Posts about scientists

The Amazing Reality of Genes and The History of Scientific Inquiry

cover of The Gene

The Gene by Siddhartha Mukherjee is a wonderful book. He does a great job of explaining the history of scientists learning about genes as well as providing understandable explanations for the current scientific understanding of genes and how they impact our lives.

As I have mentioned before, I find biology fascinating even though I found biology classes utterly boring and painful. I wish everyone could learn about biology with the insight people like Siddhartha Mukherjee provide. I realize not everyone is going to find the history and understanding of genes to be fascinating but for those who might this book is a great read. And don’t rule the idea out just because you found biology classes painful.

Life may be chemistry, but it’s a special circumstance of chemistry. Organisms exist not because of reactions that are possible, but because of reactions that are barely possible. Too much reactivity and we would spontaneously combust. Too little, and we would turn cold and die. Proteins enable these barely possible reactions, allowing us to live on the edges of chemical entropy – skating perilously, but never falling in.
– page 134

Whether it is the physics of our solar system or our biology there is a precarious band that allowed beings such as ourselves to evolve.

most genes, as Richard Dawkins describes them, are not “blueprints” but “recipes.” They do not specify parts, but processes; they are formulas, not forms. If you change a blueprint, the final product is change in a perfectly predictable manner: eliminate a widget specified in the plan, and you get a machine with a missing widget. But alteration of a recipe or formula doesn’t not change the product in a predictable manner: if you quadruple the amount of butter in a cake, the eventual effect is more complicated than just a quadruply buttered cake (try it; the whole thing collapses in an oily mess).
– page 454

The is a powerful idea. And when combined with turning genes on and off it is understandable how complex determining genetic impacts on biology and disease are. A few diseases or results (e.g. blue eyes) are nearly as simple as 1 or a few genes being altered in a specific way but most are not nearly so easy. And it isn’t like even that is so easy but with the amazing efforts scientists have made and the advanced tools those scientists created it can now seem simple to identify some such diseases.

The genetic code is universal. A gene from a blue whale can be inserted into a microscopic bacterium and it will be deciphered accurately and with near perfect fidelity. A corollary: there is nothing particularly special about human genes.
– page 480

This is something I have known and understood but it is still amazing. Genes and proteins and how they act to create the incredible diversity of life is something that is awe inspiring.

This book is a wonderful adventure for those interested in life and scientific inquiry.

Related: Epigenetics, Scientific Inquiry and UncertaintyHuman Gene Origins: 37% Bacterial, 35% Animal, 28% EukaryoticUnexpected Risks Found In Editing Genes To Prevent Inherited DisordersEpigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeWhy Don’t All Ant Species Replace Queens in the Colony, Since Some Do

Nobel Prize Winner Criticizes Role of Popular Science Journals in the Scientific Process

Randy Schekman, 2013 Nobel Prize winner in physiology or medicine has written another critique of the mainstream, closed-science journals. How journals like Nature, Cell and Science are damaging science

Mine is a professional world that achieves great things for humanity. But it is disfigured by inappropriate incentives. The prevailing structures of personal reputation and career advancement mean the biggest rewards often follow the flashiest work, not the best. Those of us who follow these incentives are being entirely rational – I have followed them myself – but we do not always best serve our profession’s interests, let alone those of humanity and society.

We all know what distorting incentives have done to finance and banking. The incentives my colleagues face are not huge bonuses, but the professional rewards that accompany publication in prestigious journals – chiefly Nature, Cell and Science.

There is a better way, through the new breed of open-access journals that are free for anybody to read, and have no expensive subscriptions to promote. Born on the web, they can accept all papers that meet quality standards, with no artificial caps. Many are edited by working scientists, who can assess the worth of papers without regard for citations. As I know from my editorship of eLife, an open access journal funded by the Wellcome Trust, the Howard Hughes Medical Institute and the Max Planck Society, they are publishing world-class science every week.

