By Way of Science     
Exploring the lesser-known byways of modern biological science with occasional forays into other topics.

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Back in May I had written a guest post at the Marmorkrebs blog detailing why I think the Marmorkrebs or marbled crayfish is an excellent model system (or could become one).

Doctor Zen also posted the second part of my post as well--so check it out!

You can read the post here or recap the first part here.

Thanks to Doctor Zen for sharing my thoughts and supporting my #SciFund project!


K.S. MacLea, Ph.D.

Posted Fri Jun 29 21:08:18 2012 Tags:

I've got a new post up as a guest blogger at Doctor Zen's Marmorkrebs blog.

The first post is titled "Never send a sibling to do a clone's job" (part one) and talks about why I think Marmorkrebs or marbled crayfish are a model system that should be of interest to scientists, and not just those that study crustaceans.

You can read the post here.

I will post part two when it is up for reading as well.


K.S. MacLea, Ph.D.

Posted Tue May 22 15:03:08 2012 Tags:

My project in the second crowdfunding-for-science extravaganza known as #SciFund has been fully funded--and beyond!

In fact, with generous donations, I am at 167% of my original goal ($1302 out of $780). (Update 5/22/12: $1616 or 208%!!) (Update 5/30/12: $$1779 or 229%!!)

Thanks to all you donors with great taste and foresight--clearly great things await for the genetics of crayfish and our understanding of this unique parthenogenetic creature, the Marmorkrebs or marbled crayfish.

Currently, the following beautiful, intelligent, and wonderful people have contributed to my Project, Crayfish Clone Wars. Thank you to all.

  • Lindy Gullett & Kate Reilly
  • Anthony Salvagno
  • Kalani Kirk Hausman
  • Greg Crowther
  • Sean Sterrett
  • Lauren Kuehne
  • Aleks Ksiazkiewicz
  • Claudia Makeyev
  • Rob Denton
  • Mandy and Jayson Boyers
  • Jennifer MacLea & Peter Harmon
  • Robert & Lorraine MacLea
  • Terese, Rob, and Patrick MacLea
  • Amanda White
  • Katie Ritcheske
  • Lynn Chambers
  • Gil & Jeanne Slater
  • Edwin & Katherine Anderson
  • Elanor Pickens (added 5/12/12)
  • Joel Green (added 5/12/12)
  • Michelle & Tom Kidwell (added 5/20/12)
  • Jared Foo (added 5/20/12)
  • Nicole Soucy (added 5/20/12)
  • Yagya Sharma (added 5/22/12)
  • Andrew Piskorski (added 5/22/12)
  • Susan Roy Greenbowe (added 5/22/12)
  • Rose Hamel Scovel (added 5/22/12)
  • Maureen Ruth (added 5/26/12)
  • Annukka Pasi (added 5/26/12)
  • Francis Portland (added 5/29/12)
  • Suzann Brehony (added 5/29/12)
  • Natalie Pitts (added 5/30/12)

You guys are the best.


K.S. MacLea, Ph.D.

Posted Sat May 12 02:49:25 2012 Tags:

The 2nd #SciFund Challenge is now live!

What is SciFund? It is "crowdfunding" to support scientific research. If you've heard of crowdfunding, it's probably because of sites like Kickstarter and RocketHub that have raised money for musicians to create albums, for programmers to create video games, and even for people to make feature-length films, among a lot of other projects, mostly in the artistic arena. SciFund is an effort to do the same thing for scientists--allowing them to raise money for small(ish) projects from individual donors.

But you want details, right?

The SciFund Challenge is asking the general public to open their wallets for small-amount donations organized through the RocketHub website, which handles the administration of the project (and takes a small cut of the proceeds). You can think of this as the model charities have always used (bundling lots of donations to do good works), but with an internet/social media twist.

As in 2011 when the #SciFund Challenge started, scientists from a wide variety of disciplines (ecology to psychology to astronomy) have signed on to crowdfund their research. And I've decided to join them in SciFund 2!

Crayfish Clone Wars My project is called Crayfish Clone Wars and you can watch video I made for the project on YouTube: Crayfish Clone Wars video.

So, I can hear you wondering, what exactly are you planning to do?

I've worked in the past with two types of decapod crustaceans, crabs (2 species) and lobsters. But the decapods also include shrimp and crayfish and to broaden my exposure to this fascinating group of creatures, I've decided to take on a research project studying the unusual "clone" crayfish Marmorkrebs (also called the marbled crayfish). This crayfish is unique among the ~15,000 or so decapod crustaceans in that it is the only one that can reproduce parthenogenetically. As a result, female Marmorkrebs reproduce without sex, and produce only daughters that are genetically identical to the mother.

But how identical is identical?

Turns out this is not as easy of a question as you might imagine. It's taken us a long time to prove that even human monozygotic (identical) twins are really genetically (mostly) identical. We don't really know how genetically identical these parthenogenetic crayfish are. So, this means that we don't really know how different that different lines of Marmorkrebs are (those that are not descended, at least to our knowledge, from the same ancestor). In Crayfish Clone Wars, I will use DNA sequencing to minutely examine genes from the different "lines" and see how the genes differ (that is, I will pit clone versus clone in a "Clone War" at the DNA level!). And since we have only a few DNA sequences from the marbled crayfish in the entire GenBank database, every gene we study brings us one step closer to the goal of a Crayfish Genome Project.

