Friday, January 25, 2008

Friday beautiful science

Today's Friday beautiful science comes from the Mercury Messenger mission:

One week ago, the MESSENGER spacecraft transmitted to Earth the first high-resolution image of Mercury by a spacecraft in over 30 years, since the three Mercury flybys of Mariner 10 in 1974 and 1975. MESSENGER's Wide Angle Camera (WAC), part of the Mercury Dual Imaging System (MDIS), is equipped with 11 narrow-band color filters, in contrast to the two visible-light filters and one ultraviolet filter that were on Mariner 10's vidicon camera. By combining images taken through different filters in the visible and infrared, the MESSENGER data allow Mercury to be seen in a variety of high-resolution color views not previously possible. MESSENGER’s eyes can see far beyond the color range of the human eye, and the colors seen in the accompanying image are somewhat different from what a human would see.


Sunday, January 20, 2008

Supernatural? Really?


Friday, January 18, 2008

What is peer review, really?

I am currently writing a manuscript for publication in a peer-reviewed molecular biology journal. And I’m hating it (just a little). Hopefully I’ll have this out of my hair in just a few more weeks. But it occurred to me, not all of my readers are scientists (indeed, based on the commenters alone, I would say that only a few of my readers are scientists). It occurs to me that not all of my readers know exactly how peer-review works – and why it’s the best game in town for verifying scientific work (well, aside from replication of the results by an independent lab).

So I thought I would write a little bit about how it works from the inside. The experiments that I’m writing about have been conducted over the last several years by another post-doc in the lab and I. We were working on different problems, but as it turns out, together our data shows several neat things about a protein that we study.

So. He and I have spent the last several months fighting about what belongs in the paper, and what doesn’t. Sorting the wheat from the chaff. And if he doubts any of my experimental findings, I do extra experiments to convince him. And vice versa. So over the last few months we’ve hashed out a story that we think some folks will find interesting. And we’ve managed to convince each other that this story is probably true.

But it doesn’t stop there. Next, I’ve been writing off and on over this time (and much more intensively more recently). I’ve also organized and integrated our data together into figures that are more intuitive than if I presented our data as it arrived chronologically. I gave a lab meeting just before Christmas, and had everyone in the lab look at the figures. As it happens, they hated them. They found them unclear, and at times, unconvincing. So I added a couple of experiments, and removed a couple that folks found unconvincing (so now I won’t make a couple of the conclusions I wanted to make – but I can do more on that later, and put it into a different paper).

I’m nearly at the point where I’ll hand out the manuscript and heavily revised figures to a few folks that I think are talented. These aren’t folks who are going to say, “Yes, Dr. Dr. Factician, this is the most brilliant piece of work I’ve ever seen” or “I agree with you 100%, you brilliant hunk of man, you!” Rather, I’ll hand it out to people who both don’t care what I think and have the intellectual fortitude to tear up the paper. Hopefully these folks will be ruthless with it, and help me make it into an even better paper.

After those revisions, I’ll give it to my advisor. I’ve only written one paper with her in the past. She is fairly particular about what goes and what doesn’t. More than likely, she’ll want to see 5 or more drafts of the paper before she’s happy (keep in mind, by the time she sees it, this paper will have been through more than 30 drafts).

After that, I clean up the paper one last time, checking for typos, casting about for logical errors, and off it goes to the journal. At the journal, it goes through 2 types of review. The first review is by the editorial staff. They will read the paper and decide if it’s proper material for their journal (i.e. topical) and if it’s sexy enough. There’s not much that I can do about sex appeal – that’s a pretty subjective area. Granted, I’ll try to make my work sound as interesting as possible, but hand it to 3 different people, 1 will say it’s Super-Sexy, 1 will say it’s interesting and 1 will say it’s banal tripe.

So, supposing I make it past the editor, it will be sent to 3 ad hoc reviewers. These are folks who are experts in my field. People in the position of my advisor (professors and the like at major medical schools). My advisor often gets me to review papers for her, so it’s possible my paper will get reviewed by post-docs, but it will be reviewed by people in my field. All 3 of them have to think that the paper is interesting and that the science is solid. Any one of them is sufficient to torpedo the paper.

Finally, if my paper is accepted, it will be printed in a journal for everyone to see. If there are problems with it, we will hear about it in other peoples’ papers. If it fits with other peoples’ data, and helps them to do other experiments in the field, they will cite my paper in their own papers, raising the visibility of my paper. (For example, my most successful paper has been cited 128 times).

