Hummingbirds and sweets – a great example of how evolution works

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Dinosaurs lost the ability to taste sugar; hummingbirds re-evolved it
[Via Ars Technica]

Chickens are not fussy eaters. Any object resembling food is worth an exploratory peck. But give a chicken the choice between sugary sweets and seeds, and they will pick the grains every time. This is odd. Many animals, including our own sugar-mad species, salivate for sugar because it is the flavor of foods rich in energy. New research suggests that many birds’ lack of interest in sugar is the result of genes inherited from their dinosaur ancestors.

Most vertebrates experience sweet taste because they possess a family of genes called T1Rs. The pairing of T1R1 and T1R3 detects amino acids and gives rise to the savoury “umami” taste, while the T1R2-T1R3 pair detects sugars, giving us our sweet tooth.

Maude Baldwin, a postgraduate student at Harvard University, searched the genomes of ten species of birds, from chickens to flycatchers. She found that insectivorous and grain-eating birds possess the gene pair that detects the amino acids present in insects and seeds, but none of them had the T1R2 gene responsible for the ability to taste sugar. These modern birds evolved from carnivorous theropod dinosaurs that had diets that were rich in proteins and amino acids, but lacked sugar. So Baldwin reasoned that without a need to detect sweetness, ancient birds lost their T1R2 gene.

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Birds lack the receptors to detect sweets, apparently inherited from their dinosaur predecessors.

So how do hummingbirds taste the sugars that they eat exclusively? urns out that they did not    regain this by reactiviating the old genes. Those are dead and gone.

They took the genes that were present, that normally detected proteins. These genes are mutated in hummingbirds to now detect sugar.

This is seen a lot: once a function is lost, it is regained only by adapting a current gene, not by reforming the old  one.

AAAS creates an open access journal that is not really open access

 Key to the open door

The biggest scientific society is joining the open access movement — sort of
[Via The Raw Story]

Access to research is limited worldwide by the high cost of subscription journals, which force readers to pay for their content. The use of scientific research in new studies, educational material and news is often restricted by these publishers, who require authors to sign over their rights and then control what is done with the published work. In response, a movement that would allow free access to information and no restrictions on reuse – termed open access – is growing.

Some universities and funding organisations, including those administered by governments, now mandate open access, recognising its potential to increase the impact of research paid for by public money. The United Nations is considering the importance of open access to ensure the “right to enjoy the benefits of scientific progress and its applications”.

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In reading the details, it sounds like a semi-open access journal. Digital only but there is a 33% surcharge to make it really open access. And a 50% surcharge if it is longer than 10 pages.

For a digital publication where pages do not  really matter since nothing is printed.

Typical authoritarian response to a distributed effort.

Science conferences – too often mundane rather than magical

 Army kicks off science conference

 

Scientific conferences, the too-slow movement of ideas, and giving an engaging talk
[Via Small Pond Science]

I went to a bunch of scientific conferences this summer. Four of ‘em. I have a smorgasbord of reflections on the whole experience to share with you.

Yes, this is a lot of travel. 

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Very accurate description of science conferences. They should be places for rapid exchange of information.

But too often they are simply places for a bunch of white men to hang out.

Far too many talks are like every other. And many have little relevance to anyone else. The same information could have been exchanged by telephone.

I suspect this is self-evident to anybody that’s been in science for a few years. We might be studying animals or plants or microbes or rocks, but science is still a human enterprise. The indicator of a good talk — especially for a junior scientist who needs to get and stay employed — is the fact that the talk was impressive. If you had to choose between giving people the impression that: A) you’re an awesome scientist, or B) a particular scientific idea 

Yep, way too many speakers simply do a data dump to show the crowd how hard they have been working, to awe the crowd.

“60 slides in 15 minutes. That’ll do the trick.They will be awed by how hard we have worked!”

Now I have seen the masters of this approach,who also managed to get across big ideas also. In pre-digital days. Lee Hood would have two separate projectors going on two screens at the same time – sometimes popping back and forth between them, other times leaving one slide up for a long time as he discussed another, seldom looking at the screens , never appearing to read from notes and always on point with the idea.