While this subject may seem esoteric, there is so much we don't know about crustacean biology, and crayfish are particularly understudied at the genetic level amongst the decapods (where most research goes to crabs, lobsters, and shrimp, depending on your part of the world). Every gene we study in crustaceans helps us to understand these animals better. I'm not going to promise that we're going to cure cancer with this information, but I think the discovery of new genes and how they work in new organisms is every bit as worthy of study.

What your contribution will support:

  • Sample collection from Marmorkrebs (marbled crayfish) individuals.
  • Sample processing (DNA and/or RNA isolation, reverse transcription, gene cloning, quantitative polymerase chain reaction, preparation for and carrying out of conventional Sanger sequencing and/or next-generation sequencing (NGS) methods).
  • Bioinformatic sequence analysis.
  • Deposition of sequences in the GenBank gene database, contributing to knowledge of genetics in crustaceans and other organisms.

What you will receive for your contribution:

  • Periodic updates via my blog and by email on the status of work.
  • Rewards that are listed on the RocketHub project page and that commemorate your contribution in fun ways

I originally released a "teaser" video for Crayfish Clone Wars in the month of April, to whet your appetites, which you can view here: Teaser video for Crayfish Clone Wars

If you would consider a donation to my project, I would be grateful for your help. I'm raising only $780 to fund the modest costs associated with the collection of tissues or blood (hemolymph) from the crayfish and purification of genes from those samples. Because of the small pricetag for my project, if I can get everyone reading this to donate only $1 or $5, I can easily reach my goal by the end of the SciFund Challenge on May 31st, 2012.

Would you please help? Thank you very much!

If you would like to know more about me, have a look at the about me page for my blog, By Way of Science.


K.S. MacLea, Ph.D.

Posted Thu May 3 04:32:17 2012 Tags:

Crayfish Clone Wars My project in the upcoming #SciFund Challenge (SciFund 2) will be called Crayfish Clone Wars and I'll be raising a small amount of money to do some experiments on samples from these amazing clone (parthenogenetic) crayfish! Stay tuned--the Challenge opens on May 1st.

Here's the "teaser" video for Crayfish Clone Wars:

On May 1st, you'll be able to actually donate to the project, so check this space!

You can also see the "teaser" video for Zen Faulkes of UTPA, who is doing his own crustacean research project (his second SciFund project), this time in Beach of the Goliath Crabs:


K.S. MacLea, Ph.D.

Posted Sat Apr 21 20:41:25 2012 Tags:

There are a lot of other people attempting to raise money for science in SciFund 2.

SciFund logo I'm providing links here to reach their projects:

Be sure to visit these websites to learn about the other cool projects in the second #SciFund Challenge! I'll post more when I have the updated link list for other projects.


K.S. MacLea, Ph.D.

Posted Sun Apr 15 22:52:05 2012 Tags:

I visited Russia (then part of the Soviet Union) as a teenager and had a wonderful trip and met some amazing people. Since academics and intellect were (at least at that time) very highly regarded in Russia, we had several experiences that cemented that. Among the experiences I best remember was being repeated trounced at Chess on the trains as we traveled.

Molecular Basis of Domestication of the Fox at Cornell, image from Russia is also home to some truly amazing marathon scientific experiments. One of them is the work of the late Dmitry K. Belyaev and his successor Lyudmila Trut over the past 50+ years to domesticate the fox, Vulpes vulpes.

Last year, this was the subject of a great National Geographic piece "Taming the Wild" by Evan Ratliff.

Now, there's another article about the project in Slate. The take-home message is that this exciting project is imperiled by the lack of funds to keep it going and to really prove that domestication, according to Belyaev's original criteria, has indeed occurred.

You can see some further information on the project at the Cornell website on the project. (Go Big Red!)

It would be a tremendous shame to see this experimental domestication work lost as a result of loss of funding and I hope they will be able to bring additional funding in to fulfill its promise.

As an aside, this also reminds me of the Japanese "Darkfly" experiment, rearing fruitflies in the dark for over 57 years so far.


K.S. MacLea, Ph.D.

Posted Tue Apr 10 22:14:38 2012 Tags:

This year, during the month of May I'll be raising money for a scientific research project I'm conducting, using the crowdfunding collaborative project known as the SciFund Challenge.

By Way of Science I'll post a bit more about this tomorrow, and I'll be using their blog space to promote the project I'll be undertaking.

The SciFund Challenge raised over $76,000 in their 1st fundraising drive in 2011. This year, in the 2nd Annual SciFund Challenge, with almost double the projects, they hope to raise a lot more money for scientific research. I hope you'll help me be a part of it!

