Posts Tagged ‘DNA’
“Two dangers constantly threaten the world: order and disorder”*…
After two days of posts on the state of our civil society, a palette-cleanser: Jordana Cepelewicz with a possibly-consoling reminder…
When he died in 1930 at just 26 years old, Frank Ramsey [see here] had already made transformative contributions to philosophy, economics and mathematics. John Maynard Keynes sought his insights; Ludwig Wittgenstein admired him and considered him a close friend. In his lifetime, Ramsey published only eight pages on pure math: the beginning of a paper about a problem in logic. But in that work, he proved a theorem that ultimately led to a whole new branch of mathematics — what would later be called Ramsey theory.
His theorem stated that if a system is large enough, then no matter how disordered it might be, it’s always bound to exhibit some sort of regular structure. Order inevitably emerges from chaos; patterns are unavoidable. Ramsey theory is the study of when this happens — in sets of numbers, in collections of vertices and edges called graphs, and in other systems. The mathematicians Ronald Graham and Joel Spencer likened it to how you can always pick out patterns among the stars in the night sky…
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… In fact, Ramsey theory isn’t just about inevitable patterns found in graphs. Hidden structure emerges in lists of numbers, strings of beads and even card games. In 2019, for example, mathematicians studied collections of sets that can always be arranged to resemble the petals of a sunflower. That same year, Quanta reported on research into sets of numbers that are guaranteed to contain numerical patterns called polynomial progressions. And last year, mathematicians proved a similar result, about sets of integers that must always include three evenly spaced numbers, called arithmetic progressions.
In its hunt for patterns, Ramsey theory gets to the core of what mathematics is all about: finding beauty and order in the most unexpected places…
Finding order in chaos: “Why Complete Disorder Is Mathematically Impossible,” from @jordanacep in @QuantaMagazine.
* Paul Valery
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As we ponder patterns, we might send paradigm-shaping birthday greetings to a woman who found order and pattern of a different– and world-changing– sort: Rosalind Franklin; she was born on this date in 1920. A biophysicist and X-ray crystallographer, Franklin captured the X-ray diffraction images of DNA that were, in the words of Francis Crick, “the data we actually used” when he and James Watson developed their “double helix” hypothesis for the structure of DNA. Indeed, it was Franklin who argued to Crick and Watson that the backbones of the molecule had to be on the outside (something that neither they nor their competitor in the race to understand DNA, Linus Pauling, had understood). Franklin never received the recognition she deserved for her independent work– her paper was published in Nature after Crick and Watson’s, which barely mentioned her– and she died of cancer four years before Crick, Watson, and their lab director Maurice Wilkins won the Nobel Prize for the discovery.
“Judge me by my size, do you?”*…
A tiny variety of the fork fern seems altogether unremarkable– but has a genome that dwarfs the human genome in size. Max Kozlov explains what that might teach us…
A small, unassuming fern-like plant has something massive lurking within: the largest genome ever discovered, outstripping the human genome by more than 50 times.
The plant (Tmesipteris oblanceolata) contains a whopping 160 billion base pairs, the units that make up a strand of DNA. That’s 11 billion more than the previous record holder, the flowering plant Paris japonica, and 30 billion more than the marbled lungfish (Protopterus aethiopicus), which has the largest animal genome. The findings were published [on May 31] in iScience…
The world’s genomic champion, which is native to New Caledonia and neighbouring archipelagos in the South Pacific, is a species of plant called a fork fern. Its colossal number of base pairs raises questions as to how the plant manages its genetic material. Only a small proportion of DNA is made of protein-coding genes, leading study co-author Ilia Leitch, an evolutionary biologist at London’s Royal Botanic Gardens, Kew, to wonder how the plant’s cellular machinery accesses those bits of the genome “amongst this huge morass of DNA. It’s like trying to find a few books with the instructions for how to survive in a library of millions of books — it’s just ridiculous.”
There’s also the question of how and why an organism evolved to have so many base pairs. Generally, having more base pairs leads to higher demand for the minerals that comprise DNA and for energy to duplicate the genome with every cell division, Leitch says. But if the organism lives in a relatively stable environment with little competition, a gargantuan genome might not come with a high cost, she adds.
