Would you act as a consultant on a scifi movie?

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Last week in my first year seminar course “Controversial issues in the life sciences” we watched Jurassic Park and discussed a series of questions about the science included, the portrayal of scientists, and various other issues. This was interesting, because most of the people in the course are not biology majors but had done a good job learning about cloning, genetic engineering, and other topics during the semester. (This was also a nice break from giving weekly presentations, I am sure).

Anyway, as part of the discussion we also read several papers about science in movies. One of them by Kirby (2003) is about scientists as consultants for Hollywood productions. As I was reading it, I thought to myself, “I would probably do it, but not for personal payment — if they funded my research that would be ok”. Then, on the following page, I read:

Based on the available evidence, science consultants are far more likely to accept research funds, or no compensation at all, rather than actual payment for their services. One of the reasons for this situation is the unwillingness of scientists to take money for what they consider a “public service.” Many of the consultants I researched felt it was their “duty” as a scientist to impart knowledge to an uneducated public, including filmmakers, and that it would have been “unethical” for them to take money for this activity. For example, two of the consultants for the 1922 gland-based horror film A Blind Bargain(1922) felt that it would be “disreputable” for “medical researchers” to accept payment for their services, and they even requested that their names not be included in publicity material (see Riley, 1988).Likewise, Donald Francis of Genentech, Inc., who is most famous for his work on an AIDS vaccine, refused financial payment for his work as technical adviser for the film Outbreak(1995), accepting as compensation “only that his 17-year-old son, Oli, be allowed to observe the filming” (see Ganahl, 1995: 1E). Francis’ example underscores the conflict that science consultants face. On the one hand, they believe that as scientists they should give scientific advice freely to anyone who seeks knowledge. On the other hand, they are providing a specialized service for filmmakers and believe they should receive compensation of some type. To resolve this tension, consultants have come up with other forms of compensation that do not involve direct financial payment. In this regard, consultants who accept research funds rather than salary or consultation fees perceive that this action does not compromise their “ethics,” because the money will not go into their pockets but will go toward the production of “new knowledge.”

Science is an intriguing culture, no question.

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Kirby, DA (2003). Science on the set: science consultants and the communication of science in visual fiction. Public Understanding of Science 12: 261-278.

"Everlasting antibiotics", wanna bet?

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From Albert Einstein College of Medicine in New York (and several news services):

Einstein Researchers Develop Novel Antibiotics That Don’t Trigger Resistance

Most antibiotics initially work extremely well, killing more than 99.9% of microbes they target. But through mutation and the selection pressure exerted by the antibiotic, a few bacterial cells inevitably manage to survive, repopulate the bacterial community, and flourish as antibiotic-resistant strains.

Vern L. Schramm, Ph.D., professor and Ruth Merns Chair of Biochemistry at Einstein and senior author of the paper, hypothesized that antibiotics that could reduce the infective functions of bacteria, but not kill them, would minimize the risk that resistance would later develop.

Dr. Schramm’s collaborators at Industrial Research Ltd. earlier reported transition state analogues of an enzyme that interferes with “quorum sensing” — the process by which bacteria communicate with each other by producing and detecting signaling molecules known as autoinducers. These autoinducers coordinate bacterial gene expression and regulate processes — including virulence — that benefit the microbial community. Previous studies had shown that bacterial strains defective in quorum sensing cause less-serious infections.

Rather than killing Vibrio cholerae and E. coli 0157:H7, the researchers aimed to disrupt their ability to communicate via quorum sensing. Their target: A bacterial enzyme, MTAN, that is directly involved in synthesizing the autoinducers crucial to quorum sensing. Their plan: Design a substrate to which MTAN would bind much more tightly than to its natural substrate — so tightly, in fact, that the substrate analog permanently “locks up” MTAN and inhibits it from fueling quorum sensing.

To design such a compound, the Schramm lab first formed a picture of an enzyme’s transition state — the brief (one-tenth of one-trillionth of a second) period in which a substrate is converted to a different chemical at an enzyme’s catalytic site. (Dr. Schramm has pioneered efforts to synthesize transition state analogs that lock up enzymes of interest. One of these compounds, Forodesine, blocks an enzyme that triggers T-cell malignancies and is currently in a phase IIb pivitol clinical study treating cutaneous T-cell leukemia.)

