Science Connections

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What do leopard spots, striped marine angelfish, and sand dune ripples have in common? Their patterns are self-organizing Turing systems! Discovered by Alan Turing in the 1950s, these repeating natural patterns can be created by the interaction of two things that spread at different speeds, one faster than the other.

See how scientists are applying Turing’s theories today.

The geometry of DNA: a structural revision

This proposed structure for DNA is wholly founded upon mathematical principles. Although the geometrical modification to the base pairings is relatively minor, the resulting double helix manifests a clarity altogether distinct from that offered by Crick and Watson and it would appear to shed light upon a number of areas of continuing uncertainty.

• Geometric equations predict the dimensions of DNA’s structure. Not only does the pentagonal geometry predict the helical dimensions but it would also demonstrate ‘principle causation’. • The pentagonal geometry provides the dynamics required to build a consistent, stable and uniform helical structure and also establishes why there should be consistently ten bases contained within a single turn of the helix. Incidentally, when converted to the molecular dimension I would certainly predict degrees of variation, certainly between 9.5 and 10.5 bases per turn, but perhaps even more. • Both the hollow centre and side-by-side structural formation ensure instant access at any point within the helix. This would permit the DNA (even circular) to open and close during its replication functions without entangling itself. • The modification to the base pairing would appear to be able to exist in either the enol or keto formations. • While the sugar-phosphate backbones will undoubtedly prove integral to the stability of the helical structure, it is the geometry of the basepair molecules themselves that are ultimately responsible for the formation of the helix.

“Geometric equations predict the dimensions of DNA’s structure.” No, they match the dimensions of DNA’s structure. The argument is circular; of course pentagons would be able to match the helical structure, because your initial assumption was that the structure is helical.

"The pentagonal geometry … establishes why there should be consistently ten bases contained within a single turn of the helix." That’s cool and all, but it misses the entire underlying reason. The van der Waals diameter of a carbon atom (and consequently the thickness of a base) is 3.4 angstroms, whereas the distance between the glycosidic bonds between nucleotides in the backbond is 6 angstroms. The bases of DNA are hydrophobic on the flat faces and want to be in as close contact as possible (the so-called “hydrophobic interaction”). There are 10.5 base pairs per turn because at that angle of twisting, the bases are in direct contact with each other, maximizing the “hydrophobic interaction”.

"Both the hollow centre and side-by-side structural formation ensure instant access at any point within the helix." Yes, but once again this completely ignores the underlying chemistry. A hollow center means that your bases are exposed to water. If you’ve taken an ochem class, then you’ve likely discussed the relevant intermolecular forces that govern the behavior between hydrophobic substances and water. Water would much prefer to make hydrogen bonds with itself than to lose out by interacting with the bases; remember, the formation of bonds is always exothermic. Exposed bases means you have water that isn’t making as many hydrogen bonds as it can, increasing the energy of the entire system.

"This would permit the DNA (even circular) to open and close during its replication functions without entangling itself." So there’s a family of enzymes called topoisomerases (they’re incredibly intriguing enzymes with really cool mechanisms!) that untangle the DNA as it replicates. DNA does not tangle when replicating; the consequences of that would be the entire cell cycle grinding to a halt because replication can’t be completed. 

"The modification to the base pairing would appear to be able to exist in either the enol or keto formations." I simply can’t with this statement. There are so many things wrong here. Bases generally exist in the keto/amino form rather than the enol/imino form because they’re more thermodynamically stable; the amino form of adenine is favored over the imino form by a factor of 10,000. But more important is that the enol/imino forms are ambiguous when it comes to replicating. DNA is based on the ability to replicate to make an exact copy of itself, and that relies on the hydrogen bonding capabilities of each base. Think of it as how puzzle pieces can fit together. A and T fit together, as do G and C. But if your adenine goes from the keto form to the enol form, all of a sudden, it can’t fit with T anymore. It’s become a good pairing candidate for C instead—which means you now have an error in replication. Your modification to the base pairing essentially breaks the entire concept of base pairing as it stands.

