Tag Archives: science

Some interesting essays from around the web:

On the graying of photography. Not literal aging (well, somewhat), but more like a generational clash. But nothing we haven’t read about before about progress or changes in cultural viewpoints, especially vis-à-vis ebook vs paper book debates.

Success in science is dominated by finding statistically significant differences, and the need for positive results – coupled with the metric of publications – makes us all put on rose colored glasses. In this case, it might mean using weak statistics (original paper in PNAS) without regard as to whether it makes sense.


Over dinner at Bobby Flay’s Mesa Grill, I was recommending Gordon Shepherd’s book, Neurogastronomy, to a friend, who is a foodie. He seemed really interested in it, having read Herve This’s Molecular Gastronomy and other books like it. I’ll say here what I told my friend.

Shepherd brings with him both expertise and experience on the subject, having actually worked in olfaction for many years. The people he works with are my friends and peers, as I have also worked in olfaction until recently.  The way this book is presented is a model I wish to emulate; it is a  synthesis of both scientific findings and their meaning to us. By combining these elements with clear descriptions of the experiments involved, Shepherd is able to place the mechanics of smell within the context of odor and flavor perception. How the system works, how quality of life can be impaired, possible evolutionary consequences, and ultimately how we can subvert human flavor perception to improve our diet, nutrition, and yes, pleasure. 

Gordon Shepherd has made a huge impact in neurophysiology and in the field of olfaction. I think it is wonderful that he has written this book, to emphasize that olfaction is an important sense, playing a role in shaping human culture by its role in flavor perception. This is a direct counter to the notion that the human (and primate) olfactory system compares “poorly” against other sensory systems because the amount of brain space devoted to processing olfactory data seem so small. It also counters the perception from an olfactory detector consideration, such as that other mammals have both a greater number and variety of odor sensors, and thus as a result that they are better smellers than humans.

For me, I also had the vicarious thrill of seeing people I know depicted in a book meant for a wider audience.


From the standpoint of a neuroscientist, it was refreshing to see how a distinguished scientists view as the most important pieces of neurophysiological evidence fitting into the concept of flavor perception.  This is the bit of curation that I am such an enthusiast for. We have a wealth of data, and often, scientific reviews are a great place to being reading about a field. Reviews are as much about synthesis of existing scientific threads as much as about historical perspective and charting future research directions (i.e. what hasn’t been yet addressed).  With so much great writing today, having forty or fifty years of experience may not be necessary to provide proper context for a given research environment.

With that said, it is always nice to see someone with the stature of Gordon Shepherd present such a broad picture of the field and to hew closely to underlying research.

He spends the first chapters discussing some anthropology findings, laying the groundwork for the importance of flavor in shaping human culture. It seems that cooking – with its transformation of food at the molecular level and in the unlocking of huge stores of nutrition – provides a huge impetus in humans retaining a strong smell sense. The rest of the book recounts both his own and others’ contributions to the field of olfaction.

His presentation of neural activity is that brain works by encoding and extracting information that can be described as literal, physical patterned activity. Evidence from open brain surgery, to anatomical tracing, to functional imaging supports this idea. In each case,  patterns arise from ephemeral neural activity, grouped into physically discrete locations on the brain. Hence one hears about the visual and audio cortices, the somatosensory cortex, the hippocampus as a site of early memory formation, and so forth.

For the olfactory system, this is also true: at increasing levels of topologic precision, we can say that the main olfactory processing structures include the olfactory bulb, the olfactory cortex, and the orbitofrontal cortex. As we progress to more microscopic descriptions, we can describe groups of active neurons within these structures. The whole point of the brain’s wiring is to funnel external stimuli into combinations of activated neurons.

The connections between these neurons tend to lead to reactivation of the same groups of neurons to the same stimulus. Brain centers located downstream than operate on these patterns, recognizing them, storing them, retrieving them, and matching them. At some point, this stream of information is combined with other sensory inputs (aural, visual, taste, smell, and touch), resulting in higher order, conscious thoughts.

What I say next is not meant as a criticism but as a way to understand why Shepherd is so effective at presenting the science behind “neurogastronomy”. He left out a significant area of research, that of timing. A full description of how the brain works will have to include not only which neurons are active, but when they are active. There is not enough space in such a book to detail the underlying mechanism of smell: the identity of active neurons, how they are connected, and the timing of their activity.

My old boss (among others) was combining smell discrimination-decision making behavior task with simultaneous neural recordings. He, and others, have shown that within a sniff a rat can gain sufficient information to make a decision. This is on the order of a quarter of a second. Such a system likely functions as a time-based code. This is a huge part of understanding how the brain works.

Yet I have to say, it isn’t necessary to Shepherd’s story. Shepherd paints a compelling picture by simply presenting neuronal activity as a pattern, allowing him to describe a huge arc in a few strokes. But this stroke does reveal his thinking; he clearly places a central role in the anatomical organization of the brain, which groups neural activity into patterns. At ever more minute levels, the specific connections underlie the feature extraction processes going on in the brain. In a sense, the fact that neurons, at some point, activate represents the mechanics of actualizing information processing that we had already determined to take place in these neurons, based simply on how they are connected.

