Evolution Explains Taxonomy

 
Charles Darwin advanced many different arguments in support of his claim that life has evolved. One of the most potent arguments is that evolution explains the classification scheme proposed by Linnaeus and used by all naturalists in the early part of the nineteenth century.

The following passage is from the summary of Chapter 4: Natural Selection in Origin of Species.

It is a truly wonderful fact the wonder of which we are apt to overlook from familiarity that all animals and all plants throughout all time and space should be related to each other in group subordinate to group, in the manner which we everywhere behold namely, varieties of the same species most closely related together, species of the same genus less closely and unequally related together, forming sections and sub-genera, species of distinct genera much less closely related, and genera related in different degrees, forming sub-families, families, orders, sub-classes, and classes. The several subordinate groups in any class cannot be ranked in a single file, but seem rather to be clustered round points, and these round other points, and so on in almost endless cycles. On the view that each species has been independently created, I can see no explanation of this great fact in the classification of all organic beings; but, to the best of my judgment, it is explained through inheritance and the complex action of natural selection, entailing extinction and divergence of character, as we have seen illustrated in the diagram.

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Nature tells the world scientific community about Canada's lack of support for science

 
The latest issue of Nature reports on Prime Minister Stephen Harper's plan to slash the budgets of the major granting agencies [Cash concerns for Canadian scientists].

Billions of dollars in science infrastructure investments have been overshadowed by cuts to major grant-funding programmes in Canada's federal budget....

Although the budget does contain Can$87.5 million for graduate-student scholarships, the research community is perplexed by the government's decision to cut funding to Canada's three federal granting councils. Over three years, the budgets of the Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council and the Social Sciences and Humanities Research Council will be reduced by almost Can$148 million. "It's an unfortunate consequence of getting poor advice or not listening to good advice," says Aled Edwards, a structural biologist at the University of Toronto, Ontario, and director and chief executive of the international Structural Genomics Consortium. He argues that the most efficient way to invest in research is through the funding councils, where peer review determines where the dollars are spent....

But the long-term effect of cutting funds for research may be that Canadian scientists will take their research south of the border, says Edwards. Canada's research funding pales in comparison with that in the United States, and the latest budget threatens to widen the gap between the two countries, he adds. "We're at serious risk of a brain drain."

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Nobel Laureates: John B. Fenn and Koichi Tanaka

 

The Nobel Prize in Chemistry 2002.

"for their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules"

John B. Fenn (1917 - ) and Koichi Tanaka (1959 - ) were awarded the Nobel Prize for developing techniques using mass spectrometry to determine the molecular mass of proteins and peptides. Here's the Press Release describing their achievements.

THEME:
Nobel Laureates

Mass spectrometry is a very important analytical method used in practically all chemistry laboratories the world over. Previously only fairly small molecules could be identified, but John B. Fenn and Koichi Tanaka have developed methods that make it possible to analyse biological macromolecules as well.

In the method that John B. Fenn published in 1988, electrospray ionisation (ESI), charged droplets of protein solution are produced which shrink as the water evaporates. Eventually freely hovering protein ions remain. Their masses may be determined by setting them in motion and measuring their time of flight over a known distance. At the same time Koichi Tanaka introduced a different technique for causing the proteins to hover freely, soft laser desorption. A laserpulse hits the sample, which is “blasted” into small bits so that the molecules are released.

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The images of the Nobel Prize medals are registered trademarks of the Nobel Foundation (© The Nobel Foundation). They are used here, with permission, for educational purposes only.

Darwin Birthday Party in Toronto

 

Darwin Birthday Party

Starts: Friday, February 13th 2009 at 5:30 pm
Ends: Friday, February 13th 2009 at 7:00 pm
Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

Come celebrate Darwin's Birthday! There will be cake, games and a toast to one of the greatest men in science who ever lived. Stick around for the Pre and Post Darwin Science talks that follow.

A CFI Members Exclusive Activity!

Pre- and Post-Darwinian Science

Starts: Friday, February 13th 2009 at 7:00 pm
Ends: Friday, February 13th 2009 at 9:30 pm
Location: Centre for Inquiry Ontario, 216 Beverley St, Toronto ON (1 minute south of College St at St. George St)

What was science like before Darwin, and how did it change after Darwin?

Larry Moran will be discussion our modern scientific world in light of the impact Darwin and his theory of evolution due to natural selection has had on it.

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto.

