It was a really bad week for Homo sapiens: 

First, it turns out rats have regrets just like we do:
http://www.nature.com/neuro/journal/vaop/ncurrent/abs/nn.3740.html
At least when they fail to maximize their food intake. That primitive circuitry is highly active in grad students (cliche, I know).

Then chimps beat humans at gaming:
http://www.nature.com/srep/2014/140605/srep05182/full/srep05182.html
I’m just happy I was not one of their human subjects. The authors kindly played it down stating that chimps’ choices were “at least as strategic as human choices”. Much nicer than than the other way around.

And finally, a computer which can out-converse a human being:
http://news.sciencemag.org/sifter/2014/06/this-supercomputer-can-convince-us-it-s-human
I wonder how many times the computer had to say “like” to be so convincing…
Also, what is the reason behind Russian scientists' decision to have the computer pretend to be a Ukranian boy with a pseudo-jewish last name? Ivan Ivanov not good enough?

Now onto more scientific stuff:

A computational biology paper about predicting enhancers based on dinucleotide frequecies:
http://www.genome.org/cgi/doi/10.1101/gr.169243.113

An excellent review on genome editing using different nucleases
http://www.nature.com/nrg/journal/v15/n5/full/nrg3686.html#t

A nice back-and-forth on adaptive value of a certain mutation.
http://www.pnas.org/content/111/23/E2357.full
http://www.pnas.org/content/111/23/E2358.full
Or is it just a polymorphism undergoing some good old genetic drift? Regardless, there should be more discussions like that.

And back to non-science:

Real heavyweights on dire prospects of the research enterprise as it is:
http://www.pnas.org/content/111/16/5773.full
I think it applies more broadly, not just to the US.

There is a more optimistic counter-argument of course:
http://www.pnas.org/content/early/2014/06/11/1408267111.full.pdf?etoc

But if you are hell-bent on getting a PhD, you will need to take GRE of course. Which apparently is no good for nothin'.
http://www.nature.com/nature/journal/v510/n7504/full/nj7504-303a.html
The figure is very persuasive indeed. I would be even more persuaded if it turned out that among tenured faculty, women and minorities entered grad schools with lower average GRE scroes than the white dudes.

Enjoy!

A very nice paper on bone regeneration in zebrafish:
http://dev.biologists.org/content/141/11/2225.full

Ongoing insertional mutagenesis of the human genome by transposons:
http://www.pnas.org/content/111/22/8131

Selective mating in Homo sapiens:
http://www.pnas.org/content/111/22/7996.full
Perhaps we should have computational geneticists play with this some 10 generations into the future. Or maybe not…

I am very disturbed by many aspects of this story:
http://www.sciencemag.org/content/344/6188/1076.full
One of them: persuading a briliant mech engineering student to get PhD in math may be considered a success. But not if all he has is a non-tenure track teaching position as a result.

Ironically, here is a mathematical model of probability to become a PI:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_06_02/caredit.a1400136

Remember that paper about wnt not really being a morphogen I highlighted back in January? Here is a paper about wnt being transported by migrating neural crest cells:
http://dev.biologists.org/content/141/10/e1002.full
It is one of the papers which make me wish (again!) we had a Dev Bio journal club...

A cautionary tale than not all genes are essential in humans:
http://www.sciencemag.org/content/344/6185/687.full
This is probably only a surprise to human geneticists who do not bother with model systems literature...

It is nice to read about a successful post-science career transition:
http://www.sciencemag.org/content/344/6186/934.full
But we do not get to read about those who don’t make the transition quite as successfully, so the sample is biased.

About a $30-million-a-year scam business:
http://thechart.blogs.cnn.com/2014/05/12/antioxidant-in-red-wine-has-no-benefit-at-low-doses/?hpt=hp_bn13
http://www.bbc.com/news/health-27371546

An entertaining column that rings true. A lot.
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_05_20/caredit.a1400126

This week’s list is more fun than science. Fitting with the Finals week here at Temple.

A synthetic yeast chromosome. Made by undergrads.
http://www.nature.com/nature/journal/v509/n7499/full/509168a.html
http://www.sciencemag.org/content/344/6179/55

Crowdsourcing at it’s best:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_05_05/caredit.a1400112
Turns out “big science” can be fun, too.

Your pick: either cool dudes are having a “chilling” effect or are men stink up biomedical studies.
http://www.sciencemag.org/content/344/6183/461.full

Very disturbing news: working harder leads to better results.
http://news.sciencemag.org/education/2014/05/scienceshot-why-asian-american-students-outperform-their-white-peers?rss=1
The author needed to hypothesize as to why the outperforming student group spends less time hanging out with their friends. Really?!