That could help to provide an explanation — although a rather boring one — for the fork fern’s large genome: it might be neither detrimental nor particularly helpful for the plant’s ability to survive and reproduce, so the fork fern has gone on accumulating base pairs over time, says Julie Blommaert, a genomicist at the New Zealand Institute for Plant and Food Research in Nelson.
For now, researchers can only speculate on answers to these questions. The largest genome to be sequenced and assembled belongs to the European mistletoe (Viscum album), with about 90 billion base pairs. Modern techniques might not be sufficient to do the same for the fork fern’s genome: even if it’s sequenced, there’s still the computational challenge of taking the data and “sticking them together in a way that biologically reflects what’s going on”, Leitch says.
Finding ways to analyse enormous genomes could yield crucial insights into how genome size influences where organisms can grow, how they are able to flourish in their environments and their resilience to climate change, independent of their specific DNA sequence, she adds. Pellicer says it’s remarkable that a tiny, non-flowering plant that most people “wouldn’t bother to stop and look at” could offer such important lessons. “The beauty of the plant is inside.”
“Biggest genome ever found belongs to this odd little plant,” from @maxdkozlov in @Nature.
* Yoda, “The Empire Strikes Back”
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As we rescope scale, we might send insightful birthday greetings to Phillip Allen Sharp; he was born on this date in 1944. A geneticist and molecular biologist, he co-discovered RNA splicing— for which he shared the 1993 Nobel Prize in Physiology or Medicine (with Richard J. Roberts). His work has spurred new research in evolutionary biology, and has contributed to the development of both treatments and vaccines for infectious diseases, cancer and other ailments.
“The spirit of inquiry and the courage to challenge the status quo are at the heart of scientific progress”*…
Adam Mastroianni on the challenges– and opportunities– facing science…
Randomized-controlled trials only caught on about 80 years ago, and whenever I think about that, I have to sit down and catch my breath for a while. The thing everybody agrees is the “gold standard” of evidence, the thing the FDA requires before it will legally allow you to sell a drug—that thing is younger than my grandparents.
There are a few records of things that kind of look like randomized-controlled trials throughout history, but people didn’t really appreciate the importance of RCTs until 1948, when the British Medical Research Council published a trial on streptomycin for tuberculosis. Humans have possessed the methods of randomization for thousands of years—dice, coins, the casting of lots—and we’ve been trying to cure diseases for as long as we’ve been human. Why did it take us so long to put them together?
I think the answer is: first, we had to stop trusting Zeus.
To us, coin flips are random (“Heads: I go first. Tails: you go first.”). But to an ancient human, coin flips aren’t random at all—they reveal the will of the gods (“Heads: Zeus wants me to go first. Tails: Zeus wants you to go first”). In the Bible, for instance, people are always casting lots to figure out what God wants them to do: which goat to kill, who should get each tract of land, when to start a genocide, etc.
This is, of course, a big problem for running RCTs. If you think that the outcome of a coin flip is meaningful rather than meaningless, you can’t use it to produce two equivalent groups, and you can’t study the impact of doing something to one group and not the other. You can only run a ZCT—a Zeus controlled trial.
It’s easy to see how technology can lead to scientific discoveries. Make microscope -> discover mitochondria.
Clearly, though, sometimes those technologies get invented entirely inside our heads. Stop trusting Zeus -> develop RCTs.
Which raises the question: what mental technologies haven’t we invented yet? What brain switches are just waiting to be flipped?…
On reinvigorating science: “Declining trust in Zeus is a technology,” from @a_m_mastroianni.
Apposite to an issue he raises: “Citation cartels help some mathematicians—and their universities—climb the rankings,” from @ScienceMagazine.
[Image above: source]
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As we deliberate on discovery, we might send micro-biological birthday greetings to a woman who modeled the attitude and behavior that Mastroianni suggests: Ruth Sager; she was born on this date in 1918. A pioneering geneticist, she had, in effect, two careers.
In the 1950s and 1960s, she pioneered the field of cytoplasmic genetics by discovering transmission of genetic traits through chloroplast DNA, the first known example of genetics not involving the cell nucleus. She identified a second set of genes were found outside of the cell’s nucleus, which, even though they were nonchrosomomal, also influenced inherited characteristics. The academic community did not acknowledge the significance of her contribution until after the second wave of feminism in the 1970s.