In the Nature Chemical Biology study, Dr. Schramm and his colleagues tested three transition state analogs against the quorum sensing pathway. All three compounds were highly potent in disrupting quorum sensing in both V. cholerae and E. coli 0157:H7. To see whether the microbes would develop resistance, the researchers tested the analogs on 26 successive generations of both bacterial species. The 26th generations were as sensitive to the antibiotics as the first.

“In our lab, we call these agents everlasting antibiotics,” said Dr. Schramm. He notes that many other aggressive bacterial pathogens — S. pneumoniae, N. meningitides, Klebsiella pneumoniae, and Staphylococcus aureus — express MTAN and therefore would probably also be susceptible to these inhibitors.

Ok, here we go. How big was the population size tested? How much is 26 generations in bacterial timescales? Let’s think about this. One person taking antibiotics would have billions of bacteria in his/her gut. A week on antibiotics is about 350 generations if you consider 30 minutes per.

How about the possibility of a new mutation or lateral transfer from some other species? Yes, selection may result in resistance easily in bacteria if some individuals already carry a resistance gene, but I would never bet against some mutation occurring down the line and leading to a reproductive advantage — they don’t have to survive while all others are killed for selection to occur and therefore for the new resistant trait to increase rapidly in proportion. Natural selection is about relative reproduction, not necessarily survival alone.

Jon Stewart is awesome.

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This is not supposed to be a political blog, but the current economy is hurting scientific funding and so I feel justified in posting links to Jon Stewart’s absolute thrashing of the sort of people who contributed to the current economic mess by giving nonsensical financial advice.

(If it won’t play, go here).

To watch this in Canada, go here.

By the way, if you think Stewart only came off so well because he was on his own turf, see him on Crossfire:

Recent lab papers.

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So, what have we been up to in the lab?

Ardila-Garcia, A.M. and T.R. Gregory (2009). An exploration of genome size diversity in dragonflies and damselflies (Insecta: Odonata). Journal of Zoology, in press.

Smith, J.D.L. and T.R. Gregory (2009). The genome sizes of megabats (Chiroptera: Pteropodidae) are remarkably constrained. Biology Letters, in press.

Smith, E.M. and T.R. Gregory (2009). Patterns of genome size diversity in the ray-finned fishes. Hydrobiologia 625: 1-25.

Andrews, C.B. and T.R. Gregory (2009). Genome size is inversely correlated with relative brain size in parrots and cockatoos. Genome 52: 261-267.

Andrews, C.B., S.A. Mackenzie, and T.R. Gregory (2009). Genome size and wing parameters in passerine birds. Proceedings of the Royal Society of London B 276: 55-61.

Currently finishing up:

Ants/bees/wasps, butterflies, moths, hummingbirds, more bats, more birds

Canadian scientists are cry babies?

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Here is an excerpt from an editorial in the Toronto Star today:

There is a fundamental disconnection between the nation’s scientists and political leaders over what Ottawa is doing for research.

The scientists complain that the federal government has slashed funding for research and, as a result, Canada runs the risk of a “brain drain” to the United States, where the new Obama administration is pouring money into the field. The government, on the other hand, says it has increased research funding by billions of dollars and the complaining scientists are cry babies. They are both right.

So, even though the editorial then goes on to (correctly) explain the scientists’ position that injecting money for infrastructure (mostly at the request of universities, which is not the same as what scientists may have asked for) while simultaneously cutting basic grants, providing no new support for major agencies such as Genome Canada, and directing money increasingly toward government-preferred applied projects will likely harm Canada’s research abilities, the editor thinks we’re cry babies.

This must be just a poor choice of wording, given the actual conclusion:

There are reports that Goodyear is quietly assuring people in the field that this cut will be restored in future budgets. If so, there seems no reason why that couldn’t be done now. The amount in question is minuscule when compared to the $76.5 billion cumulative deficit projected over next three fiscal years (less than two-tenths of 1 per cent). And the danger of losing scientists and projects to the U.S. is real if the government waits until later.