Just as Wall Street needs to break the hold of the bonus culture, which drives risk-taking that is rational for individuals but damaging to the financial system, so science must break the tyranny of the luxury journals. The result will be better research that better serves science and society.

Very well said. The closed access journal culture is damaging science in numerous ways. We need to stop supporting those organizations and instead support organizations focused more on promoting great scientific work for the good of society.

Related: Fields Medalist Tim Gowers Takes Action To Stop Cooperating with Anti-Open Science CartelScience Journal Publishers Stay StupidHarvard Steps Up Defense Against Abusive Journal PublishersThe Future of Scholarly Publication (2005)The Trouble with Incentives: They WorkWhen Performance-related Pay BackfiresRewarding Risky Behavior

Introduction to Fractional Factorial Designed Experiments

Scientific inquiry is aided by sensible application of statistical tools. I grew up around the best minds in applied statistics. My father was an eminent applied statistican, and George Box (the person in the video) was often around our house (or we were at his). Together they wrote Statistics for Experimenters (along with Stu Hunter, not related to me) the bible for design of experiments (George holds up the 1st edition in the video).

The video may be a bit confusing without at least a basic idea of factorial designed experiments. These introductory videos, by Stu Hunter, on Using Design of Experiments to Improve Results may help get you up to speed.

This video looks at using fractional factorials to reduce the number of experiments needed when doing a multifactor experiment. I grew up understanding that the best way to experiment is by varying multiple factors at the same time. You learn much quicker than One Factor At a Time (OFAT), and you learn about interactions (which are mainly lost in OFAT). I am amazed to still hear scientists and engineers talk about OFAT as a sensible method or even as the required method, but I know many do think that way.

To capture the interactions a full factorial requires an ever larger number of experimental runs to be complete. Assessing 4 factors requires 16 runs, 6 would require 64 and 8 would require 256. This can be expensive and time consuming. Obviously one method is to reduce the number of factors to experiment with. That is done (by having those knowledgable about the process include only those factors worth the effort), but if you still have, for example, 8 very important factors using a fractional factorial design can be very helpful.

And as George Box says “What you will often find is that there will be redundant factors… and don’t forget about those redundant factors. Knowing that something doesn’t matter is almost as important as knowing what does.” If you learn a factor isn’t having an affect you may be able to save money. And you can eliminate varying that factor in future experiments.

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George Box 1919 to 2013 – A Great Friend, Scientist and Statistician

Reposted from my management blog.

I would most likely not exist if it were not for George Box. My father took a course from George while my father was a student at Princeton. George agreed to start the Statistics Department at the University of Wisconsin – Madison, and my father followed him to Madison, to be the first PhD student. Dad graduated, and the next year was a professor there, where he and George remained for the rest of their careers.

George died today, he was born in 1919. He recently completed An Accidental Statistician: The Life and Memories of George E. P. Box which is an excellent book that captures his great ability to tell stories. It is a wonderful read for anyone interested in statistics and management improvement or just great stories of an interesting life.

photo of George EP Box

George Box by Brent Nicastro.

George Box was a fantastic statistician. I am not the person to judge, but from what I have read one of the handful of most important applied statisticians of the last 100 years. His contributions are enormous. Several well know statistical methods are known by his name, including:

George was elected a member of the American Academy of Arts and Sciences in 1974 and a Fellow of the Royal Society in 1979. He also served as president of the American Statistics Association in 1978. George is also an honorary member of ASQ.

George was a very kind, caring and fun person. He was a gifted storyteller and writer. He had the ability to present ideas so they were easy to comprehend and appreciate. While his writing was great, seeing him in person added so much more. Growing up I was able to enjoy his stories often, at our house or his. The last time I was in Madison, my brother and I visited with him and again listened to his marvelous stories about Carl Pearson, Ronald Fisher and so much more. He was one those special people that made you very happy whenever you were near him.