Then, in the early 1970s, she moved into cancer genetics (with a specific focus on breast cancer); she proposed and investigated the roles of tumor suppressor genes. She identified over 100 potential tumor suppressor genes, developed cell culture methods to study normal and cancerous human and other mammalian cells in the laboratory, and pioneered the research into “expression genetics,” the study of altered gene expression.
“We’ve co-evolved with our microbes”*…
Allergies seem more prevalent and more severe these days because they are. Theresa MacPhail explains…
… Although allergy researchers may disagree on definitions, symptoms and methodology, all agree on one thing: Allergies have grown worse over the last few decades, and the staggering numbers of allergy sufferers worldwide is likely to continue growing. An estimated 235 million people worldwide have asthma, and anywhere from 240 to 550 million people globally may suffer from food allergies. Drug allergy may affect up to 10% of the world’s population.
There’s a consensus, looking at the last century’s data, that U.S. hay fever rates increased in the mid-20th century. Data suggests that the incidence of asthma increased beginning in the 1960s, peaking sometime in the 1990s. Since then, asthma rates have remained fairly constant. Respiratory allergic diseases and atopic sensitization (or skin allergy) have likely increased over the last few decades. But the most dramatic and visible increase has been the rise in global incidence rates for food allergies, which began in earnest in the 1990s and has grown steadily ever since.
There are, unsurprisingly, multiple theories about the cause. The hygiene hypothesis is one front-runner, positing that people who are “too clean” develop allergies. Many others think it’s our diet, that changes in the way we grow and prepare food have altered our gut microbiome, fueling allergies. Still others argue that manmade chemicals and plastics we encounter daily are making our immune systems more irritable.
What everyone agrees on is that the environment’s influence on our genes, or epigenetics, has played a large role in the rise of allergies, as does the makeup of our nose, gut and skin microbiomes. In the end, it appears, we are at least partially doing this to ourselves. Modern living is likely at the root of the recent rise in allergies…
Our very old immune systems can’t keep up with modern lifestyles and diets, leading to increases in all sorts of chronic health problems like allergies and obesity: “How Modernity Made Us Allergic,” from @TheresaMacphail in @NoemaMag. Eminently worth reading in full.
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As we stifle a sneeze, we might send infectious birthday greetings to Alfred Hershey; he was born on this date in 1908. A bacteriologist and geneticist, investigate bacteriophages, or phages—viruses that infect and replicate inside bacteria. In 1952, he and Martha Chase conducted the famous Hershey–Chase, or “Waring Blender” experiment. Their work confirmed that DNA, not protein, was the genetic material of life.
Hershey’s work with bacteriophage earned him a share of the 1969 Nobel Prize in Physiology or Medicine with Max Delbrück and Salvador Luria, “for their discoveries concerning the replication mechanism and the genetic structure of viruses.”
“The unexamined life is not worth living”*…
Diana Gitig reports on research that suggests that some of us agree more actively with Socrates than do others– and for a baked-in reason…
People who enroll in genetic studies are genetically predisposed to do so.
According to the Catalogue of Bias, ascertainment bias occurs when a sample being studied is not representative of the target population. This can produce misleading or even false conclusions, and it can be hard to detect since it cannot usually be identified by examining the sample alone. This is why many studies try to use variables other than participation in the study to make sure their samples are as representative as possible.
Studies examining how a particular treatment affects a particular health outcome often try to handle ascertainment bias by adjusting for “covariates,” things like education level or socioeconomic status, that could affect health outcomes independently of the treatment. But Stefania Benonisdottir and Augustine Kong at Oxford’s Big Data Institute have just demonstrated that we can determine if genetic studies are biased using nothing but the genes of the participants.
And they used that technique to show that there’s a genetic contribution that influences the tendency to participate in genetic studies…
People in a genetic database have segments of DNA in common unexpectedly often: “Want to have your genes tested? It might be genetic,” in @arstechnica.
The Benonisdottir and Kong paper, in Nature Genetics, is here.
* Socrates
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As we battle bias, we might send systemic birthday greetings to Sergei Winogradsky; he was born on this date in 1856. A microbiologist, ecologist, and soil scientist, he discovered chemoautotrophy (now better known as known as chemosynthesis) and the the Nitrogen cycle— which is to say that he pioneered the cycle-of-life concept.
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