I've recently been working to unearth the scientific genealogy of Carlos Bustamante's lab. With the aid of some labmates, we have made quite a bit of progress! We have the lineage to the 17th century, and it goes thusly:

Carlos José Bustamante

• 1951-present
  
• Ph.D. in Biophysics, University of California, Berkeley, 1981
  

• 1930-present
  
• Ph.D. University Wisconsin, 1954
  

• 1912-2003
  
• Ph.D., Stanford University, 1935
  

• 1894-1966
  
• Ph.D., University of California, Berkeley, 1919
  

• 1884-1959
  
• Ph.D., Universität Breslau, 1911
  
• [California Digital Library]
  

• 1860-1925
  
• Ph.D., Universität Berlin, 1884
  
• Dissertation: Über eine neue Interferenz-Erscheinung an planparallelen Glasplatten und eine Methode die Planparallelität solcher Gläser zu prüfen
  

• 1821-1894
  
• M.D., Königlich Medizinisch-chirurgische Friedrich-Wilhelm Institut, Berlin, 1842
  
• [Max Planck Institute for the History of Science]
  

• 1801-1858
  
• M.D., University of Bonn, 1822
  
• [Max Planck Institute for the History of Science]
  

• 1771-1832
  
• M.D., Ernst-Moritz-Arndt-Universität Greifswald, 1795
  
• [MGP]
  

• 1748-1831
  
• Georg-August-Universität Göttingen, 1771
  
• [MGP]
  

• 1744-1777
  
• Georg-August-Universität Göttingen, 1767
  
• [MGP]
  

• 1719-1800
  
• Ph.D., Universität Leipzig, 1739
  
• Dissertation: Theoria radicum in aequationibus
  
• [MGP]
  

• 1693-1743
  
• Ph.D., Martin-Luther-Universität Halle-Wittenberg, 1713
  
• Dissertation: De corpore scissuris figurisque non cruetando ductu
  
• [MGP]
  

• 1663-1727
  
• Ph.D., Universität Leipzig, 1685
  
• Dissertation: Disputationem Moralem De Divortiis Secundum Jus Naturae
  
• [MGP]
  

• 1644-1707
  
• Ph.D., Universität Leipzig, 1665
  
• Dissertation: Ex Theologia naturali — De Absoluta Dei Simplicitate, Micropolitiam, id est Rempublicam In Microcosmo Conspicuam
  
• [MGP]
  

Filed under biology · chemistry · physics · science · science history

Posted by H. C. Hodges at 11:19 AM | Permalink | Comments (1)

Getting the cover of a journal like Nature is a little bit like winning the scientific lottery. So we're very proud:

Congratulations all around, especially to Jin-Der, who has done a fantastic job of making this project work. Although we were the first to observe ribosome activity in real-time, there is so much yet to come!

Filed under berkeley · biology · chemistry · physics · science

Posted by H. C. Hodges at 10:23 AM | Permalink | Comments (2)

This article at the NY Times is quite disappointing. The author makes several unwarranted leaps, for example, comparing the cost of vaccinations in 1980 to today...

Getting a vaccination was not always so difficult. In 1980, it cost only about $23, or $59 adjusted for inflation, for the seven shots and four oral doses needed to immunize a child, according to data provided by Thomas Saari, who is emeritus professor of pediatrics at the University of Wisconsin.

Today, though, a child who receives all the recommended vaccines would receive as many as 37 shots and 3 oral doses by the 18th birthday — at a cost exceeding $1,600.

The 1980's were well before the biotech industry really existed (hell, recombinant techniques didn't even exist until nearly the mid-70's!); one would fully expect that vaccines developed before modern molecular biology would be technologically simpler and cost less to develop and produce. Plus we're not comparing the same thing... the above compares required vaccines in 1980 with all recommended vaccines today; when you include the newer, clearly useful, vaccines, you fully expect the price to increase. So the comparison is rather disingenuous.

Note that the argument isn't about whether or not the new vaccines should be mandatory; the Times article is mostly complaining about the cost of all recommended vaccines.

There is amongst some an expectation that any biological technology that can help people should be given away for nearly free. This attitude doesn't seem to appear in other sciences (who would expect carbon nanorods, or synthetic zeolite catalysts to be immediately affordable?). Why is biology so different?

If the fear-mongering segment of the public succeeds in taking the market out of the biological technology industry, there won't be one. Let's not get so breathless when drug prices are high, because it's worth remembering therapeutics will be cheap and abundant when their patents runs out.

It's instructive to remember that Rogaine, Claritin, Aleve, and even Tylenol were all once on-patent drugs...