George Box, Stuart Hunter and Bill Hunter (my father) wrote what has become a classic text for experimenters in scientific and business circles, Statistics for Experimenters. I am biased but I think this is acknowledged as one of (if not the) most important books on design of experiments.

George also wrote other classic books: Time series analysis: Forecasting and control (1979, with Gwilym Jenkins) and Bayesian inference in statistical analysis. (1973, with George C. Tiao).

George Box and Bill Hunter co-founded the Center for Quality and Productivity Improvement at the University of Wisconsin-Madison in 1984. The Center develops, advances and communicates quality improvement methods and ideas.

The Box Medal for Outstanding Contributions to Industrial Statistics recognizes development and the application of statistical methods in European business and industry in his honor.

All models are wrong but some are useful” is likely his most famous quote. More quotes By George Box

A few selected articles and reports by George Box

Related: It is not about proving a theorem it is about being curious about thingsBox on QualitySoren BisgaardLearning Design of Experiments with Paper HelicoptersPeter Scholtes

Scientists Don’t Look Like They Do in Movies

The Myth of the Scientist: Crystal Dilworth at [email protected]

Scientists don’t fit the stereotypical mold some people think they do. It doesn’t take much to replace those views. The main point, in my opinion, is to let kids know they can be a scientists even if they are not like the stereotypical examples – though it will take a lot of work.

Related: Movie Aims to Inspire College Students With Tales of Successful Minority ScientistsWomen Working in ScienceCitizen ScientistsScientists Singing About Science

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Science PhD Job Market in 2012

The too-big-to-fail-bank crisis continues to produce huge economic pain throughout the economy. Science PhDs are not immune, though they are faring much better than others.

U.S. pushes for more scientists, but the jobs aren’t there

Since 2000, U.S. drug firms have slashed 300,000 jobs, according to an analysis by consulting firm Challenger, Gray & Christmas. In the latest closure, Roche last month announced it is shuttering its storied Nutley, N.J., campus — where Valium was invented — and shedding another 1,000 research jobs.

Largely because of drug industry cuts, the unemployment rate among chemists now stands at its highest mark in 40 years, at 4.6 percent, according to the American Chemical Society, which has 164,000 members. For young chemists, the picture is much worse. Just 38 percent of new PhD chemists were employed in 2011, according to a recent ACS survey.

Two groups seem to be doing better than other scientists: physicists and physicians. The unemployment rate among those two groups hovers around 1 to 2 percent, according to surveys from NSF and other groups. Physicists end up working in many technical fields — and some go to Wall Street — while the demand for doctors continues to climb as the U.S. population grows and ages.

But for the much larger pool of biologists and chemists, “It’s a particularly difficult time right now,” Stephan said.

From 1998 to 2003, the budget of the National Institutes of Health doubled to $30 billion per year. That boost — much of which flows to universities — drew in new, young scientists. The number of new PhDs in the medical and life sciences boomed, nearly doubling from 2003 to 2007, according to the NSF.

The current overall USA unemployment rate is 8.2%.

The current economy doesn’t provide for nearly guaranteed success. The 1960’s, in the USA, might have come close; but that was a very rare situation where the richest country ever was at the prime of economic might (and even added on top of that science was seen as key to promote continued economic success). Today, like everyone else (except trust fund babies), scientists and engineers have to make their way in the difficult economy: and that should be expected to be the case in the coming decades.

Right now, physicians continue to do very well but the huge problems in the USA health system (we pay double what other rich countries do for not better outcomes) make that a far from a certain career. They likely will continue to do very well, financially, just not as well as they have been used to.

Science and engineering education prepare people well for economic success but it is not sufficient to guarantee the easy life. Just like everyone else, the ability to adapt to current market conditions is important in the current economic climate – and will likely continue to be hugely important going forward.

