January 2015 – Page 6 – Harmonia Philosophica

Communicating… Cells… Humans…

Bioengineers at the University of California, San Diego have discovered that mouse embryos are contemplating their cellular fates in the earliest stages after fertilization when the embryo has only two to four cells, a discovery that could upend the scientific consensus about when embryonic cells begin differentiating into cell types. Their research, which used single-cell RNA sequencing to look at every gene in the mouse genome, was published recently in the journal Genome Research. In addition, this group published a paper on analysis of “time-course”single-cell data which is taken at precise stages of embryonic development in the journal of Proceedings of the National Academy of Sciences.

“Until recently, we haven’t had the technology to look at cells this closely,” said Sheng Zhong, a bioengineering professor at UC San Diego Jacobs School of Engineering, who led the research. “Using single-cell RNA-sequencing, we were able to measure every gene in the mouse genome at multiple stages of development to find differences in gene expression at precise stages”.

The findings reveal cellular activity that could provide insight into where normal developmental processes break down, leading to early miscarriages and birth defects.
The researchers discovered that a handful of genes are clearly signaling to each other at the two-cell and four-cell stage, which happens within days after an egg has been fertilized by sperm and before the embryo has implanted into the uterus. Among the identified genes are several genes belonging to the WNT signaling pathway, well-known for their role in cell-cell communications. (1)

Cells speaking to each other.
Molecules speaking to each other.
Particles interracting with each other.

The whole world a giant organism.
A networked place, where everything affects everything.
We all communicate with each other.

It really needs a great amount of egoism and free will in order NOT to…

Grothendieck, manuscripts, burning libraries..

Alexander Grothendieck, who died on Nov. 13 at the age of 86, was a visionary who captivated the collective psyche of his peers like no one else. To say he was the No. 1 mathematician of the second half of the 20th century cannot begin to do justice to him or his body of work. Let’s resist the temptation to assign a number to a man of numbers. There are deeper lessons to be learned from this extraordinary human being and his extraordinary life.

In mathematics, he revolutionized the field known as algebraic geometry. (1)

Once upon a time there was a wise man. Who burned 25,000 pages of manuscripts before disappearing from the face of the Earth.

Once upon a time there were people who were important.

Not for what they published but for what they did not.

We lack those people today.
Burn all the bookstores.
Discover yourself…

Mammoth extinct. Resurrected. Life and death.

Scientists are one step closer to cloning a woolly mammoth, thanks to the results of a new autopsy conducted on a remarkably preserved specimen of the species discovered last year.

The 40,000-year-old mammoth, nicknamed “Buttercup,” was found in permafrost on the remote Siberian island of Maly Lyakhovsky. When scientists cut into the carcass, its fresh-looking flesh oozed dark blood, raising hopes that DNA could be extracted.

Scientists believe that the key to cloning the prehistoric beast is finding a complete copy of its DNA. That wasn’t found in this case, but the scientists did recover long fragments. Plans call for researchers from South Korea’s Sooam Biotech Research Foundation to analyze tissue samples from the carcass over the next two years, with the hopes of finding an intact genome. (1)

The dead is not dead.
What was alive, always stays so.
In a weird way you already know this.
Not through DNA.
Not through genetics.
But in a more simple and elegant way.
By simply not dying.
Check again.
There is nothing to “resurrect”.

That is not dead which can eternal lie.

And with strange aeons even death may die…

Human clocks. Human time… Life…

Human existence is basically circadian. Most of us wake in the morning, sleep in the evening, and eat in between. Body temperature, metabolism, and hormone levels all fluctuate throughout the day, and it is increasingly clear that disruption of those cycles can lead to metabolic disease.

Underlying these circadian rhythms is a molecular clock built of DNA-binding proteins called transcription factors. These proteins control the oscillation of circadian genes, serving as the wheels and springs of the clock itself. Yet not all circadian cycles peak at the same time — some peak in the morning and others in the evening. The question, is, how does a single clock keep time in multiple phases at once? Now, thanks to new findings from researchers at the Perelman School of Medicine at the University of Pennsylvania, we know.

In the current issue of the journal Cell, Mitchell Lazar, MD PhD, the Sylvan Eisman Professor of Medicine and director of the Institute for Diabetes, Obesity, and Metabolism and his team report the results of a genome-wide survey of circadian genes and genetic regulatory elements called enhancers. These are key parts of the “dark matter” of the genome; rather than encoding proteins, they control the expression of genes.

Led by postdoctoral researchers Bin Fang, Logan Everett and Jennifer Jager, Lazar’s team took advantage of new tools based on high-density DNA sequencing to measure the activity of enhancers throughout the day in the livers of mice. They found that many enhancers, like circadian genes themselves, have a daily oscillation that is in phase with nearby genes — both the enhancer and gene activity peak at the same time each day. The enhancer activities, in turn, are governed by distinct proteins called transcription factors. Grouping the enhancers into eight three-hour phases based on when they peak, the group asked which factors are capable of binding to the enhancers in each set. Remarkably, the team found that enhancers that are in the same phase tend to bind the same transcription factors. (1)

Everything in nature tuned with each other.
We are all following a clock.
We are all following many clocks.
And these clocks are winded together.

Two pendulums on the same wall.
Earth and the Moon looking at each other.
Humans living together till they die.

Tik tak tik tak tik tak…