Archive for the 'Issues in Science' category

Wow, there must be a loooooooooooot of folks who don't f*cking love science

Sep 20 2013 Published by under Issues in Science

Yes, the funding situation for science research and the career trajectories for PhDs are all sorts of suckery right now. I’m currently in that boat navigating those waters. So if you ask me, “Should we push for increasing research funding?” The answer is obvs yes. Should we push to put people in office who reflect this sentiment? Yerp. Should post docs be paid more? Yes….err...I'm open for debate (see below). Should all of these issues get "debated in the media, that sees equal time with the wars we fight and the bills we pay our aging workforce?” Absolutely.

So why do I find this WHY YOU DON’T “FUCKING LOVE SCIENCE” post misdirected?

Breaking people down into a false dichotomy of those who truly love science and those who just proclaim that they “fucking” love science dismisses the multitude of ways people (have to) prioritize matters that impact their lives. If science funding isn’t your number 1 priority...well, psshh, then you’re doing it wrong is quite frankly condescending. Ever wonder why people thumb their noses at scientists? Well…

If the point of the post is to preach to the choir, then bang up job. But if it’s to make a case to those who prioritize entitlements/earned benefits, military spending, etc. ahead of science to bump science higher on that list, then I don’t think this helps:

“No, what you love is social security, high-tech fighter aircraft, and bombing the Middle East so that it stays in the stone age where the government has assured you it belongs.”

Can anyone else taste the contempt?

Also this:

Not to mention that many graduate students are paid less than the average unemployment benefit.  That’s right: for the first five years of those two decades, most people would’ve gotten paid more if they’d not had a job at all.

Cool. Thanks for contributing to the “you’re better off doing nothing and suckling at the teat of government” narrative. One, as far as I know you can’t draw unemployment benefits for 5 years. Two, as a graduate student you agree to be trained and receive said stipend. Three, although they may not end up in their expected/intended careers, science and engineering PhDs have the lowest levels of overall unemployment (1.5%). But you know...trivializing the unemployed is *totally* ok.

As for increasing postdoc pay, this is debatable and I’ll let the peeps with more experience in the postdoc game hash it out. For me, I have several questions: Is a postdoc really about further training anymore if the intended career opportunities on the other side are dwindling? Or has it basically transitioned into a de facto midcareer position? In which case, should we really be making what is essentially a temp position more desirable by increasing its salary? Is it possible to have better paid, more permanent-y, PhD-level research positions instead?

3 responses so far

Should I start patenting the cDNAs I've made in the lab?

Jun 13 2013 Published by under Issues in Science

In a unanimous decision today, the SCOTUS struck down patents for genes by ruling against Myriad Genetics in Association for Molecular Pathology vs. Myriad Genetics. The Court, however, did leave some wiggle room for companies to patent cDNAs, or complementary DNA.

"In Myriad, the high court held cDNA is patentable, because it involves actual work in the laboratory and inverts the normal process found in nature. The synthetic DNA is an edited version of a gene, stripped of non-coding regions that the court said makes it “not naturally occurring.”

Critics say even the edited sequences are directly analogous to naturally occurring DNA."

In many labs, cDNAs are routinely made, manipulated, and used for research. cDNA is DNA that is engineered in reverse using messenger RNA (mRNA) as the template. As the above quote alludes, a cDNA is not a carbon copy of its corresponding gene. Interspersed along the length of a gene are regions of non-coding DNA sequence. These are segments of DNA that aren't represented in the sequence of the encoded protein. When a gene is initially transcribed into mRNA some of these non-coding regions, called introns, are included. Introns, however, are ultimately removed by the cell before the mRNA is translated into protein. Since mRNA is used to make cDNA, the introns are excluded from the cDNA sequence.

gene expression

During gene expression, a gene is first transcribed into a primary RNA transcript, which includes non-coding introns (blue). Through a process called splicing the introns are removed from the transcript resulting in a mature mRNA molecule. The sequences found in mRNA are called exons (red and yellow). The mRNA is  then translated into protein. Since cDNA is made from mature mRNA, it will consist only of exon sequences.

Although gene and cDNA are different, they both carry essentially the same DNA sequence for a protein. (It should be noted, however, that many genes encode multiple forms of a protein, for which each form has its own corresponding cDNA.) So, I'm not sure why the "patentable" emphasis is on cDNAs as opposed to making mutations* to the underlying sequence that result in say, new or altered function of a protein. At least there I could see an inventive process happening--or am I missing something here?

*I'm talking about generating novel mutations. Of course, I'm not sure what should happen if said mutations are discovered to be "naturally occurring" after the fact.



5 responses so far

What's the gender ratio of your references for letters of recommendation?