"… it is the geometry of the basepair molecules themselves that are ultimately responsible for the formation of the helix." Again, completely wrong. Base pairing is necessary for correct replication, but they are not the driving force in the helix formation. Hydrogen bonds are extremely weak; if they weren’t, water wouldn’t be a liquid at room temperature—it’d be a solid! The reason why DNA helix formation is favorable is because of the whole “hydrophobic interaction” thing as mentioned before. 

If you look up and read the actual article, you’ll see even more evidence against this person’s proposal. They suggest that the ribose phosphate backbone isn’t held together by covalent bonds at all, but with hydrogen bonds; even more insane is their suggestion that the bases aren’t covalently attached to the backbone covalently at all. Figure 5 shows hydrogen bonding occuring through N9 of guanine, which is patently impossible since N9 is where guanidine is covalently bound to ribose.

The issue here is that the person is blindly applying math to science, without considering the existing physical limitations already in place. Math might be a powerful tool in explaining the world, but it’s completely meaningless if you use it without looking at the context.

I took a lot of pictures of Robin’s Tesla coil last night. I did some longer exposures and then some short exposures to get only a single spark while holding down the shutter to take continuous pictures.

We also stuck a radiometer on the top of it. The radiometer contains low pressure gas which emits light when current flows through it acting similar to a fluorescent light bulb. Here’s how a radiometer normally works.

The descent into Alzheimer’s disease.  A doctor chronicles the signatures of his patient as the disease took hold of her. Our love goes out to anyone who’s dealt with this awful disease in some way. 

Aha! The moment of economic creation was not at 1650 after all! Conventional economic theory sometimes gives the impression that economists are creationists in spirit. Many historical graphs [1] only offer useful information back to the year 1650. Around 1650 or so, most economic indicators enter their exponential phase, which renders graphical information about previous eras incomparable.

But economist and modeler Max Roser [2] offers a historical view of global GDP going back 2,000 years. His “Our World in Data" website is an attempt to characterize global economics and other social phenomena as a series of visualizations. This includes maps (spatial distributions) and charts that make long-term comparisons more than a series of bad graphs. If John Maynard Keynes were to look at these data, he might say: in the long run, we are all wealthier [3].

[1] The bottom three pictures are courtesy of: Roser, M.   GDP Growth Over the Very Long Run. Our World in Data (2014).

[2]Matthews, D.   The world economy since 1 AD, in a single chart. Vox blog, August 15 (2014).

One of the first ever drawings of a fuel cell (1842)

Sir William Robert Grove, judge & physicist, was the father of the modern fuel cell. He developed his idea through experimenting with sending an electric current through water splitting it into its component parts of hydrogen and oxygen. He then tried to reverse the process and combine hydrogen with oxygen to produce electricity and water thereby producing a simple fuel cell.

In this letter from the Ri’s archive, Grove writes to Michael Faraday in October 1842 to describe his new accomplishment:

I have just completed a curious voltaic pile which I think you would like to see, it is composed of alternate tubes of oxygen and hydrogen through each of which passes platina foil so as to dip into separate vessels of water acidulated with sulphuric acid the liquid just touching the extremities of the foil as in the rough figure below…………………….

……………. I cannot but regard the experiment as an important one both as to the chemical and other theories of the pile & as to the catalytic effect of the combination of the gases by platina.

Helioseismology: seismology of the Sun

The Sun oscillates and vibrates at many frequencies, like an ocean surface or …like a bell. Certain frequencies are amplified by constructive interference(wave propagation) and the turbulence “rings” the sun like a bell. Unfortunately, sound does not carry through the vacuum between the Sun and the earth, so we have to “listen" to the oscillations by looking at the motions of material on the surface of the Sun. With the right instruments, scientists can "hear" this ringing or pulsations from the Sun. To do this, they use an instrument called a Michelson Doppler Imager (MDI), mounted on the SOHO spacecraft and the Helioseismic and Magnetic Imager (HMI), one of the three instruments that make up the Solar Dynamics Observatory (SDO).

