Tag: dna

DNA precursors in space

Consider this: we have the capability to detect the presence of very specific molecules from 25k light years away. This is just mind-boggling.

Researchers have discovered prebiotic (pre-life) molecules in interstellar space that may have formed on dusty ice grains floating between the stars. The molecules were detected near the center of our Milky Way Galaxy — specifically, the star-forming region Sagittarius(Sgr) B2(N), which is the richest interstellar chemical environment currently known. 1 of the newly-discovered molecules, called E-cyanomethanimine (E-HNCHCN) is one step in the process that chemists believe produces adenine, 1 of the 4 nucleobases of DNA. The other molecule, called ethanamine, is thought to play a role in forming alanine, 1 of the 20 amino acids in the genetic code.

2014-10-03: Isopropyl cyanide, needed for life

Astronomers have detected radio waves within a giant gas cloud in interstellar space corresponding to an unusual carbon-based molecule called isopropyl cyanide, needed for life. Organic molecules usually found in these star-forming regions consist of a single “backbone” of carbon atoms arranged in a straight chain. But the carbon structure of isopropyl cyanide branches off, making this the first interstellar detection of such a molecule


2014-12-02: DNA itself can also survive in space. This makes Panspermia (and contamination of the seas of europa by humanity’s probes) more likely.

Surviving space flight, 1000°C temperatures, re-entry into Earth’s atmosphere, and landing, 35% of the DNA retained its full biological function

2022-03-13: Peptides can form on cosmic dust

Without any of the enzymes that biochemistry provides, the production of peptides is an inefficient 2-step process that involves first making amino acids and then removing water as the amino acids link up into chains in a process called polymerization. Both steps have a high energy barrier, so they occur only if large amounts of energy are available to help kick-start the reaction.

Because of these requirements, most theories about the origin of proteins have either centered on scenarios in extreme environments, such as near hydrothermal vents on the ocean floor, or assumed the presence of molecules like RNA with catalytic properties that could lower the energy barrier enough to push the reactions forward. And even under those circumstances, “special conditions” would be needed to concentrate the amino acids enough for polymerization. Though there have been many proposals, it isn’t clear how and where those conditions could have arisen on the primordial Earth.

But now a group of astrobiologists showed that peptides, the molecular subunits of proteins, can spontaneously form on the solid, frozen particles of cosmic dust drifting through the universe. Those peptides could in theory have traveled inside comets and meteorites to the young Earth — and to other worlds — to become some of the starting materials for life.

Ethics arbitrage

In China, a research project aims to find the roots of intelligence in our DNA; searching for the supersmart

it would appear that the biggest sequencing lab in the world has no qualms about research that would not pass ethics approval in the west. of course, the results of that research will not be ignored by the west, how convenient.

World microbiome

The Earth Microbiome Project analyzes microbial communities across the globe. We propose to characterize Earth by environmental parameter space into different biomes and then explore these using samples. We will analyze 200k samples to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, 500k reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.

For example, we may have soil samples from a pH range of 4-6.5 and 7.3-11.2 at a range of different temperatures, nutrient loads, and soil types. To understand the full range of soil microbiota on earth we would need to explore samples whose pH is below 4, above 11.2 and between 6.5 and 7.3, and all at a range of different temperatures, nutrient loads and soil types.

DNA sequencing on Mars

venter is such a show off. after wining the human genome race, he sailed around the world, collecting dna samples, and doubled the number of all known genes. then he claimed to have created “synthetic life”, and now this. the man clearly has enormous talent, but i wonder if he is as insufferable as the biography suggests.

Craig Venter and Jonathan Rothberg are competing to put a DNA sequencing machine on Mars, each claiming that it is the best way to search for and confirm Marian life. “This will work only if the DNA on Mars is exactly the same in its fundamental structure as on Earth. It is very unlikely that terran DNA is the only structure able to support Darwinian evolution.” Though I lean slightly toward Venter. Some of the chemistry of DNA life has been shown to imply have the best combinations of stability and just the right breakability and attachment probabilities in the bonds.

FDA nonsense

FDA commissioner Alexander M. Schmidt

In all of FDA’s history, I am unable to find a single instance where a congressional committee investigated the failure of FDA to approve a new drug. But, the times when hearings have been held to criticize our approval of new drugs have been so frequent that we aren’t able to count them. … The message to FDA staff could not be clearer.

