(Roughly) Daily

Posts Tagged ‘DNA

“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


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.

The Nitrogen Cycle (source)


“For you formed my inward parts; you knitted me together in my mother’s womb. I praise you, for I am fearfully and wonderfully made.”*…

DNA is indisputably important to biological development. But, Alfonso Martinez Arias argues, far from being a blueprint for an organism, genes are mere tools used by life’s true expert builders: cells…

… Over the past century, scientists have discovered a material explanation for the source of life, one that needs no divine intervention and provides a thread across eons of time for all beings that exist or have ever existed: deoxyribonucleic acid — DNA. While there is little doubt that genes have something to do with what we are and how we come to be, it is difficult to answer precisely the question of what their exact role in all of this is.

A closer look at how genes work and what they can accomplish, compared to what they are said to achieve, casts doubt on the assertion that the genome in particular contains an “operating manual” for us or any other living creature. When it comes to the creation of organisms, we’ve overlooked — or, more accurately, forgotten — another force. The origin and power of that force are cells.

What makes you and me individual human beings is not a unique set of DNA but instead a unique organization of cells and their activities…

A fascinating essay, adapted from Martinez Arias’ forthcoming book, The Master Builder- How the New Science of the Cell Is Rewriting the Story of Life: “Cells, Not DNA, Are The Master Architects Of Life,” in @NoemaMag.

[Image above: source]

* Psalm 139: 13–14


As we delve into design, we might send insightful birthday greetings to Ernst Mayr; he was born on this date in 1904. A  taxonomist, tropical explorer, ornithologist, philosopher of biology, and historian of science, he is best remembered as one of the 20th century’s leading evolutionary biologists. His work contributed to the conceptual revolution that led to the modern evolutionary synthesis of Mendelian genetics, systematics, and Darwinian evolution, and to the development of the biological species concept.

His theory of peripatric speciation (a more precise form of allopatric speciation which he advanced), based on his work on birds, is still considered a leading mode of speciation, and was the theoretical underpinning for the theory of punctuated equilibrium, proposed by Niles Eldredge and Stephen Jay Gould. Mayr is sometimes credited with inventing modern philosophy of biology, particularly the part related to evolutionary biology, which he distinguished from physics due to evolutionary biology’s introduction of (natural) history into science.


“History repeats itself, in part because the genome repeats itself. And the genome repeats itself, in part because history does.”*…

The original Human Genome Project map of the human genome was largely based on the DNA of one mixed-race man from Buffalo, with inputs from a few dozen other individuals, mostly of European descent. Now, researchers have released draft results from an ongoing effort to capture the entirety of human genetic variation…

More than 20 years after the first draft genome from the landmark Human Genome Project was released, researchers have published a draft human ‘pangenome’ — a snapshot of what is poised to become a new reference for genetic research that captures more of human diversity than has been previously available. Geneticists have welcomed the milestone, while also highlighting key ethical considerations surrounding the effort to make genome research more inclusive…

The draft genome, published in Nature on 10 May, was produced by the Human Pangenome Reference Consortium. Launched in 2019, the international project aims to map the entirety of human genetic variation, to create a comprehensive reference against which geneticists will be able to compare other sequences. Such a reference would aid studies investigating potential links between genes and disease.

The draft pangenome follows the 2022 publication of the first complete sequence of the human genome, which filled gaps that had been left by the original Human Genome Project. But unlike the original draft human genome and its successor, both of which were derived mostly from the DNA of just one person, the draft pangenome represents a collection of sequences from a diverse selection of 47 people from around the globe, including individuals from Africa, the Americas, Asia and Europe…

More at “First human ‘pangenome’ aims to catalogue genetic diversity,” in @Nature.

See the paper on the Pangenome Project here; and for more background, “This new genome map tries to capture all human genetic variation.”

* Siddhartha Mukherjee, The Gene: An Intimate History


As we go wide on genetics, we might send microscopic birthday greetings to Christian Anfinsen; he was born on this date in 1916. A biochemist, he won the 1972 Nobel Prize for Chemistry for his research on the shape and primary structure of ribonuclease (the enzyme that hydrolyses RNA), in whihc he found that found that its shape and consequently its enzymatic power could be restored– leading him to conclude that ribonuclease must retain all of the information about its configuration within its amino acids.


Written by (Roughly) Daily

May 14, 2023 at 1:00 am

“I have all these great genes, but they’re recessive. That’s the problem here.”*…

DNA Sequence chromatograms produced by automated sequencing machines

When the Human Genome Initiative published its first findings in 2002, the world was shocked. Genetic biologists, however, had long ago come to realize that DNA sequences are only part of the story of how organisms develop…

Fueled by the expectation that knowing the sequence of our DNA would tell us who we are, US funding agencies launched one of the most ambitious scientific efforts of all time in 1990. I refer, of course, to the Human Genome Initiative. Since then, the pace of that effort has been furious:even before the decade was over, the finishing line was clearly in view. When in February 2001, two rival teams announced the results of their first analysis of this invaluable information, their report made front-page headlines around the world. Humans, it seems, have far fewer genes than had been expected — in fact, only a third more than the lowly roundworm. How can this be? And what does it mean? Are we really so similar to, and so little more than, mere worms? News of the extent of our commonality with all living species is as stunning as it is humbling. But at the same time, it invites a certain incredulity — and that not merely because of human pride. Simple observation of the manifest diversity of life also makes us resist, for it is impossible not to wonder: what is it, if not the number (and in many cases, even the structure) of the ‘genes’ encoded in our DNA that accounts for the extraordinary differences among living organisms? For the answer to this question, it seems that we will have to look to the regulatory dynamics that determine how the sequence information of the DNA is to be used by the cell. Here, in the complex regulation of genetic transcription, of translation, of protein structure and function, is where we will find what makes us human beings rather than worms, flies or mice. Knowledge of the sequence of our DNA can tell us an enormous amount, but it can almost certainly not tell us who we are.