To give you a little teaser, I'll just say this much right now: I'll be studying the genes of the parthenogenetic crayfish known as marmorkrebs. If you want to learn a little bit about marmorkrebs before my next post, please see Zen Faulkes's excellent website on the critter.

In the mean time, watch this space to learn more about crowdfunding science. (In addition to the SciFund Challenge, another project, is a new entrant into the crowdfunding-for-science world. Check it out! I'm going to stick to just the one project for now, though.)


K.S. MacLea, Ph.D.

Posted Sat Apr 7 06:01:27 2012 Tags:

There are, of course, many cultural differences between "East" and "West." I've had a growing awareness that intellectual property is one of those areas.

Now, I am no IP lawyer, patent agent, or anything of the sort.

By Way of Science But I have taught Chinese students here at Colorado State and elsewhere and I've noted that they often don't seem to understand plagiarism very well. That is not to say that American students understand it well, either, but I've always gotten the impression that the undergrad Chinese students understand what it is, but don't consider it to be important. (The American students who don't follow the rules on the other hand, are usually either taking short-cuts because they think they can get away with it, but are aware it's wrong, or they are plain ignorant of its importance.)

I'm not the only one to notice this aspect of Chinese academic culture, of course. Peter Friedman in Forbes had a substantial article about this very topic in 2010.

And what I've seen in other areas of Chinese intellectual endeavor suggests to me that this is by no means isolated. Just ask the Russians if Chinese collaborators can be trusted to respect other countries' intellectual property (in this case, Russian made MiG fighter aircraft).

It will be interesting to see how thoughts on IP develop in China going forward. The US is by no means a clean player in all of this. Since the beginning of the Republic, the country was known for producing cheap knock-offs of European goods. In a way, entrepreneurship and invention is a no-holds-barred rush for the next technology. Those who only copy others' goods will never get ahead in the long run. Those who work to develop the new technologies that will push us to new and great advances--those people will be the victors, no matter their country.

Can the "West" continue to innovate? Can the "East" develop its ability to invent in new areas, not just to rehash or extend technology developed elsewhere? The answers to these questions will be important in determining the outcome of economic competition in the next couple of centuries.


K.S. MacLea, Ph.D.

Posted Sat Apr 7 05:44:58 2012 Tags:

Fraud in scientific publications appears to be on the rise. At least if you can believe all the anecdotes you hear.

By Way of Science You need only look at two excellent websites to get an idea of what's going on out there: Retraction Watch and Abnormal Science.

I enjoy reading both blogs, even though I have great faith in the scientific system. Perhaps even because of that faith. I want to see Science (with a capital S) correct its wayward members and bring the enterprise back onto the "straight and narrow."

If you spend any time looking at either site, you will immediately notice one of the great problems in molecular biology today: image manipulation. By image manipulation I mean copying or altering "bands" (those little smudges of DNA or protein) visualized on gels or membranes. These techniques, including RT-PCR and western blots, are mainstays of most molecular research today in biology, in fields from agriculture to cancer to physiology and beyond.

Compared to the insidious (and also common--I'm looking at you, undergrads I've taught!) phenomenon of plagiarism, image manipulation is both easier and harder to detect. By easier, I mean some of the image enhancement techniques that immediately lay bare all kinds of malfeasance. (Check out some of the comments in this Retraction Watch article, for example.) By harder, I mean simply this: A Google search or use of software such as Turn It In can easily detect plagiarism. Image duplicates usually take a lot longer to detect however.

I was thinking about this this morning in the Responsible Conduct in Research course I am auditing.

What about Image Search?

Unlike common text searches on Google, etc., image search is not yet commonly used. But it has a lot of potential to pick up some kinds of image manipulation (particularly duplicates) in the scientific literature. I hope journals will be proactive and start including this kind of filtering pre-publication for all scientific articles. Might prevent us seeing the cases we're seeing now, where individual scientists or research groups are retracting dozens of papers, each full of duplication, falsification and fabrication.

You can do a simple Google Image Search and it works quite well for normal images. Will it work for gels and blots? I'm sure someone must be working on it. Let's hope so!

You may be asking yourself: What is the government doing about this? It varies a lot by country, but if you want to read about the US government's role in policing science, there's a logical place to start. The ORI website has some great resources, including summaries of prior misconduct inquiries.

On a personal note, I feel strongly about the importance of keeping an eye on science and keeping it honest. Mistakes happen. But I remember as a grad student, a postdoc found a paper in which someone had obviously manipulated an image (to hide "non-specific" bands on a western blot--although to be fair, you had to blow the image way up to be able to see the distortions). Although we thought it should be reportable, he was concerned about retaliation from a big name in the field. I can't blame him, but if I had been in his shoes, I would have reported the incident. For his part, I think he was happy to know at least why he saw two bands on his gel when others had seen only one with the same antibody.

But the literature stayed wrong due to this misconduct. Science needs to stay on top of this and bring its malcontents to justice, or it will continue. Not only that, but "errors" will remain in the literature, poisoning progress in these areas for some period of time.


K.S. MacLea, Ph.D.

Posted Sat Apr 7 05:09:41 2012 Tags:

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