Jun 12 2013 Published by under Issues in Science, Late-stage PhD student

A few weeks ago while going through old resumes and updating my CV, I noticed that my references have historically been women-centric. I started wondering what the gender ratios were like for other people's references, so I threw this question out into the Twitterealm.

Here were some of the responses:

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What's the gender ratio of your references?

  1. Peoples - what is the gender ratio of your references?
  2. @AmasianV Mostly men. Most of them seem to be called "Al".
  3. @AmasianV all women currently. Historically about 3/4 women.
  4. Depends on job/app. For any single app my range was 0-33% female. MT @AmasianV: what is the gender ratio of your letter writers?
  5. @AmasianV @27andaphd 50/50. The strongest and most influential = female.
  6. @AmasianV @27andaphd Most of my women colleagues very familiar w/ me and my work are at similar stage as I am, grad students, postdocs, etc.
  7. @AmasianV @27andaphd I've met more senior women who do great work in my field, but I don't know them well enough to ask for reccomendation
  8. @AmasianV @27andaphd Oh, absolutely. In my case it's just a matter of probabilities of being in same place/same time and getting their time
  9. @AmasianV @27andaphd Just like any other important, more senior researcher that I want to know well.
  10. @AmasianV @N3OX fo sho. Sadly, I've only had 1 female mentor in my field since I started grd school 10 yrs ago #structuralbiology

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Racial disparities in accruing debt during graduate school

May 09 2013 Published by under Issues in Science

According to a new report from the American Institutes for Research, black and Hispanic STEM PhD students are more likely to accrue larger amounts of debt during grad school than their non-underrepresented minority (URM) peers (read: white, Asian, & biracial). The Chronicle of Higher Education article is a little clunky in trying to summarize a report that compares debt incurred by graduate students in STEM programs versus those in social, behavioral, and economic (SBE) programs. I suggest reading the actual report itself.

Figure 5. Graduate Student Debt for STEM Phd Recipients by Race-Ethnicity and Gender- 2010

The report also found that these disparities existed regardless of the source of funding (institutional vs external) or the time it took students to complete their PhD studies.

Other factors that may be worth exploring include the distance that students travel to attend graduate school, spending patterns during graduate school, the family commitments of PhD students during graduate school (e.g., marital status and number of dependents), and salary expectations after leaving graduate school. If graduate students’ spending patterns during graduate school are related to the expected financial pay-off of their PhDs, then differences in graduate student debt may be related to differences in students’ inflated estimates of their future salaries.

I'd add socioeconomic and debt status upon entering grad school to that list. Identifying which factors contribute to debt could help us better position students to shoulder less of it.

As graduate programs make more of an effort to recruit underrep'ed minorities, however, I wonder whether these disparities will become greater or smaller...

6 responses so far

(data not shown) Hypocrite

Apr 25 2013 Published by under Issues in Science, Late-stage PhD student

Earlier this week, I spent a good chunk of time complaining about data not being shown in two papers I had read. Normally, I'd be apt to take their word for it because "data not shown" results tend to be inconsequential footnotes to the larger story and conclusions. This time it was different, though. The data not being shown was being used to make claims that were pertinent to a little thing I've been working on called my thesis. It didn't help matters that the results that were published were less than convincing. I really would have liked to see the data--I mean, isn't that what Supplemental Information is for? Some have suggested that I contact the authors to see if they'd send me the data but I'm not sure how to craft that correspondence without broadcasting a big, fat "Yo, I don't believe you."

Well anyway, now's a good time as any to check myself since I'm totally guilty of pulling the "data now shown" card, too.



5 responses so far

An "Acceptable" GMO?

Apr 05 2013 Published by under Issues in Science, Science

Soybean Field

For many opponents of genetically modified foods, the idea of fiddling with an organism’s genome doesn’t quite sit well in their stomachs. The type of genetic tweaking that renders soybean plants resistant to the herbicide Roundup strikes some not only as unnatural but something that borders on playing God. Similarly, another common objection to genetic engineering is that the transfer of genetic material/DNA genes violates a so-called “species barrier.” Such is the case for Bt corn, which harbors the bacterial gene for Bt toxin, a compound that is poisonous to insect pests. This argument, however, disregards the fact that Nature ignores this barrier all the time. In the wild, DNA is often transferred between species through processes collectively known as horizontal gene transfer. So, not even Nature plays by antiGMO rules.

But what if an already existing gene variant with a desired trait from one organism is genetically engineered into another organism of the same species? Would this make GMOs a little bit more palatable to their detractors?

Soy is one of the most important crops grown in the US and it is nearly ubiquitous in the market. It’s in our food, drinks, biodiesel fuel, even cosmetics. If you rummage through my mom’s kitchen you’ll find soy sauce in the pantry, tofu in the fridge, and edamame in the freezer. Back in the day, she used to keep soybeans on hand for when she’d press her own soy milk.

