Dan Rhoads
Dan is a postdoc working at the University of Cyprus in developmental biology. He has a BSc in molecular biology and a PhD pharmacology and biochemistry.
Articles by Dan Rhoads:
Book Review: On Growth and Form
Unlike most naturalists and biologists before and since, who were only satisfied if they could understand a particular form by the configuration of its immediate precedents, D’Arcy Thompson was quite satisfied with a mathematical description or a physical analogy. He truly viewed the variety of biological forms that he looked at with the eyes of…
Nobel Prizes in Molecular Biology
There are a lot of places to read about the history of molecular biology, but one theme that generally seems to emerge is that discoveries are dependent upon the experimental technology. Take this list of Nobel prizes for molecular biology for instance.
How Science Is Changing What We Eat
From about the time our ancestors traded the nomadic lifestyle for more urban settings, agriculture has been important. It’s no coincidence either — selective breeding and domestication of crops made civilization possible. And in an era when the capacity for cultivating the primary grain and vegetable crops of the world is being stretched to its…
Expectations for a Young Researcher
I find myself asking, what expectations would I have for me, starting out in a new lab?
Against Animal Rights Terrorism
In research relating to molecular biology, it is common for animal models of disease to be used, especially in projects directed towards making biomedical discoveries and breakthroughs. So I find it very important to occasionally read about and blog against animal rights’ terrorists.
Selfish Genes and Gene-Centered Evolution
But despite Dawkins’ notoriety, maybe there are some readers here who haven’t read The Selfish Gene – I didn’t until two years ago, actually. So, what specifically is The Selfish Gene about?
A Stephen Jay Gould Highlight Reel
With it almost being Darwin Day, it seems only right to review a book on perhaps the best popularizer of evolutionary biology in the 20th Century, Stephen Jay Gould.
Writing a Lot in Academia
We all know that surviving in the publish-or-perish world of academia requires that we write a lot. For myself, I view blog-writing as a form of writing practice — I used to really suck at it. Okay, actually I still get stuck sometimes when trying to write, especially for grants.
Stem Cell Century: The Law of a Controversial Science
Russell Korobkin’s book Stem Cell Century: Law and Policy for a Breakthrough Technology is the first book to address not just embryo destruction but the full range of important policy questions raised by stem cell research and regenerative medicine.
Science as Progress, and More on the Philosophy of Science
Following up on my recent post about The Nature of Scientific Observation, I left two-thirds of Chalmers’ book What is This Thing Called Science untouched, including discussions on Bayes’ theorem and the New Experimentalism.
A Grad Student, a Postdoc, and a Professor are Walking…
A grad student, a post-doc, and a professor are walking through a city park and they find an antique oil lamp. They rub it and a Genie comes out in a puff of smoke. The Genie says, “I usually only grant three wishes, so I’ll give each of you just one.” “Me first! Me first!”…
Gates Foundation Innovations on Funding Science
All fields in Science thrive on fresh ideas that contest accepted theory. Yet, researchers seeking funded face ever greater competition for limited funds – funds that are overly wedded to safe, unadventurous research.
The Nature of Scientific Observation
Currently I’m reading Alan Chalmers’ What is this thing called science?, with specific interest in the questions of expertise and the uniqueness of science as a foundation for knowledge.
Revising the NIH Grant Review Process
NIH analysis indicates that an increasing number of meritorious applicants that were ultimately funded had to resubmit their applications multiple times which increased burden on applicants and reviewers alike. How should the NIH address this problem?
Assessing the Bitesize Bio Experience
With the new design for Bitesize Bio, I thought it appropriate for a re-assessment of what blogging here means to me. Nick started this site as a blog for molecular biology, with a bit of a dream to turn it into a community for aspiring molecular biologists. By providing a mix of personal development, technique…
Dance, Scientists, Dance!
Are you the sort of scientist who taps her toes while working in the laboratory? Didn’t I see you pirouette on your way to the fume hood? In fact, doesn’t your entire scientific career feel like one big dance?
Biotechnology Imitates Nature
“A collaborative effort of Janine Benyus’ Biomimicry Guild and Gunter Pauli’s ZERI Foundation, Nature’s 100 Best brings to light fascinating secrets of nature capable of revolutionizing nearly every aspect of our economy, and changing our destructive relationship with the environment to one of mutual benefit.”
Science and Entrepreneurship
Scientist entrepreneurs have an inherent advantage over other entrepreneurs. They are closer to the future than the rest of us. That proximity to the cutting edge gives them the opportunity to start businesses based on science that are truly breakthrough in nature.