Depending on your viewpoint, when the neurons activate may prove important in these processes. Is timing then a peripheral phenomenon, since the most important observation is how these neurons are wired, or could the same wires actually transmit different “information”, depending on the sequence of activity? These are questions researchers continue to spend entire careers answering.

I can imagine a different investigator may have written the same book, but emphasize the ephemeral nature of neural ensembles where the real significance may lie in timing of the activity. In this case, the sequence of neurons firing, how their activity coincide, and the precise synapses activated in downstream neurons are just a few of the parameters that affect perception.

It isn’t a matter of discrediting one versus the other; it is just a point about presentation. In no way am I suggesting that the viewpoint put forth by Shepherd as deficient, merely that he probably made an editorial decision to provide a coherent framework for the edification of non-scientists. I really admire this book, as an exemplar of a rigorous book meant for popular consumption. Most importantly, I feel that he has described the wealth of experimental detail about how current theories of olfaction and flavor perception were arrived at.

I spent too much time on my last post, but I really wanted to push it out. I realized I never came out and stated my idea. Partly, it’s because it might sound controversial unless I develop it properly. I’m glad I waited, because Joshua Timmer, of Ars Technica, pointed to a new study that is relevant to my points here.

In  my previous essay, I had presented Stephen Jay Gould’s idea of dual magisteria, which addresses how one engages with the world. In Rocks of Ages, Gould places undue emphasis on religion as a major counter-point to the scientific descriptions of the physical world. He does mention that there could be other domains of thought, but Gould writes they would encompass other magisteria. Here, Gould did not go far enough; it suffices to group religion as one of many intuitive, personal ways of finding meaning in the world. Simply, there should be two magisteria: science, and all of non-scientific, intuition based ways of looking at the world.*

*The distinction is clear: there is a way to examine the material world, with experiments (although not necessarily their interpretation) providing a common frame of reference. Experiments are placed in this rarified realm because it is expressly constructed so that when methods are made available, other investigators can observe the same results. That is why one of the worst things you can say about a scientist’s findings is that it is not reproducible. 

In this context, my idea for how one might deal with science is that, functionally speaking, they can ignore it. This is possible since science itself, in the realm of meaning in one’s life, may have a lesser impact than other emotional, intuition based thinking. Second, when one aims to counter scientifically based policies, it is more about risk/benefit analysis, trade-offs, and marshalling political support, which actually has less to do with the underlying science and more about rational discourse. In other words,  it is possible to arrive at policies that are directly opposed to the recommendations based on scientific findings.

There is a distinct lack of courage from those who are opposed to science and distrust it because it is considered a Liberal domain (i.e. American Liberals tend to favor governmental intervention in regulating markets but  less  in one’s personal and social lives. The story goes that academia is populated by these liberal types.) These anti-science laymen lack courage because they avoid saying that their policies are at odds with the scientific consensus because they thought other considerations were more important.

So they couch their objections in scientific terms, and rather shoddily*. The proper argument for creationism in school isn’t in to make it an alternate scientific theory in biology class, but in a social studies or literature class, perhaps even an actual religious study. The goal of religion and these classes, as Neil Postman and Joseph Campbell realized, is to attempt to connect the impersonal world to human perception. At best, it can be as invigorating as a philosophy course and as an art appreciation course. It is interesting to me that so many myths do share elements in how they describe how the world began, with many such stories pre-dating even the gods of pharoanic Egpyt, let alone Christianity. There is power in these stories because while they are rudimentary attempts at explanation, in actuality they help us deal with the mysterious and the fear of dying at an approachable human level.

* Hence this strange, if not ironic call, for more facts. Again, my last essay about experts focused on this idea of splitting hairs, where all of a sudden hyper-specific observations are used and not the general theory. My point in that essay is that just simply emphasizing specific examples over the rule is not a simple act. The divergence may be due to chance – acceptable within almost all scientific frameworks – or may indicate an actual alternate cause. If that’s the case, not only must the new model explain why this observation happened, but it must also address why all the other observations we’ve seen arose and was addressed by the other theory. Some type of analytical closure is needed to address how we could have gotten things so wrong. One might argue that Occam’s Razor helps us avoid this situation where we go with an explanation that agrees with most observations – one clear example of this is the models for an earth-centric versus a heliocentric model of the solar system.