$5, $3 for students and FREE for Friends of the Centre

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Genomics, Proteomics and Mass Spectrometry

The explosion in sequence information as a result of various genome projects has resulted in many unexpected payoffs. One of them has to do with the identification of tiny amounts of unknown protein.

Many experiments in biochemistry and molecular biology lead to the recognition of a novel protein that hasn't been identified. For example, one could go fishing for proteins that bound to other proteins or look at the protein composition of various complexes.

Often the only thing one knows about the protein is its molecular weight on an SDS gel. You can cut out the band containing your protein of interest and extract the protein but that only gives you a tiny amount of denatured protein.

With the development of protein mass spectrometry it becomes possible to determine an accurate molecular weight of the protein [Biochemistry and Mass Spectrometry]. In theory, one could then compare this molecular weight to all the calculated molecular weights of all the proteins encoded in the genome. These calculated molecular weights can be determined from the genome sequence—if you're lucky enough to be working with an organism whose genome has been completely sequenced.

Unfortunately, there are many proteins with similar molecular weights so this straightforward technique doesn't work. However, if you digest the protein with enzymes that cut it several times at specific sites, you create group of peptide fragments. The molecular weights of the peptides can be determined by mass spec and the "fingerprint" of your unknown protein can be compared to calculated fingerprints of every protein in the proteome.

Here's an example of a tryptic digest of an unknown human protein of M_r = 90,000. The sizes of the various fragments can be measured accurately and compared to the predicted fragment sizes based on the known DNA sequence of the gene. If you're lucky, there is only one protein that will give rise to the observed peptides. Thus, the unknown protein can be unambiguously identified from the mass of its peptides.

In this case, the protein is Hsp90. As you might have guessed, the success of this techniques owes almost as much to the development of efficient software and databases as it does to the advances in mass spectroscopy.

The technique is powerful but the equipment is expensive and requires well-trained technicians.

There are many different kinds of mass specs and every lab will have its own customized setup. The one shown here belongs to Joseph Loo of Chemistry & Biochemistry, UCLA (Los Angeles, CA, USA). I "borrowed" it from his website [Joseph Loo].

Modern research facilities will have access to special labs where protein fingerprinting is routinely performed. In some cases, a major facility will serve as a regional center for analyses and charge a fee ($50-150) for each sample.

The image of the tryptic peptides of Hsp90, above, are from the website of such a facility in the Department of Biochemistry at the University of Buffalo (Buffalo, NY, USA) [Proteomic Capabilities]. Now that you know how the technique works, the description on their website will look much less intimidating.

The MALDI-TOF facility housed in the Department of Biochemistry provides access to mass spectrometric fingerprinting of unknown proteins. MALDI-TOF (Matrix-assisted, Laser-Desorption-Ionization/Time of flight) mass spectrometry is presently the method of choice for identification of unknown proteins via mass analysis of proteolytic peptides, and for characterization of post-translational modifications. This technique is rapid, highly sensitive, and applicable to a wide variety of research problems. Applications include direct characterization of mutated proteins, estimating the extent of protein derivatization (e.g., biotinylation), and identification of unknown proteins isolated from polyacrylamide gels. Depending on the specific application and complexity of the system, reliable data can be obtained in the fmol-pmol range.

In practice, the identification of a protein from its predicted fingerprint doesn't always work. The determined molecular weights aren't precise enough to unambiguously identify the protein and some peptides don't "fly." In addition, post-translational modifications of the protein will interfere with the molecular weights calculated from the gene sequence.

In most cases when you send out your sample you get back a list of possibilities that has to be narrowed down by other means (e.g., another protease digest).

This limitation has led to the development of coupled mass specs where the peptides from one are fragmented and fed into another. What this gives you is the sequence of each peptide by a technique called MS/MS. With sequence information you can search all the databases for sequence similarity and identify proteins even if the gene for that particular species hasn't been cloned and sequenced.

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Biochemistry and Mass Spectrometry

 
The following description is from Horton et al.,Principles of Biochemistry 4/e. It explains the use of mass spectrometry in a biochemical context.

Mass spectrometry, as the name implies, is a technique that determines the mass of a molecule. The most basic type of mass spectrometer measures the time that it takes for a charged gas phase molecule to travel from the point of injection to a sensitive detector. This time depends on the charge of a molecule and its mass and the result is reported as the mass/charge ratio. The technique has been used in chemistry for almost one hundred years but its application to proteins was limited because, until recently, it was not possible to disperse charged protein molecules into a gaseous stream of particles.