Career Options After Academia
It’s a good article. But what really makes it a must-read for students thinking about grad school is the fact that these 26 one-time grad students have ended up in a truly diverse range of careers.
Small World Competition Open for Voting
Small World is regarded as the leading forum for showcasing the beauty and complexity of life as seen through the light microscope. For over 30 years, Nikon has rewarded the world’s best photomicrographers who make critically important scientific contributions to life sciences, bio-research and materials science.
Terrorism: The Animal Research War
After some of the blog posts that I’ve written on animal rights’ extremists and violence against animal researchers, there’s now a review of a most appropriate book on the topic available in Science – Scientists Under Siege. Suppose you are a scientist and a finalist for the position of vice president for research at the…
Evolution of Lager Yeasts
For something a bit more on the fun side, at least if you enjoy a pint of beer now and then – a genomic-based study has reconstructed the origins by hybridization of the lager yeast Saccharomyces pastorianus, published in the journal Genome Research [Press release]. For thousands of years, ale-type beers have been brewed with…
Expectations of a Grad Student
Graduate school in Biology is very different from undergraduate education, Medical School, Law School, or other professional graduate training programs. In graduate school, you will become your own teacher and your own motivator… Experiencing self-doubt is typical, and is best countered by keeping the lines of communication open between yourself and fellow students, and between yourself and your advisor.
Debunking the ‘GE Crops are Bad’ Myth
Pamela Ronald has an article up for anyone interested in the pro’s and con’s of genetically engineered or genetically modified crops. In 10 Things About GE Crops to Scratch from your Worry List, there are brief but succinct explanations of why common arguments against GE crops are without merit.
A Presidential Candidate on Science Policy
What do Obama’s responses tell us about him and his support of scientifically-sound policies? Well, not necessarily that he is personally good on science – but he does apparently know how to hire decent scientific advisers, and listen to them. That is huge.
Nourishing Innovation: Open Science and Federal Support
“An urgent problem is how to nourish the goose of basic research [and innovation],” wrote Arthur Kornberg. The solution: Open Science and Federal Support.
NIH and English as the Language of Science
While there’s a lot in “For the Love of Enzymes” to talk about, for this post I’m focusing on just one passing reference that Arthur Kornberg makes on NIH and the use of English as the language of science. In it, Kornberg is describing the factors that made NIH a huge success…
Animal Rights Terrorism, Redux
Last Thursday’s post on the animal rights firebombing in Santa Cruz earned me a couple outraged comments, so I suppose I did something right. I’m not too concerned with what they think, but they’re comments reflect what I was saying.
Polarity, Diffusion, and Cellular Aging
Two recent articles provide the theoretical and experimental proof that polarity and asymmetry are reducible to something as simple as diffusion – even in a complex cellular process such as aging.
Animal Rights’ Firebombings
It would seem that animal rights’ extremists are at it again, this time with a spate of firebombings in Southern California. One might be sympathetic, if one were superbly naive.
A Microcosm for Biology
The theme running throughout is that E.coli is a microcosm for understanding all of life. Zimmer reinforces this theme with repeated mention of a Jacques Monod quote, “What is true for E.coli is true for the elephant.
New Search Engine for Biology
Here’s something that I’m sure all our readers will find interesting, if they haven’t heard it already: there’s a web search engine out now for specifically designed for biologists.
Science as Culture
Dan shares some commentary on a review of the World Science Festival by Lawrence Krauss. At its core, science is a cultural phenomenon, complete with social customs. There are some differences between the culture of science and other cultures however…
Sir Paul Nurse on Information in Biology
In an opinion piece in Nature, Sir Paul Nurse suggests that we supplement reductionism with studying the information content in cells. Take a look at the modern version of holism in biology.
Notes of a Biology Watcher
Part science, part prose, Lewis Thomas’ books Lives of a Cell and The Medusa and the Snail are creative, thought-provoking, and entertaining.
A Not So Good GM Crop – Pharma Corn
On Tuesday I talked about an example of a good GM crop. Now I highlight one that I think may not be such a good idea.
Good GM Foods – Bt Corn as an Example
Dan takes a look at a potentially good GM crop already in use, and links to a couple informative resources regarding the risks and benefits of using genetics to improve the food we harvest.
The Chinese are Coming… to Grad School
It is now more likely that the next graduate student you meet in the US is from one of two Chinese alma maters than from any other U.S. university?
