Epigenetics

Trigger warning!: Donald Trump mentioned. 😉 From Nicholas Staropoli at Epigenetics Literacy Project: This week’s features: A professor’s troubling politicization of epigenetics in Gizmodo, Men’s Health quotes me on male fertility but mistakes correlation for causation. Plus see what’s trending on the Epigenetics Literacy Project. On a larger scale, the amount of stress that Americans are going through now, because of Trump—there is going to be an evolutionary consequence. Peter Ward Professor, Department of Biology, University of Washington More. Although Ward’s appointment is in biology at U Washington, as Staropoli notes, his main publications have been in astronomy and paleontology. One of Ward’s better-known works is Rare Earth (2000), on why Earth is especially habitable (now free at the link as Read More ›

The paper discusses epigenetics. Of course it’s true that we are more than the sum of our genes but you know things are changing when researchers dare say so. From ScienceDaily: Epigenetics between the generations He and his team at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany used fruit flies to explore how epigenetic modifications are transmitted from the mother to the embryo. The team focused on a particular modification called H3K27me3 that can also be found in humans. It alters the so-called chromatin, the packaging of the DNA in the cell nucleus, and is mainly associated with repressing gene expression. The Max Planck researchers found that H3K27me3 modifications labeling chromatin DNA in the mother’s egg Read More ›

So genes don’t rule?  From ScienceDaily: Mice have a reputation for timidity. Yet when confronted with an unfamiliar peer, a mouse may respond by rearing, chasing, grappling, and biting — and come away with altered sensitivity toward future potential threats. What changes in the brain of an animal when its behavior is altered by experience? Research at the University of Illinois led by Professor of Cell and Developmental Biology Lisa Stubbs is working toward an answer to this question by focusing on the collective actions of genes. In a recent Genome Research publication (DOI: 10.1101/gr.214221.116), Stubbs and her colleagues identified and documented the activity of networks of genes involved in the response to social stress. “The goal of this study Read More ›

Does anyone remember the Altenberg 16, a group of dissenting evolution theorists who met so nervously at the Konrad Lorenz institute in Austria that they locked a journalist out of the meeting?* They seem to be continuing to write papers, according to Massimo Pigliucci, I have just spent three delightful days at the Konrad Lorenz Institute for theoretical biology in Vienna, participating to a workshop of philosophers and biologists on the question of how to think about causality, especially within the context of the so-called Extended Evolutionary Synthesis, the currently unfolding update to the standard model in evolutionary theory. Here’s one: Susan Foster, Incorporating the environmentally sensitive phenotype into evolutionary thinking: phenotypic plasticity mediates the relationship between selection and genotype Read More ›

From ScienceDaily: Scientists have looked at all 14,500 participants in Children of the 90s and found that if a girl’s maternal grandmother smoked during pregnancy, the girl is 67 percent more likely to display certain traits linked to autism, such as poor social communication skills and repetitive behaviors. … The discovery, published today in Scientific Reports, is part of an ongoing, long-term study of the effects of maternal and paternal grandmother’s smoking in pregnancy on the development of their grandchildren, who are all part of Children of the 90s. By using detailed information collected over many years on multiple factors that may affect children’s health and development, the researchers were able to rule out other potential explanations for their results. Read More ›

From ScienceDaily: The impact of environmental change can be passed on in the genes of tiny nematode worms for at least 14 generations — the most that has ever been seen in animals — scientists have discovered. … “We discovered this phenomenon by chance, but it shows that it’s certainly possible to transmit information about the environment down the generations,” says Lehner. “We don’t know exactly why this happens, but it might be a form of biological forward-planning,” adds the first author of the study and CRG Alumnus, Adam Klosin. “Worms are very short-lived, so perhaps they are transmitting memories of past conditions to help their descendants predict what their environment might be like in the future,” adds Vavouri. … Read More ›

From ScienceDaily: Paper. (paywall)Our genome is made up of 6,000 million pieces of DNA that combine four “flavors”: A, C, G and T (Adenine, Cytosine, Guanine and Thymine). It is our Alphabet. But to this base we must add some regulation, just like the spelling and grammar of that alphabet: this is what we call Epigenetics. “In epigenetics, there there are “accents,” called DNA methylation, which means having a C or a methyl-C. The first one usually means that a gene is expressed and active, while the second one implies that a gene is silent and inactive. Our DNA “speaks” when it produces another molecule called RNA (Ribonucleic Acid). Until very recently, it was believed that this molecule was only Read More ›

Someone asked. Essentially, a great deal of important biological information is captured and stored outside of our DNA, as opposed to arising, Darwinism-style, through random genetic mutations. Neo-Darwinian evolution means that all new traits are due to mutations in DNA, acted on by “natural selection.” Jonathan Wells summarizes the problem here: [T]he idea that embryo development is controlled by a genetic program is inconsistent with the biological evidence. Embryo development requires far more ontogenetic information than is carried by DNA sequences. Thus Neo-Darwinism is false.” (Wells, “Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA,” BIO-Complexity And in Chapter 14 of Darwin’s Doubt, Steve Meyer offers: These different sources of epigenetic information in embryonic cells pose an enormous Read More ›