This problem was solved in the late 1980s with the development of two new types of mass spectromety. In electrospray mass spectrometry the protein solution is pumped through a metal needle at high voltage to create tiny droplets. The liquid rapidly evaporates in a vacuum and the charged proteins are focused on a detector by a magnetic field. The second new technique is called matrix-assisted desorption ionization (MALDI). In this method the protein is mixed with a chemical matrix and the mixture is precipitated on a metal substrate. The matrix is a small organic molecule that absorbs light at a particular wavelength. A laser pulse at the absorption wavelength imparts energy to the protein molecules via the matrix. The proteins are instantly released from the substrate (desorbed) and directed to the detector (see Figure). When time-of-flight (TOF) is measured, the technique is called MALDI–TOF.

The raw data from a mass spectrometry experiment can be quite simple, as shown in the Figure (right). There, a single species with one positive charge is detected so the mass/charge ratio gives the mass directly. In other cases, the spectra can be more complicated, especially in electrospray mass spectrometry. Often there are several different charged species and the correct mass has to be calculated by analyzing a collection of molecules with charges of +1, +2, +3 etc. The spectrum can be daunting when the source is a mixture of different proteins. Fortunately, there are sophisticated computer programs that can analyze the data and calculate the correct masses. The current popularity of mass spectrometry owes as much to the development of this software as it does to the new hardware and new methods of sample preparation.

Mass spectrometry is very sensitive and highly accurate. Often the mass of a protein can be obtained from picomole quantities that are isolated from an SDS–PAGE gel. The correct mass can be determined with an accuracy of less than the mass of a single proton.

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©Laurence A. Moran and Pearson/Prentice Hall

Monday's Molecule #106: Winners

 
UPDATE: The machine is a mass spectrometer and the technique illustrated is matrix-assisted desorption ionization (MALDI) coupled to time-of-flight (TOF) measurement (MADLI-TOF).

The first person to get it right was David Schuller of Cornell University. The first undergraduate from the Toronto area was Nova Syed of the University of Toronto.

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This is the second week in a row that Monday's molecule has been on a Tuesday. Sorry for the delay. I promise to get back on schedule next week.

The observant among you might have noticed that this "Monday's" molecule is not a molecule. It's my version of a machine. You have to identify what kind of a machine this is and what it does.

There are two Nobel Laureates who get credit for developing the technique shown here. One of them is responsible for the specific technique and the other for a similar variant. Name the two Nobel Lauretes.

The first person to identify the machine/technique and the Nobel Laureates wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are six ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Maria Altshuler of the university of Toronto, Ramon, address unknown, Jason Oakley of the University of Toronto, John Bothwell from the Marine Biological Association of the UK, in Plymouth (UK), and Wesley Butt of the University of Toronto

Bill and John have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

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Mendel's Garden #28

 
The 28th edition of Mendel's Garden has just been posted on Quintessence of Dust [Mendel’s Garden 28th Edition].

Hello and welcome to the 28th edition of the genetics blog carnival known as Mendel's Garden, where we celebrate blogging on topics related to anything touching on what Mendel discovered (or thought he discovered). While reading these interesting and informative pieces, please think about work that should be featured in a future edition and/or blogs (like yours) that would serve well as future hosts.

So do tomato seeds get you excited? No? Oh. Well, they should, if you're at all interested in evolutionary genetics.

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This is what we're up against.

 
PZ posted the first video on Pharyngula. I think it's important to watch both of them to see what goes on in church basements. How can we deal with this level of ignorance about science? It's especially frustrating because these young women are obviously intelligent enough that they should know better.

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Monday's Molecule #106

 
This is the second week in a row that Monday's molecule has been on a Tuesday. Sorry for the delay. I promise to get back on schedule next week.

The observant among you might have noticed that this "Monday's" molecule is not a molecule. It's my version of a machine. You have to identify what kind of a machine this is and what it does.

There are two Nobel Laureates who get credit for developing the technique shown here. One of them is responsible for the specific technique and the other for a similar variant. Name the two Nobel Lauretes.

The first person to identify the machine/technique and the Nobel Laureates wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize.

There are six ineligible candidates for this week's reward: Bill Chaney of the University of Nebraska, Maria Altshuler of the university of Toronto, Ramon, address unknown, Jason Oakley of the University of Toronto, John Bothwell from the Marine Biological Association of the UK, in Plymouth (UK), and Wesley Butt of the University of Toronto

Bill and John have offered to donate their free lunch to a deserving undergraduate so the next two undergraduates to win and collect a free lunch can also invite a friend. Since undergraduates from the Toronto region are doing better in this contest, I'm going to continue to award an additional free lunch to the first undergraduate student who can accept a free lunch. Please indicate in your email message whether you are an undergraduate and whether you came make it for your free lunch (with a friend).