The reason to get a undergraduate or graduate science or engineering education is because you are interested in science and engineering. The economic prospects are likely to continue to be above average (compared to other education choices) but those choosing this path should do so because they are interested. It makes sense to me to factor in how your economic prospects will be influenced by your choices but no matter what choices are made a career is going to take hard work and likely many frustrations and obstacles. But hopefully a career will provide much more joy than hardship.

Related: Career Prospect for Engineers Continues to Look PositiveAnother Survey Shows Engineering Degree Results in the Highest PayThe Software Developer Labor Market

Scientists Singing About Science

Fun video with scientists singing about science.

More scientists singing science songs: Friday Fun, Large Hadron RapCambrian Explosion SongThe Sun is a Miasma of Incandescent PlasmaProtein Synthesis: 1971 Video

One Scientists 20 Year Effort to Defeat Dengue Fever

As I have said many times scientific breakthroughs often follow many years of effort. Here is a great example of a scientist putting in great work for years and it looks like it is about to payoff for hundreds of millions of people.

A Scientist’s 20-Year Quest To Defeat Dengue Fever

Now as I said, Scott’s been pushing this idea of using Wolbachia to control dengue for decades, for a most of that time without any success. I asked Scott what it takes to stick with something for that long.

“I think being obsessive,” he replied. “Being maybe a little ill in that regard. And it’s just that I seem to have focused my obsession onto Wolbachia instead of on to postage stamps or model trains.”

And even though his obsession has brought him to the point where he’s shown he can get his Wolbachia-infected mosquitoes to spread in the wild, that’s not the success he’s ultimately after. “Success for me is having a significant impact on dengue disease in communities,” he says.

To do that, he’ll have to release his mosquitoes in a place where there’s a lot of dengue, and then see if that brings down the number of cases of the disease in humans. Those studies are being planned now.

The stakes are high. By some estimates, more than a billion people around the world are at risk for getting dengue. Even if it doesn’t kill you, I’m told a case of dengue can make you feel so bad, wish you were dead.

But Scott says it’s not yet time to celebrate.

“We’ve got some good preliminary data, and we’re on the path. And it’s looking good. But you know I am a realist. It could fall over at any day,” says Scott.

Related: Engineering Mosquitoes to be Flying VaccinatorsScientists Building a Safer Mosquito (2006)Video showing malaria breaking into cellTreated Mosquito Nets Prevent Malaria

Citizen Science

Citizen science enters a new era

Another online program, Phylo, is advancing scientists’ knowledge of genetics by making a game out of DNA matching. If areas of genetic sequence are roughly similar between species, it suggests strongly that they could have an important function. Finding them has been beyond the scope of computer algorithms. But earlier this month, researchers published a study where gamers outsmarted the best computers – they made the best possible DNA sequence match between up to eight species at a time.

The potential for regular people contributing to science is great. This has a long history. For most of human history science was done by non-scientists since there were no scientists. Calling is science might be a stretch but to me it was (passing on what health cures worked for various sicknesses, how to use various tools, how to grow crops…). As scientists came into being they were primarily unprofessional – that is they practiced science but were doing so as a hobby, they were not paid and had no requirements to get a PhD or anything.

Today regular people help by collecting data (counting birds, documenting plant growth [time of year], migration data, weather data…) sharing knowledge with scientists who ask, sharing their computer to be used to analyze data, analyzing data (for example, in astronomy hobbyists often make new discoveries) and the latest way people help is through games (that essentially tap human brainpower to analyze data – such as Foldit, which I have posted about previously).

I like the contributions people can make to science but I think the biggest value is the scientific understanding people gain while participating. As Neil Degrasse Tyson says the scientifically literate see a different world.

Cornell University provides an online tool to find opporunities participate in scientific research.

And we shouldn’t forget the amazing science done by students like those honored with Intel Talent Search, though the work those winning the awards do I would lump with science by “real scientists” (I believe now most of those who win are working on projects with university scientists).