Molecular Movies and Animations
In a recent issue of Cell, there’s an interesting commentary on Molecular Movies… Coming to a Lecture Near You. The article got me thinking – wouldn’t it be useful if there were more skilled graphics and animation experts at the disposal of researchers? Conveying the information content of your average proposal, report, lecture, or public…
Falling for Molecular Biology
Last week’s issue of Science has a book review that might appeal to any Bitesize Bio reader: First Adventures in Science. The book in question is Falling for Science, a collection of essays by grad students (current and former) and mentors on the crucial roles particular objects played in sparking their choice of science as…
The Slowing of Drug Discovery
The June 20th issue of Science had an interesting story worth noting (interesting to anyone into molecular pharmacology, anyway), on Drugs, Industry, and Academia. It caught my attention because of some conversations that I’ve been having recently with colleagues and friends in the industry – how is Big Pharma going to maintain itself amid slowing…
Ignorance and Democracy
Catching up on the news after being away for two weeks – Lawrence Krauss had short comment in the New Scientist, Stop creationists undermining school science. The very quote-worthy punchline being: Say that you are in charge of developing a state-wide high-school curriculum in French-language studies, and that you need the advice of a group…
Reductionism and Biology
Here is an excerpt from a great article that I found recently on Reductionism in Biology from The Stanford Encyclopedia of Philosophy.
Thinking About Grad School
Searching for a grad school? This 7 minute video with advice from from students, staff and faculty at Duke University might help.
Switching Disciplines
In evaluating my own job prospects in a difficult job market and limited by personal circumstances that confine me to a very small region, I have been forced to widen my job search to related disciplines. There just isn’t a bounty of jobs in cell and molecular biology out there for young researchers. As a…
Transferable Job Skills in Science
Relating to my post last week on jobs in industry, concerning the slight disconnect between jobs in academia versus industry — the NatureJobs podcast has a special episode this past week from NatureJobs: From Academia to Industry [mp3]. In it, Pfizer’s Anthony Harrison talks about transferable skills that could help you move from a university-based…
Thoughts on Industry Jobs
Sandra at Discovering Biology in a Digital World has some interesting thoughts on Life science PhD’s as industrial strength technicians. What I thought interesting was this bit: This wasn’t for a technician job, but a few years ago, I was in the position of hiring someone to help me on an education project. I interviewed…
Birth of the Cell Doctrine
As a general rule of thumb, it is recommended to be familiar with the history of one’s scientific field, and not merely the contemporary trends of thought. That’s generally why I liked The Birth of the Cell so much when I read it. Dissatisfied by the standard accounts of the origin of the cell doctrine,…
How I Chose a Grad School
A reader recently asked for an explanation “about choosing grad schools, taking the GREs, visiting campuses, speaking to potential advisors, and how you guys decided on where to go.” For me, to be honest, I think that I was astoundingly naive in my decision-making for where to go for graduate school.
Building Science in a Small Country
Dan makes some interesting observations on the grant funding system in Cyprus, the country he recently relocated to.
Post-Modernism versus Science
The methods of science aren’t foolproof, but they are indefinitely perfectible. Just as important: there is a tradition of criticism that enforces improvement whenever and wherever flaws are discovered.
How Cancer Begins
Every major field has its leading thinkers, and the biology of cancer is no different. What makes their impact heard better is when one of those leaders writes a book about it. Given my interest in molecular biology of cancer, I naturally have my favorite such book on the topic – Robert Weinberg’s One Renegade…
Defining Life Itself
What is this thing called ‘Life?’ One popular game in the relevant area of philosophy is to provide robust counter examples, which reveal failures in operational definitions of life. Failed attempts include physiological, metabolic, biochemical, genetic and thermodynamic definitions of life, all of which face problems. For example, a metabolic definition finds it hard to…
Enduring Grant Writing Edits
Staying in science – getting funding and getting peer reviewed – is tough. That’s one of my main gripes with creationist simpletons who imply that scientists are uncritical of their peers, and that criticism is directed solely at those who refuse to take their claims at face value. They have no clue whatsoever what they’re…
Antibiotics as a Carbon Source