Although direct study of its interior is impossible —mostly because the Sun is nearly opaque to electromagnetic energy, insights into the conditions within the Sun may be gained by observing oscillating waves, rhythmic inward and outward motions of its visible surface. These oscillations on the surface are due to sound waves generated and trapped inside the sun. Sound waves are produced by pressure fluctuations in the turbulent convective motions of the sun’s interior. These trapped sound waves set the sun vibrating in millions of different patterns or modes. Using this acoustic energy, we can “see into the Sun”, just as geologists use seismic waves to study the structure of the Earth, the discipline of helioseismology makes use of acoustic pressure waves (infrasound) traversing the Sun’s interior. These oscillations are seen as volumes of gas called granules near the Sun’s surface that rise and fall with a particular frequency. It is like seeing the rolling motions of convection cells on the surface of  boiling water. This happens very close to the surface where the flow of energy that started in the nuclear reactions in the core reaches the surface and suddenly escapes. The sound from the convection is then trapped and filtered inside the sun to produce the solar music. 

Helioseismologists can use the properties of these waves to determine the temperature, density, composition, and motion of the interior of the sun. The spectral lines emitted from gas moving upwards will be slightly Doppler-shifted to the blue; spectral lines from gas moving downwards will be slightly Doppler-shifted to the red. In this way the rolling motions of convection near the Sun’s surface can be mapped out. There are three types of oscillations. Pressure modes (p-modes) are sound waves trapped in the temperature gradient (like an echo bouncing around inside a cavern). Fundamental modes (f-modes) or surface gravity waves are caused by gravitational interactions with the sun’s surface and resemble ocean waves. Gravity modes (g-modes) are not completely understood, but they are believed to be the result of buoyancy effects. All the known pressure and fundamental modes (some 10 million) have oscillation periods of less than 18 minutes, and most are around 5 minutes. The gravity modes are not known conclusively to exist, but they are predicted to have periods of 40 minutes or longer (160-min).

Further readings:

Imaging sunspots using helioseismic methods

Helioseismology and the Sun’s interior

Global Oscillation Network Group

Helioseismic and Magnetic Imager

One chart says it all about the government and female bodies 

We’re only halfway through 2014, and state legislators have already introduced a whopping 468 restrictions intended to limit, control or otherwise regulate women’s reproductive rights.

How many comparable bills have been introduced to regulate men’s reproductive health care during this period? Zero. 

Something’s very wrong with this picture.

Type of Spirals: A spiral is a curve in the plane or in the space, which runs around a centre in a special way. Different spirals follow. Most of them are produced by formulas:The radius r(t) and the angle t are proportional for the simplest spiral, the spiral of Archimedes. Therefore the equation is: (3) Polar equation: r(t) = at [a is constant]. From this follows (2) Parameter form:  x(t) = at cos(t), y(t) = at sin(t), (1) Central equation:  x²+y² = a²[arc tan (y/x)]².

You can make a  spiral by two motions of a point: There is a uniform motion in a fixed direction and a motion in a circle with constant speed. Both motions start at the same point.  (1) The uniform motion on the left moves a point to the right. - There are nine snapshots. (2) The motion with a constant angular velocity moves the point on a spiral at the same time. - There is a point every 8th turn. (3) A spiral as a curve comes, if you draw the point at every turn(Image).

Figure 1: (1) Archimedean spiral - (2) Equiangular Spiral (Logarithmic Spiral, Bernoulli’s Spiral). Figure 2 : (1) Clothoide (Cornu Spiral) - (2) Golden spiral (Fibonacci number).

More Spirals: If you replace the term r(t)=at of the Archimedean spiral by other terms, you get a number of new spirals. There are six spirals, which you can describe with the functions f(x)=x^a [a=2,1/2,-1/2,-1] and  f(x)=exp(x), f(x)=ln(x). You distinguish two groups depending on how the parameter t grows from 0.

Figure 4:  If the absolute modulus of a function r(t) is increasing, the spirals run from inside to outside and go above all limits. The spiral 1 is called parabolic spiral or Fermat’s spiral. Figure 5: If the absolute modulus of a function r(t) is decreasing, the spirals run from outside to inside. They generally run to the centre, but they don’t reach it. There is a pole.  Spiral 2 is called the Lituus (crooked staff).

Figure 7: Spirals Made of Line Segments.

Source:  Spirals by Jürgen Köller.