I would only point out that the religious studies curriculum would be at odds with what the American (Religious) Conservatives (i.e. less government regulation for economic markets but more constraints in personal lives) desire because any such comparison of religion would naturally lead students to question how Christianity, Islam or (religious) Judaism differ from the myths that had been so callously discarded.* Again, these zealots lack the courage to say that the strength of religion lies specifically in helping believers come to terms with the cycle of life and death and the harshness of the world. By continually using stories of a Jewish guru, who lived 2000 years ago, as a basis to counter scientific findings made from observations with modern equipment, it cheapens Christ and makes the religious look silly. Are we really to think that these Holy Books are relevant to how one interprets molecular biology data showing how closely related humans are to primates and mice? Scientific interpretation and finding meaning germane to our emotional needs (or explaining the human condition) are two different things. There are any such stories one can concoct from religion, because so many stories in holy books are allegorical. We can change stories to fit the facts.

* I once asked my friend, who is a scientist and evangelical Christian, why he believes in Christianity and not, say, Zeus. He replied that Christianity is real and Zeus isn’t. He pointed to the archaeological evidence for the history of the Jews in the Old Testament and of the documentary evidence of Christ and his Apostles for the New. To which I can only suggest that, there is also evidence that the Trojan War happened. We have many stories of the Greek gods and much archaeological evidence of the beliefs of the Homeric Greeks. Does that in itself proves that the Greek pantheon of gods exists? 


At this point in American political culture, we are overly concerned with expertise, the irony of which is that we tend to pigeonhole these distinct voices, rather than to heed their advice. The pushback from scientists is that they tend to dismiss laymen as cranks. These approaches are antagonistic.

On occasion, I hear fellow scientists, when they get annoyed with lay people, brush off by claiming that their bit of science is hard and that laymen shouldn’t comment. That may be true, but as I wrote in my last essay, the tradeoff from academia is that at some point, we publicize our research to other scientists. I go further and suggest that if we are already doing this, we might as well write explicitly to laymen. In the end, it is hoped that our research is of significance and worth including in curricula – for educational purposes.

Naturally, scientific discussions tend to be easier between scientists, even if they ply their trade in different fields. We know the lingo. More importantly, we recognize that there are benchmarks for good research (control experiments, multiple trials, randomized sample sets, published methods and analysis techniques, blind trials where necessary, experiments specifically designed to test for alternate explanations, and so forth) and generally scientists do tend to read broadly. As a result, they do tend to ask questions, not as pointed as an expert might, but they aren’t at a rudimentary level either.

My own background can provide an example. My undergraduate background was biochemistry; my graduate work and one post-doc stint focused on neuroscience, specifically olfactory physiology. My current work as a staff scientist is as a cell-biologist/image analyst, running cell based assays and writing high-content analysis algorithms. Lately, my group has pushed our technology for clinical application in clinical immunology. This is not to say that I understand all these fields to the same degree as people who have spent many more years than I. The common skillset of doing science allows people like me to expand into new fields.

It isn’t as if I ignore biochemistry concepts even now, nor did my work in olfactory physiology meant I simply looked at neuronal function. The point of the latter research was to show how animals use different sniffing patterns to elicit specific neuronal response types that might be important for the animal’s understanding of its odor environment. Being aware of the overarching questions driving specific aims is crucial to a scientist’s success. Another example: Gordon Shepherd, an important researcher in olfaction, recently published a book on flavor perception titled Neurogastronomy. In it, he synthesizes olfactory and taste physiology, fluid dynamics and modeling of air flows in the human nose, the physico-chemical properties of food molecules, and human perception. His bread and butter, however, was in neuronal circuits, with emphasis on the olfactory bulb. Although his ultimate interests is in the mechanism by which neurons give rise to perception, much was unknown and so one must settle on sub-systems (such as olfaction, in “lower” life forms like honeybees, tiger salamanders, fruit flies, and rodents) for research and begin there.

So yes, I firmly believe that even if one is ignorant of a subject, one can come up to speed. It takes work and time. I am not arrogant enough to think that I am exempt from the Kruger-Dunning effect, but I do think that having the ability to identify gaps in knowledge, knowing what to read, finding experts to talk to, one can work to gain a competence in unfamiliar fields. If thinks that this cannot be the case, then there is no point in talking to one another or in reading.

I’ve only lately come to realize that science can be interpreted as a method for communication. We do this a very precise and stylized manner – introducing new ideas, detail methods, publicizing results, and discussing how our observations fit extant theory. Again, this has partly to do with the most basic elements of experimental design, geared to helping scientists remove their biases during analysis. The assumption here is that we argue interpretation and whether experiments were designed correctly. This can only work if the “recipe” and “results” are reported faithfully and  reproducible by anyone else.

Thus science differs from other forms of communication because we work to make transparent our work. Other fields have the luxury of using allegorical, indirect language. Scientific ideas are hard enough without putting some artistry in our language: for example, think of “as an object accelerates, it cannot reach the speed of light since its mass increases” or “if we know the position of an electron, we cannot know its momentum” or that “mass and energy are equivalent.” Because we scientists do try to simplify descriptions, we cannot turn around and tell laymen that what we do is hard to understand. Science is hard to do, especially to do well, but the telling of it can be straight-forward (I’m thinking of essay level exposition, not sound-bites.)