Soybean cyst nematode and egg SEM

"Low-temperature scanning electron micrograph of soybean cyst nematode and its egg. Magnified 1,000 times."

Latte drinkers, vegetarians, and us Asians aren’t the only ones who love soy, however. Lurking underground are parasitic worms known as soybean cyst nematodes, which find the roots of the soybean plant irresistible. These agricultural pests invade the roots of the soybean plant where they do a bit of their own agriculturing. These nematodes are capable of inducing the root cells on which they feed to divide thereby creating a steady supply of food for themselves. Whereas males leave the comforts of their “root homes” in order to find mates, females remain there where they continue to feed and swell in size until eventually their bodies burst through the root. Once mated and having laid her eggs, the female dies and her cuticle hardens to form characteristic the cysts on the roots of the soybean plant. The damage to soy crops is damages to the tune of $500 million to $1 billion annually in the US alone.

Segment of soybean root infected with soybean cyst nematode. Signs of infection are brown-white females or cysts with egg masses that are attached to root surfaces.

"Segment of soybean root infected with soybean cyst nematode. Signs of infection are brown-white females or cysts with egg masses that are attached to root surfaces."

Soybean plants aren’t entirely defenseless, however, as there are soybean plant strains, such as the Forrest cultivar, that are resistant to nematode attack. In this cultivar, the feeding cells that the nematodes “cultivate” in the roots of the soybean plant die off and the worms starve before they can reproduce. (Conversely, there are also soybean cyst nematodes that are resistant to resistant soybean plants. It wouldn’t be Nature without the wrinkles, now would it?)

While exactly how the feeding cells in the Forrest cultivar degenerate in response to soybean cyst nematode is unknown, a team of scientists led by Shiming Liu (Southern Illinois University) and Pramod Kandoth (University of Missouri) has recently identified mutations in the serine hydroxymethyltransferase (SHMT) gene that are responsible for nematode resistance. Serine hydroxymethyltransferase is an enzyme involved in the shuttling of one-carbon units between molecules--folate in particular--until the carbon is ultimately freed up for the cell to use in important processes such as DNA and protein synthesis. For instance, one of the consequences of serine hydroxymethyltransferase activity is the conversion of the serine to glycine, both of which are amino acids found in proteins.

One of the reactions that serine hydroxymethyl transferase catalyzes is the conversion of the amino acid serine to glycine.

One of the reactions that serine hydroxymethyl transferase catalyzes is the conversion of the amino acid serine to glycine.

Since the mutations in the Forrest SHMT gene are located near the active site, or the “business end” of the SHMT protein where the shuttling of carbons occurs, it’s possible that the mutations affect the activity of the SHMT protein. Since To test this model, Liu and Kandoth expressed the mutated SHMT Forrest gene to see if it could restore the growth of an E. coli strain that is unable to survive because it can’t manufacture it’s own glycine. They found that the mutated version of SHMT was less effective than the unmutated form of SHMT in restoring growth of the E. coli strain indicating that the activity of the Forrest SHMT protein was probably reduced due to mutations.

More importantly, soybean plants that were susceptible to SCN infection became resistant when Liu and Kandoth transferred the Forrest SHMT gene in the susceptible plants. This demonstrated that the mutated Forrest SHMT was responsible for soybean cyst nematode resistance. The scientists speculate that the decreased activity of the mutated SHMT reduces either the “nutritiousness” of the feeding cells or their ability to divide, and as a result the nematodes that infect the Forrest cultivar starve to death.

So, this brings me back to my original question of what, if anything, would constitute an “acceptable” GMO to opponents of genetic engineering? Would detracters object to a scenario where an already existing mutation* that confers resistance to an agricultural pest is engineered into other soybean plants. Directly transferring the existent Forrest SHMT variant would be more efficient over traditional methods of breeding, since only the Forrest SHMT gene would be introduced into another soybean plant without carrying over any unwanted traits or genes. There are, after all, many different cultivars of soybean plants used for different applications that may benefit from nematode resistance.

*I’ll avoid saying “naturally-occurring” since the Forrest cultivar was developed by a USDA breeding program.



Liu, S., Kandoth, P., Warren, S., Yeckel, G., Heinz, R., Alden, J., Yang, C., Jamai, A., El-Mellouki, T., Juvale, P., Hill, J., Baum, T., Cianzio, S., Whitham, S., Korkin, D., Mitchum, M., & Meksem, K. (2012). A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens Nature, 492 (7428), 256-260 DOI: 10.1038/nature11651

Crossposted at Amasian Science.

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