Now we know the reason Dracula is forever young
http://news.yahoo.com/studies-young-blood-rejuvenates-aging-mice-191130330.html
http://news.sciencemag.org/biology/2014/05/young-blood-renews-old-mice
http://www.bbc.com/news/health-27282832
You decide which kind of story telling you prefer. Or maybe the actual paper?
http://www.nature.com/nm/journal/vaop/ncurrent/full/nm.3569.html
How can I get hold of a batch of K-Creb AAVs?

Were the Terminator movies a beginning of a new film genre: futumentary?
http://www.independent.co.uk/news/science/stephen-hawking-transcendence-looks-at-the-implications-of-artificial-intelligence--but-are-we-taking-ai-seriously-enough-9313474.html
It would not be smart to dismiss Stephen Hawking…

Stem cell therapy for “broken heart" monkeys
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13233.html
Note that the trial was non-randomized.

And apparently only trials with design flaws show effectiveness of stem cell therapies for myocaridal infarction in humans.
http://www.nature.com/news/doubts-over-heart-stem-cell-therapy-1.15122
http://www.nature.com/news/false-positives-1.15119

Finally, an excellent review on functional annotation of the human genome
http://www.pnas.org/content/111/17/6131.full

Now onto the easy stuff:

How to think like a scientist:
http://www.pnas.org/content/111/17/6119.full
Imagination IS important (see my post from last week :-)

Not completely surprisingly but very disturbingly, a professor’s reaction to a letter from a prospective graduate student depends on the name on that letter:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_04_29/caredit.a1400107

Have a great weekend everyone.

A couple of very cool papers in the current issue of Development:

On dual nature of transcriptional enhancers...
http://dev.biologists.org/content/141/9/1906.full

...and a technique paper describing multi-color labeling of the retina
http://dev.biologists.org/content/141/9/1971.full

And onto "not directly scientific but kinda important" stuff.

An excellent “prospects” diagram for those considering getting a PhD in life sciences.
http://www.ascb.org/ascbpost/index.php/compass-points/item/285-where-will-a-biology-phd-take-you
The conclusion? Don’t do it. Unless you can’t imagine yourself doing anything else. And here is your catch-22: imagination may be important for a PhD-level career...

A bit on the dream job of teaching in academia:
http://www.philly.com/philly/jobs/Adjunct_professors_see_selves_as_colleges_temp_workers.html
Teaching K-12 is way better...

After reading the above, being a postdoc doesn’t sound so bad, does it?
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2002_08_30/nodoi.4149859741665864757
Every research-active faculty member will gladly tell you that postdoc was the best time of their career. Because they were lucky enough and good enough to land a decent faculty position after their postdocs.

Not to say some that the process is entirely anguish-free:
http://www.nature.com/nature/journal/v508/n7497/full/nj7497-555a.html

Of course if you wish to be positive, you could counter that libreal arts grad students have it worse:
http://news.temple.edu/news/2014-04-15/public-history-partnership-leads-full-time-work-temple-graduate?utm_source=templetoday&utm_medium=email&utm_campaign=Print_Center_Internship
I gather a one-year job offer is a big deal in that field.

I will try find some more positive news next time.

Here is a massive (and outstanding) piece of work on promoters:
http://www.nature.com/nature/journal/v507/n7493/full/nature13182.html
Too many authors to list…

And as if identifying transcription start sites was not enough, they used presence of bidirectional unspliced transcripts to identify a few enhancers:
http://www.nature.com/nature/journal/v507/n7493/full/nature12787.html
Well, “only" 43,011 of them.

Now onto the easy stuff:

Is your dad a neanderthal?
http://www.nature.com/news/human-evolution-the-neanderthal-in-the-family-1.14932
Seriously, the picture enforces every damn stereotype about men. Pure sexism. I guess I should be upset.

More on online lab notebooks
http://www.nature.com/nature/journal/v507/n7493/full/nj7493-523a.html
I did consider making all lab notebooks electronic back in 2007, but perhaps now is the time. Fully searcheable etc.

We absolutely do need a pipeline of talented students going into biomedical careers:
http://news.sciencemag.org/education/2014/03/panel-launches-study-precollege-role-nih?rss=1
Of course most of them will be going nowhere with their careers in the current/foreseable funding environment, but who cares?

And here is why grad students must get some teaching experience:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_03_24/caredit.a1400076
Contrast it with the article/experience cited within.

Have a great weekend.

How do transcription factors find their targets and how long do they stay bound?
http://www.sciencedirect.com/science/article/pii/S0092867414001974?via=ihub
I suppose this is the reason for transcriptional heterogeneity among cells

A very complicated - but hopefully precise and reasonably high-throughput- way to do lineage tracing:
http://dev.biologists.org/content/141/7/1589/F1.expansion.html
Not sure is this would be better than brainbow in zebrafish, need to read more thoroughly.