Here’s the context: “Eighty years after Alexander Fleming discovered penicillin on a moldy culture dish, the battle against killer bugs is faltering. More and more bacteria – including insidious tuberculosis strains that have cropped up2 – now shrug off almost all antibiotics. Meanwhile, few new antibiotics are reaching the clinic. Medicine is on the defensive,…
More on the Promise of Biomedical Breakthroughs
Following up on my post last week about Emerging Biomedical Technologies and their Promise, Nature had a timely editorial in last week’s issue. In Broken Promises, the article describes precisely the phenomenon that I was referring to: Intense public support for clinical research can be a mixed blessing – and the hunt for a vaccine…
Management Skills in Science
Amid growing recognition that a successful scientific career requires skills beyond scientific acumen, institutions are racing to provide management training for newly minted principal investigators. Young scientists spend years conducting complicated experiments and crunching data, but when they are finally given the keys to their own lab, they suddenly face tasks they were never trained…
Emerging Biomedical Technologies and their Promise
Do you remember how around ten years ago, gene therapy was supposed to cure various inheritable diseases? Or how various discoveries herald the expected development of new vaccines (AIDS being a notable example)? Most scientists would agree that they try to ‘sell’ their research to publishers and foundations by exaggerating the importance of findings or…
Comments on Communicating Expertise and Knowledge
Amid the misguided rhetoric of some who suggest that the science community cease trying to share their expertise and knowledge with the public, and the all-to-common response to expertise, I came across a thoughtful piece worth commenting on here. Over at Pure Pedantry, Jake Young posts on the problem of expertise. He writes: The problem…
Genome Structure and Modularity
A minireview recently in Genomics caught my eye with the title Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes that sounded just like a passage that I recalled from Richard Dawkins’ The Selfish Gene: …the ‘environment’ of a gene consists largely of other genes, each of which is itself being selected for its…
On Animal Rights Activism
Creationism isn’t the only form of pseudoscience. One form that specifically targets biomedical, and especially pre-clinical, research is that of animal rights activism. Often resorting to terrorism, they are not above arson, home invasion, and vandalism. Groups such as the Animal Liberation Front (ALF) and the Animal Liberation Brigade (ALB) in Southern California and their…
Wellcome Image Awards 2008
After yesterday’s bit of whimsical late-night creativity, I thought that today might be a good time to share the results of the 2008 Wellcome Image Awards. These images have been captured using both traditional and cutting-edge imaging techniques, from the simple light microscope to the latest in computer-aided imaging. Their artistry is astounding, and brings…
Late Night Lab Entertainment
And now for something completely different… It’s always good to introduce a little levity to the lab, before we as researchers begin to take ourselves too seriously. With that in mind, below the fold, I have a handful of YouTube videos shared by molecular biology grad students who apparently needed to introduce a little creativity…
Why Have Journal Club?
Relating to my recent comments on seminars, a beginning grad student or undergrad researcher might wonder why journal club is such a good thing. Or you might not be wondering, since the benefits are more or less the same: digesting, discussing and analyzing research findings. But whether or not you realize the benefits of journal…
Top 5 Books from Experimental Biology
I just got done reading Ernst Mayr’s The Growth of Biological Thought, which is on the history and philosophy of biology, from Aristotle to ~1980 (written in 1982). Of particular interest to me was the section on the Modern Synthesis, where the views on evolution of the geneticists and other experimental biologists were reconciled with…
Stop and Enjoy the Seminars
Continuing in the same frame of mind as my last post, What Comes After Grad School, I was thinking about something that Alex said: It reminds me of a bit of advice given to a fellow postdoc by Dr. Richard Hynes – try to attend every seminar. I would also add that in my comparatively…
What Comes After Grad School
For many of us, grad school immerses us so deeply in first-hand laboratory research that we begin to think that that’s all there is, and when faced with either limited opportunities for postdoctoral and (later) faculty research positions, we become blind to our other options. Others simply want to get out of academia and don’t…
Zebrafish: Making Development Transparent
With the recent development of transparent Zebrafish, allowing scientists to directly view its internal organs, and observe processes like tumor metastasis and blood production after bone-marrow transplant, it seems appropriate to describe Zebrafish as a model organism.