He did not need 60 slides to awe us. I’d look in awe at just ONE slide that I knew represented perhaps 10 graduate student years. On one freaking slide! And he has tens of these slides. 

You had to bow down to the awesomeness of Lee Hood and his lab. But he was also providing tremendous ideas with the data – at that time about how the tremendous antibody repertoire we all have came to be.

Later with sequencing the human genome.

He is still pursuing big ideas – P4 medicine just the latest. But he has had to bow to technology and only uses a single projector these days.

The talks I always have remembered, that had an impact on my research and whose speakers I sought out were the ones that said. “Here is a great idea. We do not have it all figured out but here is some interesting data. Anyone one have any other ideas?”

Hearing how someone has been successful with a project is useful but we can read the papers about that. Describing an interesting phenomenon that has no full explanation is always more interesting to me

And more universal, as all scientists run into problems and have to figure out how to move forward.

Make it magical, with dark corners of unknown wealth, that could hold tremendous riches if we illuminate them.

Rather than a clean, sterile progression  from point A to point B.

Hack reporting? writing about creation science without understanding science

 darwin

Why covering “creation science” is like covering cricket.
[Via KSJ Tracker]

If I were assigned to cover the upcoming cricket matches between Australia, Zimbabwe, and South Africa, I’d be writing without knowing how the game is played or scored. Or without knowing that “the injured Shane Watson and rested opener David Warner [are] not making the trip.” What’s an “opener”?

I probably wouldn’t do very well. Sadly, that happens too often when general-assignment reporters–even the best of them–try to write science or medical stories. It’s tough to do if you don’t have the background.

Last week, Scott Farwell–a general assignment reporter at the Dallas Morning …

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Not only stenographic but poor writing to boot.

What bugs me more than the sloppy writing about important things (i.e. how does a swamp become a cell, what are shape-shifting cells, or evolution is a wall? Really?) is its attempt to provide sympathy for people who are fringe.

They are ostracized for their beliefs? Yep. By scientists because they do not do science. Science is not about beliefs. It is about acknowledging the world around us, not making it fit a preconceived notion.

As mentioned by the one scientist quotes (with no one rebutting the idiocy of the ICR the reporter simply quotes):

“The problem is, they’re not scientists,” said Ron Wetherington, who teaches human evolution and forensic anthropology at SMU. “They cherry-pick data in order to use it to justify the Genesis account of creation.

”Real science, he said, works the opposite way. Researchers don’t line up facts to support a hypothesis. Natural laws and theories like evolution are constantly pressure-tested by the scientific community, checking for flaws and leaks in the logic.

Of course, this happens at the very bottom of a long article. Well, after lots of discussion about the poor ICR.

As the KSJ writer mentions, it is like reporting about the poor ostracized scientists at the Tobacco Institute, waiting until the end to have a single quote from a researcher elsewhere who mentions cigarette smoking causes cancer.

Croquet – Best way to determine authorship ever

I smiled a lot. It is better than the current way, which is usually to wait until the person who did the work leaves the lab and then put your name first.

When is free access not really free? Jonathan Eisen checks out AAAS

Figure 2 

AAAS – Blocking Access to the Scientific Literature Even When They Say It Is “Free”
[Via The Tree of Life]

Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999.  The paper was, I think, kind of cool.  It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium.  Alas, I did not have a copy on me, and the only electornic device I had with me was my phone.  The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of Windows operating system, so I looked at it and panicked and said “Maybe you should drive” (as in, maybe they should be the one controlling the computer).

So this person, who shall remain anonymous mostly because of the ancientness of their computer, did the kind of obvious thing, and opened a web browser (don’t even ask which one) and typed in “Pubmed.Com”.  OK – that would work.  I might have preferred going to Google Scholar, but I use Pubmed about as frequently.  And though I do not have a Windows machine or the weird web broswser they used, I have recreated what happened next.

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In order to read a 15 year old paper, he had to spend an hour, giving up all sorts  of information and rights, open himself up to spamming emails and generally giving over all sorts of information.

This is what I hate about so many close, for-profit journals – they continue to charge or to make money off of works that are really ancient. 

Elsevier wants $36 for me to access one of my papers from 1991 – 23 years old!