Despite science being a means of communication, it is not a debate in the sense of law; the point of distinction is not in whether the rhetoric is convincing, but whether the data best explain an idea that describes reality. There is no audience per se. Rather, the “audience” is whether the next experiment is consistent with the older findings. This is the predictive aspect of science: If what this other scientist published is true, than it affects my idea like so, and thus I should see this in my experiment.

But as soon as we step away from the realm of validating theories, we have descended into the muck surrounding the ivory tower. This isn’t bad at all; while basic research may be a worthwhile pursuit, I see no contradiction in having to justify that concept to the tax payers. While other scientists might scoff at having to consider applied research, I see this as necessary. In my field, we apply to grants from the National Institutes of Health. In fact, we must always suggest ways in which the research will ultimately benefit the clinicians who treat patients.

My bias is that I see applied research as compelling, and I see, as a red herring, the idea that all research must be pure and unsullied. In other words, I see the realm, or domain, or magisteria of science, as a rather small one. As soon as we start talking about funding, applicability, significance, whether we should pursue a line of research, we get into that fuzzy idea of the “other” magisteria.

This is the part where laymen falter. Laymen tend to argue from a grounding based more on non-scientific criteria than any scientific objections (based on methods, findings, or analysis). I have a very definite view that scientific discussions require the language and methods of science. It helps scientists tease apart assumptions, biases, and the empirical findings. It isn’t that all scientists can compartmentalize their thoughts, or that personal politics, background and temperament do not affect their thinking. It is that the whole system is set up to at least force scientists to justify their ideas (or biases) with data. Questioning scientific findings can only concern methods, analysis, interpretation, counter-evidence, and alternate hypotheses. Alternate ideas are always there; best idea or consensus by no means imply 100% certainty. It might simply be that the idea is the best of the worst.

However, if one were to discuss why the research is worthwhile, why a scientist pursued it, why something should be funded, what applications does it have, what are the resulting policy recommendations: all these are subject to debates. We have facts, as discovered by science, and then there is how we deal with facts. All of us must come to grip with them.  That is why I modified Gould’s opposed magisteria to contain two domains – science and not-science. The former speaks to objective truth, or at least a description of the material world that can be replicated by any sufficiently educated experimenter. The latter has to do with how humans perceive these hard truths.

While it seems like science is given a preeminent position, I would say that it is a rather small domain. Its language and methods are  precise – it is limited. The not-science magisterium encompasses everything else: our experience, our philosophical bent, our religious background, and so forth. These are bundled together because its “truth” is but an interpretation of how we look at the world. At the same time, it is much richer because it is unbounded by hard facts – it can be as fanciful as whatever the imagination can come up with. Its purpose is to help us with that vague concept of “meaning.” It is from this sphere that we might find compelling arguments and vivid imagery to help convince a lay audience.

Non-scientists can lay claim to the other half of the problem, that of receiving the message. Even if scientists write for the public, interested laymen need to listen. When laymen apply the label of “expert”, it is done with opprobrium, suggesting that the expert has narrow knowledge, but no “real world” experience. The ivory tower as therefore a prison rather than a place for undisturbed rumination. Non-scientists can apply the rigid standard to voices they do not like, simply by claiming that one’s expertise is not in the topic at hand. Naturally, the point is to keep experts corralled and voiceless. It is every bit the same exclusionary tactic that some scientists take in keeping laymen out of the realm of science.

My problem with it is that it allows opponents to treat each other not as individuals but as a belonging to the “other”, and eventually as caricatures. Instead of engaging with the science, it is the scientist who is attacked and demonized as mad or playing god and the laymen portrayed as ignorant, religious zealots. If nothing else, people are generally shrewd. Even if they do not appreciate the nuance of an experiment, they are probably experts in some other domain. This goes for scientists and non-scientists. Are we to suggest that they cannot do anything else, simply because they are competent in one field? Surely, all of us at various times and on numerous topics can hold incorrect opinions, but we can learn enough to become informed. To say that this is not possible is to argue that education is pointless.

No one claims that we can all become experts, but we can all learn enough to appreciate the current thinking. So the problem in how laymen and scientists relate to one another is that there is a vested interest in ignoring the fact that we all live in the world. In that sphere of public influence, rightly or wrongly, scientific facts and religious thoughts are just two of many points of view. In examining the greater good, one cannot argue in isolation.

For example, coal-fired and nuclear generated electricity provide one such example. Science and engineering have both resulted in these plants providing the most power efficiently. We already know that burning coal leads to increases in greenhouse gases. Nuclear power is generally cleaner at the point of origin, but it sure is spectacular when things go wrong or when we dispose of spent radioactive fuel. Science will not help us decide which power source to use, or whether we should re-wire our electrical grid and redesign our houses and appliances to consume less power, or whether we should build up hydroelectric power, wind farms, and solar power plants, or whether the trade-offs are worth it. Wisdom and knowledge is a tapestry. We would all do well to remember that we must argue using appropriate tools.