Filed under chemistry · patents · science

Posted by H. C. Hodges at 4:16 PM | Permalink | Comments (0)

As you may recall from my previous post, a company called Ariad is suing Lilly & Co. over alleged infringement of a patent related to NF-κB activity. NF-κB is a protein which regulates inflammation and immune response in cells; as such, it is considered by many to be a great target for new drugs.

In my previous post, I expressed skepticism that the so-called 'Baltimore patent' will be upheld. I have since bothered slugging through some of the patent code (U.S.C. 35), and have refined my thoughts a little more.

One of the strongest arguments I can think of against Ariad is that the Baltimore patent had simply not reduced the claimed invention to practice. According to 35 U.S.C. § 112:

The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.

As an example, consider two fairly representative claims from the Baltimore patent:

1. A method of inhibiting expression, in a eukaryotic cell, of a gene whose transcription is regulated by NF-κB, the method comprising reducing NF-κB activity in the cell such that the expression of said gene is inhibited.

6. A method for diminishing induced NF-κB-mediated intracellular signaling comprising reducing NF-κB activity in cells such that NF-κB-mediated intracellular signaling is diminished.

Obviously creating a particular drug requires vastly more resources than claiming what amounts to a big-picture idea for a research project. The court will have to decide whether or not the Baltimore patent ever actually reduced to practice their claimed invention. It is a fundamental requirement that a patent describe an invention well enough for a person having ordinary skill in the art (of biochemistry, in this case) to be able to create and use the invention. This is what The People receive in exchange for granting an exclusive license to the inventor.

Furthermore, according to 35 U.S.C. § 102(g), Lilly need only show that it conceived of the two drugs and worked "with reasonable diligence" to create them before the priority date of the Baltimore patent. Lilly also has to show that it didn't "abandon, suppress, or conceal" those two drugs. Since Lilly claims it disclosed the medical properties of Xigris and Evista before the Baltimore inventors conceived of their idea, it will be very difficult for Ariad to show that Lilly had concealed Evista or Xigris before the Baltimore patent's priority date.

The courts must consider "not only the respective dates of conception and reduction to practice of the invention, but also the reasonable diligence of one who was first to conceive and last to reduce to practice." Lilly, it seems to me, need only prove that they worked with reasonable diligence to reduce their two drugs to practice, while Ariad and the patent holders have to prove that they have sufficiently disclosed their invention such that any skilled worker could create and use it.

As a fairly skilled worker in the art of biochemistry, I wouldn't have any idea where to start to create and use some of the claimed inventions in the Baltimore patent. It is pretty clear to me that the Baltimore patent has not sufficiently disclosed their invention; as such I continue to expect that the appellate court will decide for Lilly & Co. and set aside the jury's previous verdict.

Filed under biology · chemistry · patents · science

Posted by H. C. Hodges at 10:31 PM | Permalink | Comments (0)

Last night, I read an old paper by Ernst Mayr on the position of biology amongst the sciences (Quarterly Review of Biology, 71(1): 97-106, 1996). In it, he posits that biology is rather radically different from other physical sciences; as a result, he says biology ought to be considered an autonomous branch of science, and not a provincial branch of physics or chemistry.

This, along with a more strident defense of biology (Science, 133: 1745-1748, 1961), surprised me more than a little bit. Since I do biophysics, I am not properly a biologist or a physicist, per se, but I do research that straddles the traditional boundaries of both fields. So I tend to look for good questions to be answered, and have not worried myself about whether my work is more "physics" or more "biology."

However, in his review, Mayr argues that there are questions dinstinctly biological in nature, and that these questions (along with some conceptual and methodological differences), make biology unique amongst the sciences. I thought I would paraphrase a few of the most interesting here:

Conceptual differences in biology

• The importance of historical narrative as an explanatory device.
• The prevalence of indeterminacy owing to the high frequency of stochastic processes, unknown factors, the presence of constraints, the interaction of multiple causes.
• The importance of quality (structure, form, function) in the properties and actions of objects, and a correlated reduction in the importance of purely quantitative differences.
• Presence of an historical constituent in the inherited program; hence legitimacy of "why" questions; capacity for the storage of historical information.

Methodological differences in biology

• The importance of observation in addition to experiment.
• The frequency of independent multiple solutions to the same problem.

Other autonomous aspects of biology

• All biological phenomena have two sets of causations, those controlled by the historically accumulated information of the genetic program (evolutionary or ultimate causations), and those controlled by the properties of the interacting system (proximate causations). The study of the historical components of each system is as legitimate a concern of biological science as the study of proximate causations.
• The outcome of biological processes is usually affected simultaneously by multiple causations, owing to the complexity of the systems interacting with complex biotic and physical environments
• Many properties of systems cannot be explained by a study of their isolated components.