But not everyone was taken aback by this news. While readers of the popular press may have been stunned, few biologists working at the frontiers of research in molecular genetics were astonished. True, they had expected a larger number of human ‘genes’, but they had long ago come to realise that DNA sequences are only part of the story of how organisms develop, and even of what we mean by a ‘gene’. They recognise, for example, that the spatial and temporal patterns of expression of a gene are even more crucial to the specification of an organism than the structure of that ‘gene’ is. They also know that no single definition of this word ‘gene’ can suffice. Of the many different definitions that are required to make sense of current usage, two stand out with particular clarity: one referring to a particular region of the DNA, and another to the unit of messenger RNA that is used in the synthesis of a particular protein. The number of genes of the second kind is in fact very much larger than that of the first kind (current estimates suggest more than ten times as many), for the fact is that many different ‘genes’ can be constructed out of a single specified region of the DNA. Because the particular context in which they use the word makes its meaning quite clear, ambiguities in usage rarely create problems for practising biologists. Not so, however, for most readers. Outside the laboratory, such linguistic uncertainties can lead to both confusion and misunderstanding — not only around the question of how many genes we have, but also of what genes are made of, where they reside, what they do and, perhaps most important, what genes are for.

The good news is that research in genetics has never been more exciting, and over the last few decades both the depth and the breadth of our understanding of the nature of genetic activity have grown spectacularly. With each advance, the picture of the role of genes in development that biologists learn to draw grows ever more complex and sophisticated, and in ever more conspicuous defiance of the simple mantra with which they began. The word ‘gene’ does not begin to do justice to the ingenuity of the mechanisms required to put biological organisms together — no more than the concept of the neuron does to the ingenuity and dynamic complexity of neural organisation, and no more than talk of individual minds to the complexities of language and cognition…

Unpacking the genome hasn’t turned out to be the master key to understanding life that many thought it would be– but that’s no reason not to celebrate what it does illuminate: “The century of the gene,” from Evelyn Fox Keller in @EngelsbergIdeas.

* Calvin, in Calvin and Hobbes (Bill Watterson)


As we investigate inheritance, we might spare a thought for D’Arcy Wentworth Thompson; he died on this date in 1948.  A classics scholar who was also an accomplished biologist and mathematician, Thompson is best remembered for On Growth and Form (1917, new ed. 1942), a profound consideration of the shapes of living things, starting from the simple premise that “everything is the way it is because it got that way.”  Thus one must study not only finished forms, but also the forces that molded them: “the form of an object is a ‘diagram of forces’, in this sense, at least, that from it we can judge of or deduce the forces that are acting or have acted upon it.”

The book paved the way for the scientific explanation of morphogenesis, the process by which patterns are formed in plants and animals.  Thompson’s description of the mathematical beauty of nature inspired thinkers as diverse as Alan Turing and Claude Levi-Strauss, and artists including Henry Moore, Salvador Dali, and Jackson Pollock.  Peter Medawar, the 1960 Nobel Laureate in Medicine, called On Growth and Form “the finest work of literature in all the annals of science that have been recorded in the English tongue.”


Written by (Roughly) Daily

June 21, 2022 at 1:00 am

“The world is bound in secret knots”*…

Everyone knows what a knot is. But knots have special significance in math and science because their properties can help unlock secrets hidden within topics ranging as widely as the biochemistry of DNA, the synthesis of new materials, and the geometry of three-dimensional spaces. In his podcast, The Joy of Wh(Y), the sensational Steven Strogatz explores the mysteries of knots with his fellow mathematicians Colin Adams and Lisa Piccirillo

How do mathematicians distinguish different types of knots? How many different kinds of knots are there? And why do mathematicians and scientists care about knots anyway? Turns out, there’s lots of real-world applications for this branch of math, now called knot theory. It started out with the mystery of the chemical elements about 150 years ago, which were, at the time, thought to be different kinds of knots tied in the ether. Nowadays, knot theory is helping us understand how enzymes can disentangle strands of linked DNA. And also, knot theory has potential in basic research to create new kinds of medicines, including some chemotherapy drugs. But in math itself, knot theory is helping mathematicians work out the riddles of higher-dimensional spaces…

The study of knots unites the interests of researchers in fields from molecular biology to theoretical physics: “Untangling Why Knots Are Important,” from @stevenstrogatz in @QuantaMagazine. Listen here; read the transcript here.

Athanasius Kircher


As we take stock of tangles, we might might send nicely-tied birthday greetings to a beneficiary and user of knot theory, Francis Collins; he was born on this date in 1950. A physician and geneticist, he discovered the genes associated with a number of diseases, led the Human Genome Project, and served as the director of the National Institutes of Health.


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