Related: Backyard Scientists Aid Research8-10 Year Olds Research Published in Royal Society JournalTeen diagnoses her own disease in science class

I Always Wanted to be Some Sort of Scientist

A nice simple post by a soon to be Dr. of Genetics and Molecular Biology on what being a scientist is like for her. I like her take, which I think is much more accurate than some of the generalities people use. The main reason people (men or women) become scientists because they want to be scientists.

photo of almost-Dr. Caitlin

Photo the almost-Dr. Caitlin

The truth is science requires you to be social. We share ideas, techniques, and equipment. A good scientist knows her limitations and uses someone else’s expertise when her own is not enough. The modern scientist communicates not only through conferences and journals, but also through blogging and Facebook.

When a non-scientist (usually my parents or some other close relative) asks me about what I do, they inevitably want to tie it back to how I’m curing a disease and saving the world. I am not curing a disease or saving the world.

I study science because it’s cool. I study basic science — asking questions for the purpose of learning the answer. That doesn’t mean what I do isn’t important. Lots of ground-breaking medical advances have been made just because someone asked a question no one else thought to ask.

To all you ladies fighting the good fight in other fields, keep at it, because the numbers are going up for women with advanced degrees.

I’ve always wanted to be some sort of scientist. When I was in elementary school I wanted to be a paleontologist because dinosaurs are awesome (and so was “Jurassic Park”). When I was 11, I read the Hot Zone and knew I wanted to be a biologist. Though there were times that I flirted with the Dark Side, i.e., medical school, but mostly only because when my teachers figured out I was good at science they said go to medical school. No one even suggested becoming a scientist.

Great stuff. Good Luck, Caitlin.

Related: Movie Aims to Inspire College Students With Tales of Successful Minority ScientistsKids on Scientists: Before and After Talking to Real Live ScientistsWomen Choosing Other Fields Over Engineering, Math, Physics and Computer Science

Science is at its best when curious people are just trying to find things out

Brian Cox has a new television show, Wonders Of The Universe (a co-production of the BBC, the Discovery Channel, and the Science Channel), that looks like it will be wonderful. I would love more great shows on science. BBC has done some great stuff, so has PBS and the Discovery channel. I’ll be exploring what kind of access those channels have provided over the internet in the next year. I hope it is good. I was going to link to the web site for the show but the first 2 videos I tried to click on to view they wouldn’t show, so I don’t see the point in linking – hopefully eventually people that care about promoting science will make decisions to use the internet sensibly).

Interview of Professor Brian Cox

That’s a very important point about scientific discovery in general. Most scientists are interested in just looking at the universe, looking at nature. I don’t think there are many great discoveries that you can point to that were the result of someone wanting to find the answer to a particular question. If you look back at Einstein or Newton, you find that people are fascinated often by the smallest things, actually. In terms of Einstein, cosmology—which is a real part of the way the universe evolved, the way the universe began, the Big Bang—all that stuff came from Einstein really just being interested in the speed of light. He was just interested. It was a question he’d always asked. He’d always wondered about how light travels. It’s a useful lesson, in general, not only to the theories, but that science is at its best when curious people are just trying to find things out.

There’s a very famous quote from [Alexander] Fleming, when he discovered penicillin, he said something like, “On September something 1928, I didn’t expect to wake up and revolutionize medicine.” He woke up playing around with little bits of mold in his kitchen, basically. He was just interested in moldy things. [Laughs.] And he revolutionized everybody’s life. Everybody. Virtually everybody who is over the age of about 40 or 50 is alive today because of antibiotics. Virtually everybody would have died if it hadn’t been for that. And it wasn’t someone trying to discover antibiotics that did it. It was someone exploring nature. So, the argument, “Couldn’t we just spend our money making everybody’s lives better?” We are doing that. That’s what exploration actually does.

Related: Why Do People Invest Large Amounts of Time and Money? (Neil deGrasse Tyson)Brian Cox Particle Physics WebcastScience and Engineering WebcastsScientifically Literate See a Different WorldScience and the Excitement, the Mystery and the Awe of a Flower

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