It's interesting that many older biologists saw the successes of biochemistry and biophysics as a danger to the field of biology proper. Many early critics complained that such interdisciplinary research gave much to the other field, while returning relatively little to biology. In this light, the point about multiple causations (evolutionary and proximate) is still quite relevent, because the evolutionary causes are often unaddressed in many of the recent "hot" papers in biophysics.

Filed under biology · chemistry · physics · science

Posted by H. C. Hodges at 4:34 PM | Permalink | Comments (2)

Well, I read a rather surprising post from Derek Lowe today. Turns out, he thinks that most common buffer reagents are a bunch of hocus-pocus:

There's some reducing agent in there, naturally. Can't have those thiols turning into disulfides and balling up the protein, I understand - but does something bad happen if it's not in there? Generally, no one finds out, because, hey, why mess with it? And there's some EDTA, and some salt, and their function is? Well, as far as I can tell, they're also in there because they've sort of always been. Same goes for the squirt of detergent (Brij-35 or some such), and the tiny bit of bovine serum albumin, of all things. It's just part of the old-fashioned recipe from Grandma's Protein Kitchen.

Now, organic chemistry has a little of this, true, but it hasn't reached quite the Ancient Runestone levels of enzymology.

Lowe unexpectedly sounds like so many of the physicists I know that make snap judgments about how biology is done without the requisite background. As it turns out, many people do understand each reagent's use and shortcomings. We use many of those reagents for reasons that we understand pretty well:

1. Reducing agents protect methionines and cysteines from oxidation. If the protein is an intra-cellular protein, then this mimics the reducing environment of the cell. If there are structurally or functionally important cysteines on the protein, this prevents them from forming intra- or inter-molecular disulfide bridges. Generally, one doesn't want those, because they can lead to the protein becoming insoluble. You may also need them if you're going to do mass spectrometry, because you want to know the molecular weight of the monomers (not the disulfide-linked Nmers). Plus there are multiple types of reducing agents, and there are situations where you'd use one and not the other.
2. EDTA is in there because the researcher wants to prevent magnesium or other divalent cations from somehow affecting the molecule of interest. This "somehow" can include metalloprotease degradation or bacterial growth. Sometimes you have your own reasons for not wanting a protein to bind Mg²⁺ (like if an enzyme gains a certain reactivity upon binding). Also, magnesium is required by some nucleases, so the addition of EDTA can also prevent nucleases from degrading DNA or RNA, if those are present in solution.
3. Salt is just silly to question. Most proteins depend on salt for stability and solubility. Salt helps screen attractive and repulsive ionic interactions.
4. Depending on the protein, you may require the presence of detergents to make the molecule soluble. There are many different types of detergents, and you'd choose one (believe it or not) rationally, depending on the type of interaction you want with the protein. There are cationic, anionic, zwitterionic detergents, and polar (but uncharged) detergents too. These are especially important for hydrophobic proteins that would otherwise aggregate were detergent not present.
5. BSA may sound silly, but it's a stabilizing adjuvant. Not only does it tend to keep the test tube feeling like the cell by acting as a crowding agent, it also acts as a sink for protease degradation in the case that some contaminant makes it in the tube accidentally. In our lab, we use it regularly as a blocking agent to prevent nonspecific protein-protein interactions and protein-surface interactions. I imagine Lowe would be shocked to also find out that we use α-casein from milk for the same purpose. The reason we use these animal-derived proteins are because of their cost; they are also abundant, have no relevant enzymatic activity, and work well.

Thankfully, Lowe doesn't question the actual buffer itself, which is probably the most critical ingredient because it stabilizes pH. There are dozens of commonly used buffers, each one optimized for particular chemistries and with different pK_a values. For example, you might need a buffer without primary amines that buffers well at pH 8, in which case you may pick triethanolamine over the more common tris.

Each of these ingredients—even if one doesn't understand how it works—is often a required buffer component. These reagents are the moral equivalent of the glass flask in chemistry. Sure, I could deride Derek for using such stone-aged materials as "super-heated sand" for his Erlenmeyer flask, or "baked mud" for his Büchner funnel, but that would be silly and take a rather healthy amount of hubris. Instead, I recognize that these are the basic tools of chemists, and we move on.

In much the same way, these buffer reagents are some of the most basic tools in biology; they combine to provide a tightly controlled and consistent chemical microenvironment for proteins and other macromolecules.

Filed under biology · chemistry · science

Posted by H. C. Hodges at 8:05 AM | Permalink | Comments (0)