When arguing scientific points, it makes sense to ask about the assumptions, previous empirical evidence, the methodologies, and current findings. It is a fair question to ask for clarifications between current findings and facts that seem contradictory. But scientific validity is argued from empirical evidence, not from rational arguments like two opposing lawyers. There is no such thing as “all evidence.” There is curated best evidence. And while that is still no guarantee of the scientist being right, it will certainly take a bit of work for anyone to identify the actual problems with the model (and see my previous essay on experts for some examples.)

When arguing significance, we would do well to remember that matters of judgment can be based on personal experience and informed opinions. Benefit and risk can be of equal weight, with personal caution being the only guide as to what one prefers to emphasize. It would be great if we all have informed opinions, and that is all we can aspire to when we haven’t had the luxury of time spent cultivating an expertise on a topic. It is partly the scientists’ job to make available the resources to  help citizens become informed. Telling them to trust us is a non-starter; we argue that an argument from authority (and mostly with regard to religious authority) is no argument at all.

Scientists need to set an example and show laymen our actual methods; a fact is believed so because we see it – and you can too if you do exactly as we specify. The other component to this is to realize how  quickly we step outside of our scientific domain. Facts and coherent theory are not sufficient to inspire. Rhetoric becomes an important factor. If you don’t think language matters, just recall  “irradiated foods” and the public misperception. The reference is to light, not nuclear radiation, but consumers rebelled.

For laymen, they need to be more honest about the basis for their objections. Since society pays lip service to the idea of experts being good (when they argue in your favor), it is supposed that the only way to take themselves seriously is to argue from facts, even if their strongest arguments might be based on personal experience and circumstances. The result is that even non-scientists make a push into the domain of science, not realizing it that ideas are not weighted equally. One needs affirmative evidence to show the possibility that a theory can be a valid alternative. Pointing out the holes in global warming mechanisms or evolution can at best weaken those theories. In no way does criticizing science show why creationism is valid.*

*I try to avoid being snide, but I can’t help it. Please answer me this: does taking host during Communion result in the transubstantiation of the wafer and wine into the body and blood of Christ?  A favorite question that Protestants tweak Catholics with. You would think there is an verifiable answer here. Whose creation story – excuse me, theory – should we teach? The Sumerians’? The Egyptians’? The Greeks’? The Zoroastrians’? The Buddhists’? The Hindis’? For that matter, let me know which set of gods to pray to. Maybe before we even consider teaching creationism as an alternate theory to evolution and cosmology – a distinctly American phenomenon – the religious ought to figure out which story best “fits” the data.

The point of this essay is to suggest a more constructive way to talk about science. I see no issues with using compelling imagery to push scientific ideas. This is not acquiescing. I am recognizing the fact that no one likes their beliefs challenged. But scientific facts are as they are; they change only because of more precise observations from better tools and experiments. Our personal worldviews are what must change, if the two are ever at odds. We scientists should take advantage of the metaphors and allegories allowed us by the non-science domain, showing that even something as contentious as religious ideas can be reformulated, not necessarily refuted, and make palatable the bitter pill of hard-won scientific facts.

I recently heard a fun episode of This American Life, called “Kid Politics”. Ira Glass presented three stories about children being forced to make grown-up choices. The second story is an in-studio interview of Dr. Roberta Johnson, geophysicist and Executive Director of the National Earth Science Teachers Association, and Erin Gustafson, a high-school student. The two represented a meeting of minds, between a scientist who is presenting the best evidence demonstrating human induced climate change and a student who, in her words, does not believe in climate change.

It is worth listening to; Ms. Gustafson is certainly articulate, and she is entitled to think what she wants. I simply emphasize that, Ms. Gustafson uses language that suggests she is engaged in a defense of beliefs rather than an exploration of scientific ideas.

Ira Glass, near the end of the interview, asks Dr. Johnson to present the best pieces of evidence arguing in favor of anthropogenic climate change. Dr. Johnson speaks of the analysis of ice cores, where carbon dioxide levels can be detected. This can be correlated to evidence of temperature. Ms. Gustafson points out that apparently, in the 1200s, there was human record of a warm spell – I gathered it was somewhere in Europe, although the precise location and the extent of this unseasonably hot weather was not mentioned –  where low CO2 levels at the time.

Clearly, Ms. Gustafson has shown enough interest in the topic to find some facts or observations to counter a scientific conclusion. She then calls for scientists to show her all evidence, after which she herself will get to decide. I suppose at this point, I’m going to trespass into Kruger-Dunning territory and speak about expertise, evidence, and the use of logic.

In general, I do not think it is a good approach for scientists to simply argue from authority. I admit, this comes from a bias in my interests in writing about science to a lay audience. I focus on the methods and experiment design, rather than the conclusions; my hope is that by doing that, the authority inherent in the concept of “expertise” will be self-evident. That is, I show you (not just tell you) what others (or I) have done in thinking and investigating a problem. By extension, I hope I informed myself sufficiently before I prepare some thoughts on the matter, shooting specifically for fresh metaphors and presentation. (As an aside, I suppose that this might be a mug’s game, given the findings of Kruger and Dunning.)

