enough for a few convenient coincidences to occur in.