I agree with Jonathan – I’ll never publish in any journal that does not open access all papers after 12 months.

When a major journal’s needs to not match the scientific community’s

 Rasur des Tages 02.01.09

Who governs science? | Stephen Curry
[Via Occam's corner | The Guardian]

Traditionally, science holds itself to account, primarily through internal systems of peer review. But the recent retraction of two papers on stem-cell research by the journal Nature highlights weaknesses in this self-regulatory framework that scientists need to address

To err is human, so why should science be any different? The frailties of science can be easy to overlook because it remains one of humankinds greatest cultural and intellectual achievements; working hand in hand with technology, it has transformed our understanding of the world and our capacity to shape it. But as any scientist will tell you, the daily grind of research is often laborious and repetitive and regularly punctuated by failure either through error or miscalculation, or when our cherished theories cannot withstand the pitiless exactitude of experiment. What keeps us going are the moments of revelation or insight that every now and then swell the heart and the head with a warm pulse of satisfaction. Those small victories are all the more important because science is an intensely competitive career; the endless struggles for funding or the space to publish in the most acclaimed journals, which have failure rates as high as 80 or 90%, means that there are demons of disappointment crouching in every laboratory.

The human side of science was thrown into harsh relief by news on the 5th of August of the suicide of Japanese stem cell researcher Yoshiki Sasai. Sasai was a senior coauthor on two papers published in January this year by the high-profile journal Nature that reported a remarkable breakthrough: the generation of stem-cells by subjecting mouse cells to mild stresses such as pressure or acidic conditions, a procedure dubbed stimulus-triggered acquisition of pluripotency (STAP). But soon after publication the claims made in the papers came under intense scrutiny; there were concerns about reproducibility, a key test of any scientific report, and accusations of image manipulation and plagiarism. By the beginning of April an investigation by the RIKEN Center for Developmental Biology (CDB) where most of the work had been carried out found the lead author Haruko Obokata guilty of misconduct for having manipulated data with the intent to deceive. Sasai was cleared of misconduct but criticised in the investigation report for not properly checking the experimental data. On 2nd July both papers were formally retracted by Nature for reasons of plagiarism. A month later a serious and unfortunate incident became a desperate human tragedy when Sasai took his own life.

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This all has to do with a series of papers on stem cells published by Nature that had to be retracted because apparently they were just wrong.

Nature is a journal presented as without peer for its impact and with a scarcity of pages to ensure that it has the pick of the best science. Getting published in Nearer can get a researcher tenure.

So, there is obviously an incentive to write the perfect Nature paper based on making up the data. Peer review is not supposed to replicate the experiments but to make sure the data presented match the conclusions, that confirmation and other biases have not arisen, that the protocols are ethical, etc.

Add this to Nature’s need to publish provocative papers  – thus increasing the impact factor and justifying its price – and we have a recipe for disaster.

Which appears to have happened here.

Now, scientists are people and they make mistakes. The key of to deal with those mistakes. Science over the last 400 years has determined that open investigations are the best antidote.  Secrecy opens the way for fraud.

This is what separates science from alchemy.

Yet Nature, in response to this incident, has done very little in the open – telling us to trust its processes even as it hides them from view.

So how do we know it is fixed? How can we trust any other paper in Nature if we do not know what it does to prevent being gamed? Is it really trustworthy?

In truth, we don’t. we can’t, and probably not

That is because Nature is a business that needs subscribers. Its incentives for success do not always align with science

Unfortunately, corporate nature of company (in our case NPG) is not about encouraging the openness and improving science. It’s against it! Taking in account recent retractions (6 in half of year), closed access (even decade after publication!), closed flawed peer review, shameless promotion of its impact factor (while everybody knows that IF is a joke), absence of feedback and dialogue with peers… you can see how “frontier of scientific publishing” losing its credibility and trust.

So looking at the reviewer’s comments, to get some idea of how the process failed, would be helpful. But Nature says no and to just trust it.

This might not bode well for Nature’s future. Open access approaches tend to align much better with the needs of researchers. We are seeing a sea change in scientific publishing.

Stonewalling the community may not be the best way to go.

 

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