Critical Learning Habits
One view on the aim of graduate studies towards a PhD is to foster critical learning and thinking habits, much more so than to simply learn facts. You’re supposed to learn how to “think like a scientist,” or develop and mature your intellectual behaviors in the discussions of difficult concepts (AKA, problems). “Habits of Mind…
GenePaint: Visualizing Developmental Expression
In fields describable as functional or experimental biology, one tool that could be both useful and beautiful is a digital atlas of gene expression patterns in a representative mammal during development. That’s just what GenePaint represents. In studying any individual gene product, its global function in the whole organism needs to be addressed. Clearly we…
Wrapping up a Week of Just FAK
Just Science week has been fun, reading four recent journal articles on focal adhesion kinase (FAK). It has helped me refresh myself on FAK as I got back to writing fellowship applications – although it had the added effect of taking time away from said writing activities. So today I thought a recap was in…
FAK and Phosphatidyl Inositol in Cell Polarity
After the past three days of blogging focal adhesion kinase (FAK), each focusing on an important regulator of cell adhesion dynamics and cell motility, I’m going to turn my attention to phosphatidyl inositol-3 kinase (PI3K). PI3K has a regulatory subunit (p85), and a catalytic subunit (p110) capable of catalyzing the phosphorylation of the D3 position…
Dissecting Molecular Interactions Between FAK and Paxillin
In keeping with this week’s trend of just science blogging on FAK, let’s take a look at another critical protein-protein interaction – this time with the scaffolding protein Paxillin. Specifically, how do FAK and Paxillin interact and why? Conveniently, there’s a recent paper by Danielle Scheswohl et al., from the Schaller lab: Multiple paxillin binding…
FAK and Lamellipodia
Yesterday, I ended a post about FAK, Pyk2 and regulation of RhoA activity by asking “So, what about Rac regulation by [FAK] and Pyk2?” Today, let’s discuss a paper relating FAK/Pyk2 function studies on Rac1: Regulation of lamellipodial persistence, adhesion turnover, and motility in macrophages by focal adhesion kinase. Katherine Owen, et al., focus on…
FAK, Pyk2, and p190RhoGEF in Cell Motility
Focal adhesion kinase is an important signaling molecule in integrin-mediated cell signaling and cell adhesion. In FAK genetic knockout (FAK-null) cells, its closely homologous relative proline-rich kinase (Pyk2) is upregulated in FAK-null fibroblasts to partially compensate, but the mechanisms of Pyk2 upregulation and compensation remain undefined1. A recent study by Yangmi Lim, David Schlaepfer, and…
Metabolism as Biogenesis
One of the several popular views regarding the origin of life stems from thermodynamics. Harold Morowitz refers to it as “Metabolism recapitulates biogenesis”. In PLoS Biology there’s an interesting essay that was submitted posthumously by the chemist Leslie Orgel on this subject – The Implausibility of Metabolic Cycles on the Prebiotic Earth. Orgel takes a…
Geometries of Cells
Form follows physics in the fly eye, say Sascha Hilgenfeldt, Sinem Erisken, and Richard Carthew Simple forces, complex shapes: While most biological features appear complex in their geometries and varieties of components, appearances can be deceiving. That finding is supported by a recent modeling study by Hilgenfeldt, et al., looking at the arrangement of cone…
Worms: Models of Development
Continuing with the recent theme on model organisms, there is the nematode (roundworm) Caenorhabditis elegans. This organisms is particularly useful owing to the fact that it has very defined development patterns involving fixed numbers of cells, and it can be rapidly assayed for abnormalities. Further, strains are cheap to breed and can be frozen. When…
How Should We Customize Life?
The big biotech news of the week has been the successful construction of an artificial bacterial genome by J. Craig Venter et al., chemically assembled from scratch. While the genome is little more than a watermarked version of the wild bacterium Mycoplasma genitalium, it is now technologically feasible to construct custom genomes for bacteria of…
Xenopus as a Model for Early Development
Another popular model organism is the African Clawed Frog, Xenopus laevis, which is extremely useful for studying development and cellular physiology, owing to its particularly large and easy manipulable oocytes and embryo.
Dictyostelium as a Model
As noted in the previous post on Model Organisms, Dictyostelium discoideum is a popular model for studying fundamental aspects of cell-cell communication and chemotaxis. This is a soil-living social amoeba grows as separate, independent cells that interact to form multicellular structures when challenged by adverse conditions such as starvation. Up to 100,000 cells signal each…
Model Organisms in Biomedical Research
The term “model organism” is often used in research, to describe species that are extensively studied to understand particular biological phenomena. We say “model,” because there is usually the expectation that discoveries made in the organism model will be representative of related taxonomic groups. In particular, model organisms are widely used to explore potential causes…
In Which I Agree with the Corporations
In Deserting the hungry?, a Nature essay argues today that “Monsanto and Syngenta are wrong to withdraw from an international assessment on agriculture.” The assessment, titled the International Assessment of Agricultural Science and Technology, is an ambitious, 4-year, US$10-million project that aims to do for hunger and poverty what the Intergovernmental Panel on Climate Change…
Deserving of More Media Attention
It’s no secret that science journalism is, with a few notable exceptions, very lackluster in general. It seems to a lot of biologists whom I speak to that cell and molecular biology, genetics, and related fields, are especially underrepresented in the press. Yesterday, Alex vented a bit on this, reflecting on the capacity for wonder…
Closer to the Genetic Roots of Autism
To go with this past Friday’s post on Alzheimer’s, recent progress is being made in understanding Autism. That’s the claim coming from an initial identification of a gene called CNTNAP2, which when mutated, this gene indicated a predisposition to autism in a specific population of Old Order Amish children from Pennsylvania. Three separate studies recently…
Seeing Bacterial Bones with Cryo-EM Tomography
Until this decade, the notion that bacteria had cytoskeletons that maintained their cylindrical morphologies was not seriously considered. “People more or less thought the bacterial cell was a swimming pool and the chromosome was this ball of spaghetti,” says Stanford microbiologist Lucy Shapiro. The lack of apparent internal organization to bacteria supported this view. But…
Curing Alzheimer’s through TNF?