See more on Wikipedia:  Spiral,  Archimedean spiral,  Cornu spiral,  Fermat’s spiral,  Hyperbolic spiral,  Lituus, Logarithmic spiral,  Fibonacci spiral, Golden spiral, Rhumb line, Ulam spiral,  Hermann Heights Monument, Hermannsdenkmal.

The famous theoretical physicist John Archibald Wheeler coined the term “It from Bit”. He says that ”It” — every particle, every field of force, even the space-time continuum itself — derives its function, its meaning, its very existence entirely — even if in some contexts indirectly — from the apparatus-elicited answers to yes-or-no questions, binary choices, “bits.” This concept symbolizes the idea that every item of the physical world has at bottom — a very deep bottom, in most instances — an immaterial source and explanation; that which we call reality arises in the last analysis from the posing of yes-or-no questions and the registering of equipment-evoked responses; in short, that all things physical are information-theoretic in origin and that this is a participatory universe.

Wheeler speculated that we are part of a universe that is a work in progress; we are tiny patches of the universe looking at itself — and building itself. It’s not only the future that is still undetermined but the past as well. And by peering back into time, even all the way back to the Big Bang, our present observations select one out of many possible quantum histories for the universe.

At every moment, in Wheeler’s view, the entire universe is filled with events, where the possible outcomes of countless interactions become real, where the infinite variety inherent in quantum mechanics manifests as a physical cosmos. And we see only a tiny portion of that cosmos. Wheeler suspected that most of the universe consists of huge clouds of uncertainty that have not yet interacted either with a conscious observer or even with some lump of inanimate matter. He sees the universe as a vast arena containing realms where the past is not yet fixed.

from Does the Universe Exist if We’re Not Looking?

The Goldbach Conjecture

Researchers eliminate HIV from cultured human cells for first time

HIV-1, the most common type of the virus that causes AIDS,has proved to be tenacious, inserting its genome permanently into its victims’ DNA, forcing patients to take a lifelong drug regimen to control the virus and prevent a fresh attack. Now, a team of Temple University School of Medicine researchers has designed a way to snip out the integrated HIV-1 genes for good.

"This is one important step on the path toward a permanent cure for AIDS," says Kamel Khalili, PhD, Professor and Chair of the Department of Neuroscience at Temple. Khalili and his colleague, Wenhui Hu, MD, PhD, Associate Professor of Neuroscience at Temple, led the work which marks the first successful attempt to eliminate latent HIV-1 virus from human cells. "It’s an exciting discovery, but it’s not yet ready to go into the clinic. It’s a proof of concept that we’re moving in the right direction," added Dr. Khalili, who is also Director of the Center for Neurovirology and Director of the Comprehensive NeuroAIDS Center at Temple.

In a study published July 21 by theProceedings of the National Academy of Sciences, Khalili and colleagues detail how they created molecular tools to delete the HIV-1 proviral DNA. When deployed, a combination of a DNA-snipping enzyme called a nuclease and a targeting strand of RNA called a guide RNA (gRNA) hunt down the viral genome and excise the HIV-1 DNA. From there, the cell’s gene repair machinery takes over, soldering the loose ends of the genome back together — resulting in virus-free cells.

"Since HIV-1 is never cleared by the immune system, removal of the virus is required in order to cure the disease," says Khalili, whose research focuses on the neuropathogenesis of viral infections. The same technique could theoretically be used against a variety of viruses, he says.

Publishing is one of the most ballyhooed metrics of scientific careers, and every researcher hates to have a gap in that part of his or her CV. Here’s some consolation: A new study finds that very few scientists—fewer than 1%—manage to publish a paper every year.

But these 150,608 scientists dominate the research journals, having their names on 41% of all papers. Among the most highly cited work, this elite group can be found among the co-authors of 87% of papers.

The new research, published on 9 July in PLOS ONE, was led by epidemiologist John Ioannidis of Stanford University in Palo Alto, California, with analysis of Elsevier’s Scopus database by colleagues Kevin Boyack and Richard Klavans at SciTech Strategies. They looked at papers published between 1996 and 2011 by 15 million scientists worldwide in many disciplines.