If a scientist has done his or her job, one is left with a set of “facts”. These facts populate any school textbook. But the facts are more than that: they can act as, with a bit of thought and elaboration, as models. I dislike the distinction people make when they argue that we need to teach kids how to think and not a set of facts. I argue that learning “how to think” depends crucially on how well a student had been taught to deal with facts. These skills include how to deal with facts by using them as assumptions in deductive reasoning, weighing whether a fact has solid evidence behind it, and using facts as if they were models.

Here’s my issue with how Ms. Gustafson, and other anti-science proponents (like anti-evolutionists), argue. Let’s say we were told that gas expands upon heating. One might take this as a given and immediately think of consequences. If these consequences are testable, then you’ve just made up an experiment. Inflate a balloon and tie it off. If temperature increases lead to volume increases, one might immerse the balloon in hot water to see if it grows larger. One might choose to examine the basis of thermal expansion of gas, and he’ll find that the experiments have been well documented since the 1700’s (Charles’s Law). A reasonable extrapolation of this fact is that, if heating gas increases its volume, then perhaps cooling gas will lead to a contraction? One might have seen a filled balloon placed in liquid nitrogen (at – 196 deg C) solidify, but it also shrivels up.

Depending on how well facts are presented, they can be organized within a coherent framework, as textbooks, scientific reviews, and  introductions in peer-reviewed articles already do. My graduate advisor characterized this context fitting as  “provenance.” No idea is truly novel; even if one does arrive at an idea through inspiration and no obvious antecedents, it is expected that this idea have a context. It isn’t that the idea has to follow from previous ideas. The point is to draw threads together and if necessary,  make new links to old ideas. The end point is a coherent framework for thinking about the new idea.

Of course, logic and internal consistency is no guarantee of truth; that is why a scientist does the experiment. What hasn’t been really emphasized about science is that it is as much about communication as it is about designing repeatable experiments. Although scientists tend to say, “Show me,” it turns out that they also like a story. It helps make the pill easier to swallow. The most successful scientists write  convincingly; the art is choosing the right arguments and precedents to pave the way for the acceptance of empirical results. This is especially important if the results are controversial.

The error Ms. Gustafson makes is that she thinks by refuting one fact, she can refute an entire tapestry of scientific evidence and best models (i.e. “theory”). She points to one instance where carbon dioxide levels do not track with the expected temperature change. But in what context? Is it just the one time out of 1000 such points? I would hazard a guess that the frequency of divergence is probably higher than that, but unless the number of divergences is too high, one might reasonably suppose that the two correlate more often than not. (Causation is a different matter;  correlation is not causation.)

But let us move on from that; a more elemental disagreement I have with Ms. Gustafson’s point is that, let’s say that one agrees that carbon dioxide is a greenhouse gas. A simple model is that this gas (and other greenhouse gases such as water vapor, methane, nitrous oxide) absorbs heat in the form of infrared radiation. Some of this energy is transferred into non-radiative processes. Eventually, light is re-emitted (also as infrared radiation) to bring the greenhouse molecule to a less energetic state. Whereas the infrared light had a distinct unidirectional vector, radiation by the greenhouse molecule will occur in all direction. Thus some fraction of light is reflected back towards the source while some other light essentially continues on its original path. If infrared light approaches earth from space, then these gases act as a barrier, reflecting some light back into space. Absorption properties of molecules can be identified in a lab. We can extend these findings to ask, what would happen to infrared heat that is emitted from the surface of the planet?

A reasonable deduction might be that just as out near the edge of the atmosphere, greenhouse gases near the Earth surface also absorb and reflect  a  fraction of heat. Only this time, the heat remains near the Earth’s surface. One logical question is, how does this heat affect the bulk flow of air through the atmosphere? (An answer is that the heat may be absorbed by water, contributing to melting of icebergs. Another related answer is that the heat may drive evaporation and increasing kinetic energic of water vapor, providing energy to atmospheric air flows and ultimately to weather patterns.

For someone who ignores greenhouse gas induced global warming, dismissing the contribution of carbon dioxide isn’t just a simple erasure of a variable in some model. What the global warming denier is really asking that the known physical property of carbon dioxide be explained away or modified. Again, the point is that carbon dioxide has measurable properties. For it not to contribute in some way to “heat retention” is to say that we must ask why the same molecule won’t absorb infrared radiation and re-emit infrared radiation in the atmosphere, in the same way that was observed in the lab. In other words, simply eliminating the variable would require us to explain why there are two different sets of physical laws that apply to carbon dioxide. In turn, this would require a lot of work to provide context, or, the provenance to the idea.