On vasculature possibly guiding nerve growth:
http://dev.biologists.org/content/141/7/1480

Being clueless can be advantageous:
http://www.nature.com/nature/journal/v507/n7492/full/507277d.html
How does this apply to scientific exploration?

Here is a dilemma: if you have $5,000, should you buy a used car or sequence your genome?
http://www.nature.com/news/technology-the-1-000-genome-1.14901
If you just wait, both will get cheaper :-

Enjoy.

State-of-the art imaging to characterize cell migration. In zebrafish, of course.
http://dev.biologists.org/content/141/6/1282

Don’t know what to make of it, but it appears that control of lymphangiogenesis is quite different between fish and mice
http://dev.biologists.org/content/141/6/e605.full
The exception proves the rule perhaps?

A cool paper about a mutation in what one would consider a global regulator of transcripotion phenocopying Tbx1 mutation:
http://www.cell.com/developmental-cell/fulltext/S1534-5807%2812%2900329-2

A must-read review abut the role of myeloid cells in muscle regeneration
http://dev.biologists.org/content/141/6/1184.full

Not so big on big data
http://www.sciencemag.org/content/343/6176/1203.full

Of course Science is happy to point out that a Nature paper (see my list for January 31st) is likely to get retracted.
http://news.sciencemag.org/biology/2014/03/retraction-request-made-more-questions-swirl-around-simple-stem-cell-method
When you go for highest profile discoveries, some of them just might turn out to be questionable. Who knew...

Now onto easy (if not fluffy) matters:

Imagine a figure for which YOU would write a legend/caption containing phrase “...population caught in the act of evolving lighter skin”. Then go to
http://news.sciencemag.org/archaeology/2014/03/new-diet-sexual-attraction-may-have-spurred-europeans-lighter-skin
Yep, a skeleton in a grave. Not what you imagined?
Two more notes. First, use of term “ancient Ukrainians” to describe a people living there 6000 years ago is odd. It makes ancient Ukraine precede ancient Rome, Greece and Egypt. Second, I doubt the evolutionary models used account for all kinds of armies (including those of certain Genghis Khan and the Great Duke of Lithuania Vytautas) marching through what IS AND SHOULD REMAIN Ukraine today.

Here is a case of Europeans (in the US) taking up the great American tradition of resolving disputes by suing each other.
http://www.sciencemag.org/content/343/6175/1065.summary
Actually, this is anything but funny. I can not pretend to know who is right and who is wrong here. But I am pretty sure that if you are a postdoc in the same situation and you do not have a Nobel laureate standing behind you, you are done. Right or wrong.

We ALL KNOW girls can’t count.
http://news.sciencemag.org/math/2014/03/both-genders-think-women-are-bad-basic-math?rss=1
The most disturbing part is that even when presented with evidence, people still refused to give up their prejudice. But then again- victories of prejudice over facts occur every day, everywhere.

Here is another “doomsday” report on science environment
http://chronicle.com/article/Strapped-Scientists-Abandon/144921/?key=SWJzJAE5OHMVbCo1ZTtHZ2oBOnVqOBt3ZnYWOSwlblBVEQ==
I wish I could refute it…

...but US science funding just keeps getting worse
http://www.nature.com/news/don-t-hide-the-decline-1.14848


Have a worry-free weekend everyone :-)

Critical role of vascular endothelial cells in liver regeneration
http://www.nature.com/nature/journal/v506/n7488/full/506299a.html
http://www.sciencemag.org/content/343/6169/416.full

A potential alternative to Gal4/UAS:
http://dev.biologists.org/content/141/5/1167.full

How neural crest cells coordinate rapid migration and proliferation:
http://dev.biologists.org/content/141/5/1095.full

Popular science level intro to the broad utility of CRISPR/Cas9:
http://www.biotechniques.com/news/biotechniquesNews/biotechniques-350132.html#.UwVHtPaYDNF

An interesting stem cell clinical trial
http://www.bbc.co.uk/news/health-26273707

And finally just to cause you nightmares: dire notes about young academic researchers around the world
http://www.nature.com/news/extreme-workloads-plague-scientists-at-the-start-of-their-careers-1.14567
The sample is too small and non-random, but worthwhile nonetheless.

But there is a bit of good news: some professions experience shortage of workers:
http://www.npr.org/blogs/thetwo-way/2014/02/18/279032024/theres-a-clown-shortage-who-will-fill-those-big-shoes
The bad news is one has to be funny to qualify…

Enjoy.