One of the more dreaded diseases that plague our elders is Alzheimer’s disease, which robs the afflicted of not just their memories, but their dignities as well. Research on the role of cytokines in disease progression has illuminated a therapy with great potential, according to a recent study. Edward Tobinick and Hyman Gross, in a…
The Math of Free Will
One of the common arguments from religionists against scientific determinism is that of Free Will. Clearly, we humans possess the capacity for making choices, and have some influence over the direction of our lives. Our cells, too, possess the capacity for choice, as do bacteria and even molecules. For us, our choices are reducible to…
Meiosis and Mitosis Tutorial
I recently caught wind of Openlearn, at Open University, which is a UK university that is dedicated to distance learning. Apparently started in 1969, and hosting part-time students who will received real degrees, the OU’s teaching quality was listed as the fifth best in the UK. “Now anyone can access free online learning,” and “the…
New Journal Ranking Tool
Thompson Scientific is great for gaging the impact factors of various journals, but it has had a bit of a monopoly on journal rankings. As with any ranking scheme, there can be more than one valid way of comparing alternatives. Enter a new ranking tool – that’s free – the SCImago Journal Rank database. This…
Kinase Structures and Autoinhibition
Here’s a comment on work published about 6 months ago that was relevant to me, given my graduate studies on FAK with Jun-Lin Guan. The relations between protein structures and evolution are quite interesting indeed. As more structures are being solved for multimodular signaling proteins, the regulatory kinetics (on, off, and everything in between) is…
Relating to Historical Contingency in Biology
Two blog posts recently collided for me. First, in a blog discussion on Macroevolution vs. Microevolution, Allen MacNeill clarified some issues for me (thanks to TUIBG for bringing it back up): Add the newly emerging fields of evo-devo and epigenesis to the foregoing, and it is increasingly clear that macroevolution (i.e. cladogenesis) follows different rules…
The Big Story of 2007: Cellular Alchemy
Amid the political controversy and obstructions to conducting stem cell research, scientists this year managed to turn lead into gold… Genetically manipulating fibroblasts to become ESC(embryonic stem cell)-like sort of sounds like alchemy in a way, doesn’t it? The product of these papers, inducible pluripotent stem (iPS) cells, were created by transfecting four factors into…
The Challenge of the Two-Body Problem
This is a rather personal post for me, as I’m getting set to follow my wife abroad, while still seeking a research or lecturing position of some kind, whatever may happen. The situation is sometimes known in academia as the “two-body problem,” and is occasionally lamented as a fact of life for the challenging life…
BioChemWeb: Virtual Library for the Molecular Biologist
Wikipedia gets quite a bit of attention, and the student of the molecular biological sciences regularly needs a more in-depth information resource. There’s Bruce Alberts et al.’s Molecular Biology of the Cell, Harvey Lodish et al.’s Molecular Cell Biology, and David Nelson’s Lehninger Principles of Biochemistry if you have the textbooks handy. An online compilation…
Keeping up on the journals
As scientists, we have to keep up with new research coming out and follow the journals. We all have our preferred way of doing so though. Sporadic searches on Pubmed are one way, or weekly email updates on specific search terms (also offered by Pubmed) are another. Alternatively, there’s Hubmed for RSS of Pubmed updates,…
Protein Sociology: Collective Interaction Behaviors
As always, it’s these odd conjunctions of things that don’t go together that catches the eye. In this case, molecular and sociology. The actual article1 is much more mundane and true to the correct science jargon, and included in a special section of the most recent Nature on “Proteins to Proteomes.” It’s also a nice…
What’s with Europe’s Opposition to GMOs?