Yes, one might argue that scientists took a reductionist approach that somehow removed some other effector molecule if they measured carbon dioxide properties using pure samples. Interestingly enough, the composition of the atmosphere is well known. Not only that, one can easily obtain the actual “real-world” sample and measure its ability to absorb unidirectional infrared and radiate in all directions. This isn’t to say that thermodynamics of gases and their effects on the climate of Earth is simple. But it is going to take more than a simplistic type of question, such as to posit that there is some synergistic effect between carbon dioxide and some other greenhouse gas or some as-yet unidentified compound, so that we actually modify the working model physicists and chemists have about absorption and transfer of energy.

If you think that it seems rather pat for a scientist to sit and basically discriminate among all these various counter-arguments, I am sorry to disabuse you of the notion that scientists weigh all facts equally. Ideally, the background of the debaters ought not to matter. Hence, you will get scientists to weigh your criticisms more heavily if you show the context of the idea. The more relevant and cohesive your argument, the more seriously you will be taken. Otherwise, your presentation may do you the disservice of giving the appearance that you are simply guessing. That’s one problem with anti-science claimants: all too often it sounds like they are trying to throw as many criticism as possible, hoping that they will get lucky and have one stick.

Take evolution: if one suggests that mankind is not descended from primates, then one is saying that mankind was in fact created de novo. That is fine, in and of itself, but let’s fill out the context. Let’s not focus on the religious texts, but instead consider all the observations we have to explain away.

If we were to go on and to try and explain mankind as a special creation, how would we go about explaining mankind’s exceptionalism? Can we even show that we are exceptional? Our physiology is similar to mammals. We even share physical features as primates. Sure, we have large brains, among the largest brain mass to body mass ratios in the animal kingdom. Yet we differ in about 4% of our genome compared to chimpanzees. Further, at a molecular level, we are hard pressed to find great differences. We simply work the same way as a lot of other creatures. We have the same proteins, despite the obvious differences between man and mouse, a weak similarity between our proteins mean that we have only 70% sequence homology. It seems to me that at multiple levels, at a physiological level, at the level of physical appearances, and at a genomic level, we are of the same mettle as other life on earth. Yes, the fact is that we do differ from these other lifeforms, but it seems to be more logical to suggest that mankind is one type of life in a continuum of the possible lifeforms that can exist on Earth. It just seems likely that by whatever process that led to such a variety of creatures, man must also have been “created” from such a process.

 I hate to harp on this, but a fellow grad student and I had such arguments, while we were both doing our thesis work. My friend is a smart guy, but he still makes the same mistake that anti-evolutionists make: by disproving natural selection, one  therefore has provided some support for creationism. We argued about Darwin’s theory and whether it can be properly extended from a microscopic domain. He was willing to concede evolution occurs at a microbiotic level – such as for “simple” organisms, evolution makes sense, since fewer genes mean less complexity and therefore changes can be just as likely to be beneficial and deleterious.

I thought the opposite. If an organism is “simpler” – namely because it contains a smaller genome – it is even more crucial for a given organism that a mutation be beneficial. A larger genome, from empirical data, generally contains more variants of a given protein. While this in itself reflects the appropriation of existing genes and their products for new functions. Perhaps one possibility is that   an increase in isoforms of a protein also suggests how mutations can occur without the organism suffering ill effects directly. There is a redundancy of protein and function. Also, my friend seems to regard fitness as a “winner takes all” sort of game – as in the organism lives. I merely saw the “win” as an increase in probability that the animal will have a chance to mate, not organismal longevity. Sure, this is a just so story; I think his argument is better than the usual creationist claptrap, but only in the  trivial sense that, yes we need to take care not to over interpret our data or models and yes,  scientific theories – althoughswa they are our best models –  are temporary in the sense that we can revise them when better evidence comes along.

To go back to the way Ms. Gustafson and my friend argue, it behooves them to explain the exceptional circumstances by which we, or carbon dioxide, can act differently from our best model (i.e. theory) and yet conform to it most of the time.

Thus, despite Ms. Gustafson’s call for “all the evidence”, I somehow was left thinking no amount of evidence will persuade her. Part of the problem is that, like the religious who misapply ideas of meaning found in their bibles to the physical evidence generated by scientists, she misapplies her political views to provide the context through which she views scientific evidence about global warming. Whereas she should have used logic to deduce that global climate does not predict local weather and scientific principles  to determine whether global warming is part of a normal cycle for the Earth or is in fact due to circumstances like an increase in greenhouse gases, she probably thought of global warming in terms of regulations and taxes pushed, generally in the United States, by Democrats. Thus, Ms. Gustafson speaks, in Stephen Jay Gould’s term, from the magisteria of meaning (as defined by her political and religious beliefs) and not from the magisteria of science. In this case, she isn’t defending her theory about how the world works; her motivation is to fit the observations to her political and religious ideals.