OpenGoo.

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I am currently experimenting with an open source lab management program called OpenGoo. It allows users to set tasks and major milestones, to upload files, to set due dates, and to monitor progress on any number of individual projects. Aside from some minor hiccups with getting people in the lab to actually use it, I think it looks very useful. The success of software like this depends on the growth of a strong user community, so if you have a group of people in your lab and need a way to keep everyone organized and on target, I suggest you try it sometime.

OpenGoo

(About – Demo – Manual)

Posted in Lab

Obama lifts stem cell restriction.

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Finally.

“Today, with the executive order I am about to sign, we will bring the change that so many scientists and researchers, doctors, and innovators, patients and loved ones have hoped for, fought for these past eight years.”

“We will lift the ban on federal funding for … embryonic stem cell research.”

Lamarck didn’t say it, Darwin did.

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We have heard quite a lot in recent times about a resurgence of “Lamarckian” mechanisms, based largely on findings involving epigenetics. In this case, environmental differences cause changes in the patterns of expression of genes, and these alterations can sometimes be passed on through at least a few generations.

There are two reasons why it is inaccurate to consider this kind of change in heritable characteristics induced by the environment as “Lamarckian inheritance”.

One, Lamarck did not think that the environment imposed direct effects on organisms that were then passed on. He argued that the environment created needs to which organisms responded by using some features more and others less, that this resulted in those features being accentuated or attenuated, and that this difference was then inherited by offspring. As he wrote,

It is now necessary to explain what I mean by this statement: The environment affects the shape and organization of animals, that is to say that when the environment becomes very different, it produces in the course of time corresponding modifications in the shape and organization of animals. It is true, if this statement were to be taken literally, I should be convicted of an error; for, whatever the environment may do, it does not work any direct modification whatever in the shape and organization of animals. [Translated as in Kampourakis and Zogza (2007)]

What people insist on dubbing “Lamarckian inheritance” in the context of epigenetics is actually closer to the view held by Darwin than by Lamarck. In the second part of his 1858 joint paper with Wallace (excerpted from an 1857 letter to Asa Gray), Darwin wrote,

Selection acts only by the accumulation of slight or greater variations, caused by external conditions, or by the mere fact that in generation the child is not absolutely similar to its parent.

…

Now take the case of a country undergoing some change. This will tend to cause some of its inhabitants to vary slightly—not but that I believe most beings vary at all times enough for selection to act on them. Some of its inhabitants will be exterminated; and the remainder will be exposed to the mutual action of a different set of inhabitants, which I believe to be far more important to the life of each being than mere climate.

We can read similar things in the Origin:

I have hitherto sometimes spoken as if the variations—so common and multiform in organic beings under domestication, and in a lesser degree in those in a state of nature—had been due to chance. This, of course, is a wholly incorrect expression, but it serves to acknowledge plainly our ignorance of the cause of each particular variation. Some authors believe it to be as much the function of the reproductive system to produce individual differences, or very slight deviations of structure, as to make the child like its parents. But the much greater variability, as well as the greater frequency of monstrosities, under domestication or cultivation, than under nature, leads me to believe that deviations of structure are in some way due to the nature of the conditions of life, to which the parents and their more remote ancestors have been exposed during several generations. I have remarked in the first chapter—but a long catalogue of facts which cannot be here given would be necessary to show the truth of the remark—that the reproductive system is eminently susceptible to changes in the conditions of life; and to this system being functionally disturbed in the parents, I chiefly attribute the varying or plastic condition of the offspring. The male and female sexual elements seem to be affected before that union takes place which is to form a new being. In the case of “sporting” plants, the bud, which in its earliest condition does not apparently differ essentially from an ovule, is alone affected. But why, because the reproductive system is disturbed, this or that part should vary more or less, we are profoundly ignorant. Nevertheless, we can here and there dimly catch a faint ray of light, and we may feel sure that there must be some cause for each deviation of structure, however slight.