2013-11-26: as usual, the FDA is up to no good.

At the same time that the NSA is secretly and illegally obtaining information about Americans the FDA is making it illegal for Americans to obtain information about themselves.

2014-08-05: the FDA could help by eliminating its onerous rules for diseases with 60% mortality rates. Won’t happen of course, it’s easier to bury lots of innocents than to overcome cover-your-ass (pretty much the reason for the FDA to exist). Or as the onion put it, the Ebola Vaccine is at least 50 white people away.
2016-07-15: Fluoride still not available

American dentists first started using similar silver-based treatments in the early 1900s. The FDA is literally over 100 years behind the times.It seems that the future of dental treatment has been here all along but a combination of dentists wanting to be surgeons, lost knowledge, and FDA cost and delay prevented it from being distributed

Silver diamine fluoride been used for decades in Japan, but it’s been available in the United States, under the brand name Advantage Arrest, for just ~1 year. Toddlers in low-income families sometimes have to wait 1 year for fillings in an operating room. Transporting and treating frail patients, assuming they can afford to see a dentist, can be difficult. But now some patients can be quickly treated where they live.
2020-04-17: Nutrition overregulation

1 reason why food intended for restaurants is not reallocated to supermarkets: Nutrition labeling also frequently doesn’t comply with Agriculture Department and FDA guidelines for consumer sales

2020-12-05: This is nonsense. “Delay to allay” won’t convince anyone, and meanwhile people are dying.

Dr. Fauci said the politicization of the pandemic in his own country had led regulators to move a little more cautiously than the British, to avoid losing public support. There is no plausible reason why this basic analysis cannot be done in 24 hours. The FDA and external scientists have a simple task: confirm or reject the review already conducted by the trial’s independent data safety monitoring board before FDA submission.

2021-02-07: The FDA is unable to make sense.

Think of centers of expertise like the CDC or the IGM Economists Panel as giant systems for disentangling corruption and power. Their job is to produce 1 or 2 people who can get in front of the population and say something which has some resemblance to reality, even though the entire rest of the economy and body politic is trying to corrupt them. They…actually do sort of okay. Anthony Fauci is neither Attila the Hun nor Trofim Lysenko. He’s a kind of bumbling careerist with a decent understanding of epidemiology and a heart that’s more or less in the right place. The whole scientific-technocratic complex is a machine which takes Moloch as input and manages – after spending billions of $ and the careers of 1000s of hard-working public servants – to produce Anthony Fauci as output. This should be astonishing, and we are insufficiently grateful.

2021-02-15: Why isn’t there a reciprocal approval with the EU?

I’ve long argued that if a drug or medical device is approved in another country with a Stringent Regulatory Authority it ought to be approved in the United States. But, of course, the argument is even stronger in the other direction. Drugs and devices approved in the United States ought to be approved elsewhere. Indeed, this is how much of the world actually works because most countries do not have capability to evaluate drugs and devices the way the FDA or the EMA does. Although it’s the way the world works, few will admit it because that would violate pretensions of regulatory nationalism. Moreover, keeping up with pretenses means transaction costs and unnecessary delays. Regulatory nationalism has added months to vaccine delivery and now threatens to put to waste millions of stockpiled doses.

2021-03-02: millions of people die of heart disease every year. there has been no progress in artificial hearts in 50 years due to.. wait for it.. FDA:

The FDA gave Abiomed permission to implant 60 more devices, but it was clear that the heart would need to be updated, and then approved all over again—a lengthy process for which no one had the fortitude. “Abiomed threw in the towel. They were, like, ‘This is too hard!’ ”

2021-03-16: What are FDA inspectors even doing?

Grocery store workers are working, meat packers are working, hell bars and restaurants are open in many parts of the country but FDA inspectors aren’t inspecting. It boggles the mind.

Let’s review. The FDA prevented private firms from offering SARS-Cov2 tests in the crucial early weeks of the pandemic, delayed the approval of vaccines, took weeks to arrange meetings to approve vaccines even as 1000s died daily, failed to approve the AstraZeneca vaccine, failed to quickly approve rapid antigen tests, and failed to perform inspections necessary to keep pharmaceutical supply lines open.