From Jef Akst at The Scientist: While animal cells undergo two rounds of reprogramming during reproduction to wipe clear most of the methyl marks that decorate their DNA and histones, plants leave their epigenomes largely intact from one generation to the next. In plants, this results in epialleles—stably inherited alleles encoded by methylation, rather than by gene sequence—that control subtle phenotypes, such as timing of flowering or fruit ripening. Most of the differences [between individuals] that we see are caused by genetic variation,” says Colot. “But it’s not all caused by genetic variation. What would be caused by this epigenetic variation could be as important.” Whether these epialleles can be adaptively altered by the environment remains a matter of debate, Read More ›

From ScienceDaily: In a new study published in the Journal of Allergy and Clinical Immunology, researchers have now found a new principle for how epigenetic changes can occur. They have showed that one enzyme, tryptase, can be found in the nucleus of cells and that tryptase can cleave off the tails of histones. In this way, certain epigenetic modifications of the histone tails are removed. A very interesting finding was that this mechanism is important for maintaining the identity of the cells. Cells that lacked tryptase showed major changes, including a loss of their cellular identity and they also started to proliferate in an uncontrolled way. These effects were seen in mast cells which are central in allergic reactions. The Read More ›

From Ann Gauger at at Evolution News & Views: Yesterday started out as an ordinary Tuesday. Then I set out to read a recent paper published in the journal Cell, “Nuclear Localization of Mitochondrial TCA Cycle Enzymes as a Critical Step in Mammalian Zygotic Genome Activation,” by R Nagaraj et al. It reported something rather odd that caught my eye. Very early embryos (at the two- or four-cell stage in mouse or human respectively) undergo a critical transition: they have to go from relying on RNAs and proteins loaded into the egg before fertilization by the mother, to making their own RNA and protein. The phenomenon is called embryonic genome activation. In order to activate their genomes, embryos have to Read More ›

From ScienceDaily: The study examined DNA methylation — an “annotation” of DNA that alters gene expression without changing the genomic sequence itself — in a group of diverse Latino children. Methylation is one type of “epigenetic mark” that previous research has shown can be either inherited or altered by life experience. The researchers identified several hundred differences in methylation associated with either Mexican or Puerto Rican ethnicity, but discovered that only three-quarters of the epigenetic difference between the two ethnic subgroups could be accounted for by differences in the children’s genetic ancestry. The rest of the epigenetic differences, the authors suggest, may reflect a biological stamp made by the different experiences, practices, and environmental exposures distinct to the two ethnic Read More ›

From Anna Azvolinsky at The Scientist: In a study published last week (January 3) in eLife, Burchard and colleagues showed that about 75 percent of methylation signatures could be explained by the children’s genetic ancestry. The other 25 percent, however, is likely due to social or environmental factors that co-vary with self-identified race/ethnicity. The study is among the first to probe how the epigenome is influenced by genetic ancestry. Additional investigations are needed to better understand to what extent race and ethnicity are interchangeable with genetic ancestry, experts say. … It is challenging to draw conclusions from methylation analyses like this one because “a lot of the variation can be explained by background genetic variation of individuals,” noted Conley. In Read More ›

Epigenetics (changes in the course of life that alter the state in which genes are inherited) seems to offer explicitly science-based explanations for observations, rather than the decades-long usual: We can fit even this into Darwinism! For example,  “Evolutionary psychology: The grandmother thesis, yet again” And also, of course, this: “‘Grandmother’ thesis in human evolution takes a hit.” (Shrug.) That’s what’s killing Darwinism. For everything to fit in, the theory must be everything and thus nothing. For example, Evolutionary psychology does not, for the most part, explain puzzling human behavior. It offers Darwinian explanations for conventional behavior that are intended to supplant traditional ones. For example, why we are sexually jealous (not fear of abandonment, but “sperm competition”); why we don’t stick to our goals Read More ›

From ScienceDaily: Reporting research in the scientific journal Cell, Vienna-based scientists from the Institute of Molecular Biotechnology (IMBA) have discovered that not only do fertilized egg cells trigger epigenetic reprogramming of sperm DNA but this process is closely monitored to safeguard genomic integrity. “When the sperm enters the egg cell, the densely compacted male chromatin has to be entirely ‘unpacked’ and restructured around protein scaffolds called histones,” explained Sabrina Ladstätter, first author of the study. “Using fertilized mouse eggs, we showed that the egg cell actively triggers demethylation of the paternal DNA — in other words, it initiates epigenetic reprogramming by stripping any previous epigenetic memory passed on from the father. This allows the zygote to start afresh and create Read More ›