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours.

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What Timothy Sandefur says ....

 
I very much admire Jerry Coyne's article on science vs religion in The New Republic [see: Jerry Coyne on Science vs. Religion]. There's been some discussion on The Edge where participants are asked to address the question Does the empirical nature of science contradict the revelatory nature of faith?.

Timothy Sandefur discusses Coyne's article and the various commnents on his blog Freespace [The future of science teetering on the Edge]. He does such a good job that you should all hop over there as soon as possible and read what he has to say.

Timothy points out that the debate is really about ways of knowing. Can we obtain valid information using the scientific way of knowing? Yes we can. This is rationalism, in my terminology.

Can we obtain valid information using faith as a way of knowing? No we can't. This is superstition and it is the opposite of rationalism.

Is it possible to simultaneously practice both ways of knowing? Here's part of the response by Timothy Sandefur.

Keep the issue in mind: the question is not whether it is possible for someone simultaneously to hold unproven, baseless beliefs about a supernatural dimension and scientific, reasoned conclusions with regard to observed phenomena. It is possible for all sorts of people to believe all sorts of things—just as Humpty Dumpty practiced every day believing six impossible things before breakfast. But it is not possible to do these things and still have intellectual integrity. It requires instead intellectual dis-integration: the skill (if it can be called a skill) of not thinking about the possible connections between the phenomena of the universe. That is, it requires precisely the opposite effort that science requires. It requires one not to think. Alas, as Coyne observes, this effort is officially endorsed by many organizations motivated by political expediency:

It is in [scientists’] personal and professional interest to proclaim that science and religion are perfectly harmonious. After all, we want our grants funded by the government, and our schoolchildren exposed to real science instead of creationism. Liberal religious people have been important allies in our struggle against creationism, and it is not pleasant to alienate them by declaring how we feel. This is why, as a tactical matter, groups such as the National Academy of Sciences claim that religion and science do not conflict. But their main evidence—the existence of religious scientists—is wearing thin as scientists grow ever more vociferous about their lack of faith.

But it’s not just that there aren’t as many religious scientists as some claim. It’s the fact that these two ways of knowing are and always have been, incompatible by their nature, and that those who pledge allegiance to both are either dishonest or simply wrong.

It's nice to see a lawyer making sense.

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Gene Genie #43

 
The 43rd edition of Gene Genie has been posted at Pharmamotion: pharmacology animations and resources [Gene Genie #43: Personal genomics, health and evolution].

Once again, PharmaMotion is hosting a blog carnival. This time is the turn of Gene Genie, a carnival dedicated to cover the buzz around the web about genetics (with some orientation to personalized genetics). I hope that PharmaMotion readers find it interesting.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....

1. Scienceroll
2. Sciencesque
3. Genetics and Health
4. Sandwalk
5. Neurophilosophy
6. Scienceroll
7. Gene Sherpa
8. Eye on DNA
9. DNA Direct Talk
10. Genomicron
11. Med Journal Watch
12. My Biotech Life
13. The Genetic Genealogist
14. MicrobiologyBytes
15. Cancer Genetics
16. Neurophilosophy
17. The Gene Sherpa
18. Eye on DNA
19. Scienceroll
20. Bitesize Bio
21. BabyLab
22. Sandwalk
23. Scienceroll
24. biomarker-driven mental health 2.0
25. The Gene Sherpa
26. Sciencebase
27. DNA Direct Talk
28. Greg Laden’s Blog
29. My Biotech Life
30. Gene Expression
31. Adaptive Complexity
32. Highlight Health
33. Neurophilosophy
34. ScienceRoll
35. Microbiology Bytes
36. Human Genetic Disordrs
37. The Genetic Genealogist
38. ScienceRoll
39. Genetics & Health
40. Human Genetics Disorders
41. ScienceRoll
42. Genetic Future
43. Pharmamotion

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Should senior scientists be bloggers?

 
Eva asks the questions on her Nature Network blog [Bloggers]. I was going to leave a comment there but I can never remember my login name and password.

I hate sites like that.

The answer seems pretty obvious to me. Some small percentage of senior scientists will enjoy blogging but most won't. It's not a big deal. There's no reason to encourage more senior scientists to blog. They'll do it naturally if they feel the need.