Can we really separate the political from the scientific? If some scientist argues that there is a problem, it seems difficult to find ways to argue against them. My only suggestion is that Ms. Gustafson and others like her consider their arguments more carefully. Nitpicking specific examples is counter-productive. All theories can be criticized in this way. However, integrating the counter-example is not a straight-forward process, especially if simplistic criticism is at odds with some other firmer, more fundamental observation that even Ms. Gustafson has no problems accepting.


Christian Specht wrote a short, cute analysis on citation mutations. He has a follow-up. Basically, these result from typos by authors or typesetters. This isn’t the problem. The problem is that some typos are inherited. Specht speculates that the inheritance  (i.e. copied and propagated through citations in other papers)  is a  problem because it implies that authors simply copy old references from other papers. I guess the ideal would be that authors would use their own database references or to build up their citation from the actual paper.

I ‘m not sure if this problem is as distressing as Specht writes, although to be fair he isn’t exactly worried.)  He simply made a point that there is likely much copying of old references – even if we can’t detect the occurrence because most people usually copy the correct reference.

Specht worries that the incorrect references may be an indication that scientists do not always read the papers they cite. I would add, simply, that maybe some scientists are lazy; if a paper already contains a properly formatted bibliography for the journal to which a new paper is being submitted, I can see why some authors might simply save time and make a copy.

Or the level of scrutiny for a paper usually doesn’t reach into the bibliography, which, ideally, would involve the authors actually searching for  each paper and actually checking if the page numbers match those from the article.


Some interesting book reviews: Lee Smolin reviews Roger Penrose’s Cycles of Time, in which Penrose speculates about how the universe got its start. The mind-bender is that there might be no such official beginning, at least for our universe. Shame on me, although I am aware of Roger Penrose’s work, I had no idea how significant an impact he has had in physics. As Smolin writes in Nature,

We should pay attention because Penrose has repeatedly been far ahead of his time. The most influential person to develop the general theory of relativity since Einstein, Penrose established the generalized behaviour of space-time geometry, pushing that theory beyond special cases. Our current understanding of black holes, singularities and gravitational radiation is built with his tools.


In the same issue of Nature, Jascha Hoffman reviews Charles Seife’s Proofiness, where Seife creates a “taxonomy of statistical malfeasance”.



An interesting paper in Nature: a comparison of unique human genomes. The 1000 Genomes Project Consortium sequenced 882 people, with varying degrees of coverage (i.e. total nucleotides sequenced.) This has to do with time and costs. There were 2 mother-father-daughter trios who were sequenced with high-coverage, 178 individuals sequenced with low-coverage, and 697 individuals had only coding sequences within their genome sequenced. This type of research will enable researchers to categorize the genetic differences between closely and distantly related individuals. Further development of individual genome sequencing may enable both disease likelihood calculations as well as possibly tailoring drug treatments for disease, finer scale look at population migrations, and genetic correlates of phenotypic variation. Finally, the identification of the single nucleotide changes (polymorphisms) between individuals will also help researchers expand on the number of markers that are linked to a disease (and in fact have already guided researchers in expanding the probes in microarray chips that detect these new markers.)

A second interesting paper, this one published in Science. Workers were able to identify a specific neural circuit, in zebrafish, that processes visual information. Specifically, this circuit is tuned to small objects, perhaps used in the capture of the zebrafish’s prey.

The nice people at Ars Technica wrote about a Science paper published today. Through the use of precise optical clocks, researchers were able to show the effects of relativity for objects in motion and at different distances from a massive object (i.e. Earth). Traditionally, effects become “obvious” and large when objects move at near light-speed. It is interesting then to see that macroscopic objects (like huge clocks and by extension, things and people) can also experience relativity, albeit with inconsequential effects. Researchers were able to show that moving a clock at 22 mph or placing a clock about 1 ft higher off the ground will result in that clock ticking slower. Both are good reads.

The Scientist has published some advice for training post-docs. More emphasis needs to be placed on what a career in science entails. Often, the key motivation in doing science is that experiments are  fun. However, that isn’t doing science.

Being a scientist means: looking for gaps in existing literature, stringing together theses gaps to build a research program (i.e. grant proposal), write grant proposals, manage money, manage time, learn to interact with colleagues, build working relationships (or at least acquaint and introduce oneself) with researchers outside lab, expose oneself to science (be selective!), do the bench work, and analyze data.

If you are a graduate student, then your job is to turn data into figures. Doing so will train you to think about how best to communicate a finding. I would argue that, even if you have an “n of 1”, you should start making the graphs, tables, curves, and so on. Have the framework in place to receive data.

This is the corollary to displaying your hypothesis in a prominent location and thinking if it needs to reworking.

Essentially, focus on telling people what you are doing, why, and what you have found so far.

In doing this, you will naturally look into literature to fill in gaps in your knowledge and also to find novel experiments to try.

This set of observations is not meant to be authoritative. It is simply something (new) for you to try if you haven’t already done so. If you want to add to this list, let me know. I can link back or just update this post.

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