2021-04-14: the FDA is completely insane and is halting the distribution for the J&J vaccine due to very rare side effects. as before, there’s no consequences for acts of omission vs acts of commission. they’re much more worried about their “reputation” than actually saving lives, just like ethicists have been in this crisis. a disgrace.

As the Johnson & Johnson vaccine pauses in the United States, Philip Bump for The Washington Post offers a quick visualization that shows 100 vaccinations per second. A red one appears if there’s a side effect. But because the side effect is rare, currently at 1 in 1.1M, the red dot on the visualization likely never appears as you watch. The blue dots are potential lives saved if the J&J vaccine continues.

Clerical errors

after recent experiences with both the judicial system (as a juror) and as a patient of the medical system, the amount of clerical errors in both is astonishing. both systems drown in paperwork and both refuse to adapt any technology not from the 19th century to deal with it. total amateur hour, with criminal consequences.
2015-07-09:

After a hospital error, 2 pairs of Colombian identical twins were raised as 2 pairs of fraternal twins. This is the story of how they found one another

No Junk in DNA?

this is a really big deal and i am amused by the multiple google maps references. i was at a NIH workshop with the gentleman in the picture a few years ago (hi Mark Gerstein) and we talked about how google maps like visualizations can help spur discovery in science

i am glad faint echoes of that workshop led to something 🙂

“It’s Google maps”. Its predecessor, the Human Genome Project, which determined the entire sequence of human DNA, “was like getting a picture of earth from space. It doesn’t tell you where the roads are, it doesn’t tell you what traffic is like at what time of the day, it doesn’t tell you where the good restaurants are, or the hospitals or the cities or the rivers.”

The new result “is a stunning resource. My head explodes at the amount of data.”

more on this fight

“We don’t use that term anymore. It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, “turns out to be doing stuff.”

and techniques like LIGR-Seq can determine what that DNA does:

“Most researchers in the life sciences agree that there’s an urgent need to understand what ncRNAs do. This technology will open the door to developing a new understanding of ncRNA function”. Not having to rely on pre-existing knowledge will boost the discovery of RNA pairs that have never been seen before. Scientists can also, for the first time, look at RNA interactions as they occur in living cells, in all their complexity, unlike in the juices of mashed up cells that they had to rely on before. This is a bit like moving on to explore marine biology from collecting shells on the beach to scuba-diving among the coral reefs, where the scope for discovery is so much bigger. Actually, ncRNAs come in multiple flavors: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, or how they do this.

These noncoding regions may be the source of de novo genes:

The mystery of where these orphan genes came from has puzzled scientists for decades. But in the past few years, a once-heretical explanation has quickly gained momentum — that many of these orphans arose out of non-coding DNA. “Genetic function somehow springs into existence. This metamorphosis was once considered to be impossible, but a growing number of examples in organisms ranging from yeast and flies to mice and humans has convinced most of the field that these de novo genes exist.

Precision Medicine

A working model of your body, grounded in your own genome, refreshed continually with measurements from your body’s insides. This information will be collated with readings from millions of other monitored bodies. Software will produce detailed guidance about diet, supplements, exercise, medication, or treatment—guidance based not on the current practice of lumping symptoms together into broad categories of disorders, but on a precise reading of your own body’s peculiarities and its status in real time.

“And at that point you now have, for the first time in history, a scientific basis for medicine.”

turning medicine from craft into science.
2019-02-01:

However, nearly 20 years after the first predictions of dramatic success, we find no impact of the human genome project on the population’s life expectancy or any other public health measure, notwithstanding the vast resources that have been directed at genomics. Exaggerated expectations of how large an impact on disease would be found for genes have been paralleled by unrealistic timelines for success, yet the promotion of precision medicine continues unabated.

The authors of this new paper end by saying that “it is urgent that the biomedical research community reconsider its ongoing obsession with the human genome“, which is strong language. We’ve learned a lot from genomic studies, and we’re still learning more, and it’s not going away. But if by “obsession” they mean trying to apply genomic viewpoints to every problem regardless of suitability, or promising success in some of these programs once we can do just a bit more sequencing – because that’s all they’re lacking – then they have a point. The genome is great, the genome is huge, the genome is important. But it’s not the only great huge important thing out there.