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The University of Vermont Does the Right Thing

 
My impression of the University of Vermont has just gone way up. According to WCAX News in Vermont, the University has decided that Ben Stein is not an appropriate commencement speaker [Stein Withdraws as UVM Speaker].

Burlington, Vermont - February 2, 2009

Ben Stein won't be bidding UVM graduates goodbye after all.

Just last week, the university announced that Stein, who is highly acclaimed as an actor, author, and economist, would be delivering this year's commencement address. But Monday, the school announced that he has now withdrawn as speaker.

Stein has made headlines recently for his views regarding Darwin's theory of evolution, intelligent design and the role of science in the Holocaust. Several people from the academic community-- both locally and beyond the UVM campus-- quickly expressed concern over his selection and once notified of that, Stein withdrew from the ceremony.

"This is not, to my mind, an issue about academic freedom or the openness of the campus to all points of view. Ben Stein spoke here last spring to great acclaim," UVM President Dan Fogel said. "It's an issue about the appropriateness of awarding an honorary degree to someone whose views in many ways ignore or affront the fundamental values of scientific inquiry and I greatly regret that I was not attuned to those issues."

Fogel said the school's honorary degree committee has a list of potential candidates and he will consult others before extending an invitation to another potential commencement speaker.

Good for President Fogel. He's right. It is not appropriate to award an honorary degree to "someone whose views in many ways ignore or affront the fundamental values of scientific inquiry."

I wonder if Dan Fogel realizes that he has just earned himself a prominent place in "Expelled II"?

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A Message from Genome Canada

 
Genome Canada did not get the funding it requested in the latest budget. In fact, it got nothing at all. Here's a message from the Board of Directors of Genome Canada [Federal Budget 2009].

• Genome Canada is pleased with the federal government’s 2009 budget in which millions will be invested in research infrastructure over the next two years. This is good news for the scientific community across the country that needs to be at the cutting-edge of research infrastructure and new technologies in order to maintain Canada’s competitiveness at the national and international level.
• Although Genome Canada did not receive funding in the 2009 federal budget to fund new genomics research projects, this will not impact Genome Canada’s current projects that received a full commitment of funding from previous federal government investments in 2007 and 2008.
• Genome Canada has in place two five-year funding agreements with the Government of Canada for a total of $240M: $100 M (2008-2012) $140 M (2009- 2013)
• These investments flow to Genome Canada on a cash requirement basis. Thus, a total of $107M has been invested in 2008-09; and a total of $106.5M will be invested in 2009-10, creating and maintaining over 2,350 HQP positions per year.
• Over the same period of time, Genome Canada has raised over $225M from other strategic partners in the private, public and philanthropic sectors to support genomics research in Canada.
• Since its inception in 2000, Genome Canada has provided operating funds to Canadian genomics researchers, while complementing other sources of funds for infrastructure coming from such agencies as Canada Foundation for Innovation, to allow them to be among world leaders in their respective fields such as human health, agriculture, environment, forestry, fisheries, new technology, and GE3LS (ethical, environmental, economic, legal and social issues).
• Genome Canada is confident that the Government of Canada and its other financial strategic partners will do everything possible over the coming years to secure additional funding to support new initiatives in genomics research in Canada while increasing Canada’s productivity, wealth and well-being of all Canadians.

What a bunch of wimps. Here's the list of the Board of Directors.

It's one thing to praise the government for not giving you the money you requested but it's quite another to heap praise on a government that is cutting funding to the major granting councils. Yes, it's true that the budget contains money for infrastructure support but that money will be useless without operating grants. Operating grants are the bread and butter of scientific research. They are what pays for the day-to-day expenses of operating a research lab. It doesn't matter how nice your building is if you can't buy enzymes and chemicals. Modern science is expensive.

Operating grants also pay the salaries of research assistants, graduate students, summer students, and post-docs.

Myopic governments don't like to fund operating grants because that's a long-term commitment. One-time-only (OTO) money is much better 'cause you can get a big bang for your buck (publicity and votes) and you don't have to make any promises.

Genome Canada's directors should know this. They should not be sending out a press release that looks like they are backing the government decision to destroy basic research. Unless, of course, they agree with that strategy.

This brings up another point about Genome Canada. Many scientists, including me, don't think that the Genome Canada model is the way to fund research. In that sense, I'm not all that upset that it wasn't funded. If you want to learn more about the problems of co-funding and market-drive science then read the latest posting from Chris Hogue [Market Driven Science in Crisis?]. He knows what he's talking about.

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Hat Tip: iBiome: Genome Canada cut good for science?, And now, the walkback