So briefly, about a dozen people in my lab have criticized my work, and helped me make it better. Mrs. Factician has also played a large role in cleaning up my work. Several other scientists in my department will look at my paper. My advisor will read it and criticize it. An editor at the journal will read it and criticize it. Three ad hoc reviewers will read and criticize it. And finally, it will be placed in a journal, where many thousands of scientists can read and criticize it.

One bit of advice I give to starting graduate students: If you give your work to someone to read, and they say, “That was fantastic, don’t change a thing” you’re talking to the wrong person. You want the person who will say, “And on page 2, I can’t believe you started this sentence with the phrase X. It’s simply not true!”. Better to be criticized heavily by your colleagues close to home, and get your game in shape before sending it out for review.


Friday beautiful science

Today's Friday beautiful science comes from the TaMaRa lab (the lab of Francois Taddei, Ivan Matic and Miro Radman). They've worked on a lot of different projects, but these photos are intended to demonstrate that bacterial colonies are not made up of homogeneous cells. The first photo is of:

Cells expressing RFP undert rpoH and YFP under rpoS-dependent promoters.
That is, they have RFP (red fluorescent protein) and YFP (yellow fluorescent protein) expressed under two different stress-dependent promoters. The colour of the cell will indicate which stresses that particular cell is being exposed to, protein folding stress, or starvation stress. As you can see, this group of 'homogeneous' cells is far from - and different cells are experiencing different stresses, depending on their position within the microcolony.

This second photo is of a
microcolony formed from a single cell (as above) with sublethal mytomycin concenration. Brightest cells (center) stopped growing after 3rd division and were engulfed by dividing cells.
It is merely intended to show that different cells are responding to a sublethal dose of a DNA-damaging agent in different ways. This lab does all kinds of exciting work. I'll try to post on them more in the future.

P.S. I apologize for my absence. I had a massive hard drive meltdown a couple weeks ago, and I'm still recovering from it. I'm currently working on an ancient iMac while I wait for my machine to be fully repaired. Posting should pick up again shortly.


Wednesday, January 16, 2008

Scientists for better PCR



Friday, January 4, 2008

National Academies and Evolution

The National Academies of Science of the US has just released yet another report about evolution. Keep in mind here, the National Academies members are the best scientists in the world. You get invited to join the National Academies after a long and distinguished career as a scientist. Their reports tend to be on the heavy side.

This report is written for regular folks. It's an introduction to evolution in no uncertain terms, and it also blasts creationists:

In the United States, various views of creationism typically have been promoted by small groups of politically active religious fundamentalists who believe that only a supernatural entity could account for the physical changes in the universe and for the biological diversity of life on Earth. But even these creationists hold very different views. Some, known as “young Earth” creationists, believe the biblical account that the universe and the Earth were created just a few thousand years ago. Proponents of this form of creationism also believe that all living things, including humans, were created in a very short period of time in essentially the forms in which they exist today. Other creationists,known as “old Earth” creationists, accept that the Earth may be very old but reject other scientific findings regarding the evolution of living things.

No scientific evidence supports these viewpoints. On the contrary, as discussed earlier, several independent lines of evidence indicate that the Earth is about 4.5 billion years old and that the universe is about 14 billion years old. Rejecting the evidence for these age estimates would mean rejecting not just biological evolution but also fundamental discoveries of modern physics, chemistry, astrophysics, and geology.

Some creationists believe that Earth’s present form and the distribution of fossils can be explained by a worldwide flood. But this claim also is at odds with observations and evidence understood scientifically. The belief that Earth’s sediments, with their fossils, were deposited in a short period does not accord either with the known processes of sedimentation or with the estimated volume of water needed to deposit sediments on the top of some of Earth’s highest mountains.
Well said.

The report is well-written, and well placed. (And is clearly intended to mollify believers that there needn't be any conflict between science and faith). But this is probably a good choice on the part of the National Academies, as clearly their intent is to improve American science education:
The pressure to downplay evolution or emphasize nonscientific alternatives in public schools compromises science education.
This is the central point of the report. So go ahead. Download a copy of the report yourself (you need only provide them with your e-mail address). Send it to the members of your school board. Send it to your creationist aunt. Share it. Get it out there.


Thursday, January 3, 2008

Cancer cured!

From Ataraxia.


77th Skeptics' Circle

The 77th Skeptics' Circle is up at White Coat Underground. Go take a gander.


Wednesday, January 2, 2008

Bad talks