Nature sends word that there’s a big showdown in Europe looming that could affect the long-term prospects for the cultivation of genetically modified crops on the continent. Specifically, environment commissioner Stavros Dimas said “that he plans to reject applications from Syngenta and Pioneer Hi-Bred International for approval to grow two transgenic strains of maize (corn),…
Political Issues and the Science Lobby
Given the many urgent scientific and technological challenges facing America and the rest of the world, the increasing need for accurate scientific information in political decision making, and the vital role scientific innovation plays in spurring economic growth and competitiveness, we, the undersigned, call for a public debate in which the U.S. presidential candidates share…
Thinking Microbes
Cognition is a term frequently used in several loosely related ways to refer to a faculty for the human-like processing of information. Signal transduction networks certainly fit that bill, as the mediate adaptive changes in gene expression to specific sensory inputs. Melinda Baker and Jeffry Stock, in the recent issue of Current Biology, elaborate on…
Myosin Isoforms: Duplication and Divergence
Myosin II functions as a molecular motor which facilitates contraction of the actin cytoskeleton during migration, resides outside of protrusions at the front of motile cells, and acts at a distance to impact cell protrusion, signaling, and maturation of nascent adhesions. So clearly myosin II is a protein that is of great importance for understanding…
Personal Genomes and Modern Eugenics
As genetic screening becomes increasingly advanced and personal genomes become more commonplace, the potential for genetic engineering and modern eugenics is becoming a reality. “Designer babies” may not be science fiction forever, creating an ethical dilemna on the horizon. Hsein-Hsein keeps us informed on personalized sequencing companies that are coming out, including 23andMe, deCODEme, and…
miRNAs Get Flipped
On a couple other blogs, a study published in Science by Joan Steitz1 is being called “One of the biggest findings of the year,” and “If it turns out to be true, this finding just flipped the whole field on its head.” Bitesize Bio would be greatly remiss to not mention to so hot a…
Entosis: Cellular Canabalism
There might be more to cell death besides apoptosis and necrosis. In a paper that sounded a bit fishy to me, Michael Overholtzer, Joan Brugge and coworkers1 introduce “Entosis”: A non-apoptotic cell death process, that occurs by cell-in-cell invasion. As Eileen White2 described: Upon examination of mammary epithelial cell lines in suspension, Overholtzer et al.…
The Limits of Horizontal Gene Transfer
Looking at the tree of life, descent with modification is an obvious theme, where genes are passed on through ‘vertical’ lines of ancestry. It so happens though that genes can jump from one lineage to another, by a process called ‘horizontal gene transfer’ (HGT). Naked DNA uptake (transformation), viruses (transduction), and plasmids (conjugation) are the…
Science, Ethics and Controversies
An essay in today’s issue of Nature struck a contentious cord at the intersection of modern science and politics: that of the ethical regulation of science. The context of ethics and science was succinctly summed up: When in 1978 the first baby was born by in vitro fertilization (IVF) it was inevitable that there would…
Please, don’t take Bitesize Bio “on Faith”
Science is an endlessly fascinating, challenging, and intellectually-satisfying endeavor. So it saddens me any time that I see someone mistakingly make claims about taking science on faith. This isn’t the forum for taking on religion – if you want that, more of my thoughts on that can be found at Migrations. I have one request…
The Biased Choices of Cells
Here’s one of my favorite journal articles from the past year – an elegant study by Natalie Andrew and Robert Insall published in Nature Cell Biology: Chemotaxis in shallow gradients is mediated independently of PtdIns 3-kinase by biased choices between random protrusions. From the introduction: We have made detailed, quantitative observations of Dictyostelium cells chemotaxing…
Ribosomal Paralogs not Redundant Afterall
In the budding yeast Saccharomyces cerevisiae, 59 of the 79 cytoplasmic ribosomal proteins are encoded by two genes, stemming from an ancient genome duplication event. Komili et al. (2007) now report that these paralogous genes are not functionally equivalent, suggesting the possible existence of a “ribosome code.”1 Yeast and mammalian genomes are riddled with apparently…
Microtubules at the Membrane in Apoptosis
Apoptosis, or programmed cell death, is an evolutionarily conserved and neatly orchestrated process important for tissue remodeling and safe elimination of severely damaged cells. Conducted by a caspase-mediated proteolytic cascade, the cell death program results in a series of cellular changes distinct from cellular necrosis. And one of the critical aspects that distinguish apoptosis from…
Across the Comparative Oncogenomic Landscape
“How many genes are mutated in a human tumor?” That’s the question that a team of researchers at Johns Hopkins posed, and took a comparative genomic approach. By analyzing the sequences of 20,857 transcripts from 18,191 human genes, in 11 breast and 11 colorectal cancers, Wood et al. were able to generate a topographical representation…
Aptamer-DNA Chimeras
One of the neat tools in molecular biology is the ability to recombine parts of two proteins to create fusion or chimeras. They’re often extremely useful for simple experiments, some of the time for targeting protein domains to subcellular sites, or to isolate a structural component of a protein. The functional information is often quite…
Genes Linking Aging and Cancer