Two, the idea of inheritance of acquired characteristics predates Lamarck, was the dominant view in his time, and remained common long afterward. As Morse (1903) wrote,

Jean Lamarck first used the term “acquired character” to designate characters such as these and to him are are we to look for the first clear statement of the case. By this it is not to be understood that the idea of the transmission of acquired characters arose with Lamarck. No great generalization ever arose or ever can arise with one man alone. The attribution of the idea of the transmission of acquired characters to Lamarck falls in the same category as attributing evolution to Darwin.

Zirkle (1946) was more forceful yet,

What Lamarck really did was to accept the hypothesis that acquired characters were heritable, a notion which had been held almost universally for well over two thousand years and which his contemporaries accepted as a matter of course, and to assume that the results of such inheritance were cumulative from generation to generation, thus producing, in time, new species. His individual contribution to biological theory consisted in his application to the problem of the origin of species of the view that acquired characters were inherited and in showing that evolution could be inferred logically from the accepted biological hypotheses. He would doubtless have been greatly astonished to learn that a belief in the inheritance of acquired characters is now labeled “Lamarckian,” although he would almost certainly have felt flattered if evolution itself had been so designated.

Darwin, like Lamarck, invoked use and disuse and inheritance of acquired changes1; the Origin includes an entire section on it, the first part of which reads,

Effects of Use and Disuse.—From the facts alluded to in the first chapter, I think there can be little doubt that use in our domestic animals strengthens and enlarges certain parts, and disuse diminishes them; and that such modifications are inherited. Under free nature, we can have no standard of comparison, by which to judge of the effects of long-continued use or disuse, for we know not the parent-forms; but many animals have structures which can be explained by the effects of disuse. As Professor Owen has remarked, there is no greater anomaly in nature than a bird that cannot fly; yet there are several in this state. The logger-headed duck of South America can only flap along the surface of the water, and has its wings in nearly the same condition as the domestic Aylesbury duck. As the larger ground-feeding birds seldom take flight except to escape danger, I believe that the nearly wingless condition of several birds, which now inhabit or have lately inhabited several oceanic islands, tenanted by no beast of prey, has been caused by disuse. The ostrich indeed inhabits continents and is exposed to danger from which it cannot escape by flight, but by kicking it can defend itself from enemies, as well as any of the smaller quadrupeds. We may imagine that the early progenitor of the ostrich had habits like those of a bustard, and that as natural selection increased in successive generations the size and weight of its body, its legs were used more, and its wings less, until they became incapable of flight.

As was argued by Parkyn (1911),

It is difficult to understand how anyone well acquainted with Darwin’s works can come to any other conclusion than that he firmly believed in Lamarck’s principle of the transmission of characters acquired by use.

Designating epigenetics as Lamarckian greatly misconstrues what Lamarck actually argued. The parts of Lamarckian theory to which it does refer were likewise part of early Darwinian theory. In short, there is no vindication of Lamarck’s mechanism to be granted by epigenetics. That said, there is no doubt that Lamarck’s contributions to evolutionary thinking should be better appreciated. Certainly, the first step toward this would be an effort to understand what he actually proposed.

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Updated notes:
1) See the comments discussion. Wilkins has pointed out that Darwin was not simply a “Lamarckian” in terms of new traits arising through need+use/disuse (rather, he suggested that the strength of inheritability of traits is affected by use). However, Darwin did invoke disuse as a reason that traits could be lost which is enough to show that he did not throw out use and disuse as a mechanism of trait change.

Excellent comment on teaching science.

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From a comment by Linda Lin on my Nature Network blog:

Nevertheless, there is a habit of teaching the way we ourselves were taught, even if this is not the most efficient approach.

I went to a workshop for TAs and instructors addressing the issue of sort of flying blind in teaching. They emphasized on the importance of training and reading up on teaching every so often. One researcher said, well, we’ve been taught science for 20 years, surely we’d know how teach it without needing any training. His head of dept retorted that “I’ve had sex for 20 years, that doesn’t make me a qualified gynaecologist”.