This month’s Nature Genetics has an article introduced with the catchy title Aging and cancer: killing two birds with one worm. That’s referring to using C. elegans as a model organism, of course, due to its utility as a model organism for genetic research. Pinkston-Gosse and Kenyon follow a C. elegans-ortholog of FOXO transcription factors,…
Population Genetics Mechanisms on a Genomic Scale
Three papers from UC Davis have appeared on the PLoS journals in the past few days that bring together population genetics and genomic sequencing to address questions of importance to evolutionary biology. Their discussions of divergence in coding versus non-coding, and adaptive versus neutral shifts, are what caught my eye. Collectively, they’re three very densely…
What to Look for in a Good Mentor
For every half-way decent mentor or adviser that an aspiring scientist comes across, it sometimes seems as though there is another lurking, who is simply a jerk*. Let’s face it – scientists aren’t consistently “people-persons.” Maybe they had bad mentors, and inadvertently end up passing on the karma. Or maybe science just attracts a higher-than-average…
Science Writing: Selling Your Research
Browsing around on the Nature Network blogs, I came across one interesting discussion from a couple weeks ago that few researchers actually spend much time thinking about (I think). Martin asked, “I was wondering how much, if at all, the quality of the writing of a submitted paper is considered in the peer review process?”…
Gene Regulatory Networks during Development
Gene regulatory network (GRN) circuits are collections of DNA segments in a cell which interact with each other (indirectly through their RNA and protein expression products) and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA. A lot of research has gone into (a)…
A Missing Post-translational Modification
Eukaryotic cells possess a surveillance mechanisms that identifies aberrantly processed mRNA precursors and prevents their flow to the cytoplasm by tethering them near the site of transcription. Termed post-translational modification, this process includes the distinct events of 5′ capping, 3′ polyadenylation, and intron splicing. During processing, nascent mRNA assembles together with RNA binding proteins into…
History of Cell Biology
The cell theory, or cell doctrine, states that all organisms are composed of similar units of organization, called cells. The concept was formally articulated in 1839 by Schleiden & Schwann and has remained as the foundation of modern biology. The idea predates other great paradigms of biology including Darwin’s theory of evolution (1859), Mendel’s laws…
Fluorescent Neurons Over the Brainbow
Site-specific recombinases have, for the past 20 years, been one of the most powerful tools in studying the functions of all sorts of genes. Most widely used as the Cre/lox-based system for inserting or deleting genes in mice, transgenic analyses have told us volumes about animal development1. For instance, mouse genetic knockouts are routinely the…
Ubiquitination Isn’t Just for Recycling Anymore
Ubiquitin is a small protein, which can be attached to other cellular proteins – a post-translational modification called ubiquitination. Discoveries in the ’80s illuminated ubiquitin as a label for degradation and recycling of the modified protein. Recent studies however, are suggesting more nuanced roles for ubiquitin in signal transduction and cellular function.
Cells – This Side Up
Perhaps the most fundamental aspect of migration of any kind is, how do you know which way to point yourself? Heck, this isn’t just about migration, it’s about how something is oriented in its immediate environment. For orientation, there’s magnetic North, gravity, or any conceivable cue that you might choose to face towards. How do…
Arthur Kornberg, Biochemist
In memorandum of one of the pioneers of molecular biology, who was awarded a Nobel Prize in medicine for the discovery of DNA polymerase. What molecular biology blog would this be if we didn’t honor his memory? Larry Moran presents a fine eulogy, as does the NYTimes: Dr. Arthur Kornberg, a biochemist whose Nobel Prize-winning…
IRESs and Negative Data
Nature Precedings represents a step forward for disseminating experimental results in the internet age. Especially ‘negative’ results, that might not have gotten published otherwise, but is extremely helpful to other researchers in trying to avoid making the same mistakes. Refutation of a hypothesis, while not a discovery, is the goal of the well-planned experiment in…
Open Access to Science
The Public Library of Science (PLoS) defines the issue of Open Access Publication as: An Open Access Publication[1] is one that meets the following two conditions: 1. The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display…
History of Molecular Biology
As a freshman biology major in undergrad, I was introduced to molecular biology with the following description: Molecular biology represents the intersection of genetics, biochemistry and cell biology. Some people, it turns out, add microbiology and virology into the mix. So molecular biology is often used as a catch-all, to describe a wide breadth of…
Histone Methylation Determines Cell Fate
Gene expression is controlled at all sorts of levels in eukaryotic cells, and one of the hot areas is that of histone modifications and how they influence transcriptional accessibility on chromosomes – epigenetic regulation, as it’s called. Think of it as an analog annotation system for the cell’s genome, where each gene is wrapped up…
Modeling Tertiary Structure
Predicting and modeling protein structure, making protein crystallography somewhat obsolete, has been an elusive science to date. Since Linus Pauling and others determined that the most favorable secondary structures are the alpha helix and beta sheet, molecular and structural biologists have sought a set of rules with which to predict a protein’s structure from its…