Biomarkers are the answer.

But what is
the question?

Mauro F Rebelo
Is Adjunct Professor of Environmental Biophysics at
the Carlos Chagas Filho Biophysics Institute of the
Rio de Janeiro Federal University.
mrebelo@biof.ufrj.br
Mailing address
Universidade Federal do Rio de Janeiro, Instituto de
Biofísica Carlos Chagas Filho, Centro de Ciências
da Saúde, Bloco G, Ilha do Fundão, 21941-902, Rio
de Janeiro, Brasil
I once saw a movie where the “best of the best” US
Navy pilots went to a special school to become even
better. It was a kind of “graduate school” for pilots. In
the initial lecture, the commander explained that pilots
were becoming dependent on technology and
forgetting how to pilot. They were losing their piloting
skills. The same is happening with science graduate
students (and many times also their advisors)
throughout science. They can get really sophisticated
data from high-tech equipment, but do not really know
how to translate data into information and information
into knowledge. They are quite good at getting the
answers, but seemingly have lost the ability to ask the
questions. The resulting data are often uninteresting,
redundant, or simply useless.
Biomarkers are the answer
In our field of environmental-health biology, this
can be even a harder problem, because there are
many fewer standard practices than in human-health
biology. For example, if a researcher from a tropical
country wants to test the effect of a drug in humans,
starting from mice as a surrogate species, he will use
the same mice as a researcher in higher latitudes.
However, if the same researcher wants to test the
effect of a pollutant in his environment, it will be an
entirely different story. Surrogate species are not the
same, and are certainly not standardized. Some will
say fish are better, others will say mollusks are, and no
one will agree. Ludwig et al. (1993) showed in their
very interesting article about natural-resources
exploitation and conservation that environmental
problems are both technically and politically complex.
If we want to nurture a new generation of
environmental scientists with critical-thinking skills and
the ability to make decisions, we need to encourage
our students to consider some of these questions:

1 – The “Use my species” plague
Worse than the lack of surrogate species is the
competition between scientific groups to establish a
“preferred” one. It would be a good exercise for a new
student coming to your laboratory: find as many
articles as you can that begin or end with a suggestion
of a new surrogate species, based on a few toxicity
tests or biomarker analyses. It is as if the one who will
find the “ultimate” surrogate species will gain fame and
fortune. They will not, but during the attempt, they are
spending significant amounts of money to conclude…
less than they could. Understanding the limitations of
any given species as a surrogate species is at least as
important as highlighting the qualities that recommend
their usefulness in protecting an environment. There
likely will never be the “one” surrogate species for all
environments, because environments and the species
are simply too diverse to be compared in that way. We
should encourage students to stop looking for the
ultimate surrogate and to properly examine the merits
of available ones to address particular questions about
toxicity and mechanisms that may then be applied
different species.
2 – The “lack of experimental design”
syndrome
Environmental-science students and researchers
(including reviewers) often don’t really know statistics.
Surely not enough. Many studies report nothing more
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ANO I VOL 1 NUM 01
than the mean and standard deviation, which do not
apply in most cases in environmental science! I have
worked with sentinel species for 15 years and haven’t
found one yet that shows a normal distribution of
contaminant accumulation in its tissues. Beeby
(2001), in a very interesting article on sentinels,
showed that normal distributions are simply not to be
assumed! So why do people keep reporting average
concentrations with standard deviations? And why do
journals accept that? When it comes to experimental
design, the problem gets worse. Anxious to cover all
aspects of a given problem (let us say “how a chemical
affects the physiology of a given species”), in the hope
to publish faster and in a more prestigious journal,
researchers are jumping to evaluate the effects of as
many treatments on as many variables as they can.
The inevitable outcome is that they cannot use as
many replicates as are necessary to determine, or at
least to accurately express, the uncertainty or the
range of the biological variables. The results are often
meaningless, yet statistically significant correlations.
Ioannidis (2005) showed that the insistence to claim
“truth” based on statistical significance and to establish
“cause” based on statistical correlation has led to the
astonishing conclusion that most published scientific
results are false. It is imperative that we teach our
students to reduce uncertainty about our scientific
object (the species or the biological variable) BEFORE
we start to test for variables and treatments.
3 – The “publish or perish” paradigm
This is another demand that can be contrary to the
best practices in science: I can’t help speculating
whether the rush to publish actually contributes to
uncareful experimental design. Gven the complexity of
higher levels of biological organization – such as the
ecosystem – environmental science simply requires
more planning and more time to execute and publish
than do studies addressing lower levels of organization
– such as the cell. But how to address the difficulties in
the current publishing system? My guess is that we
could do that by going back to asking good,
meaningful, relevant questions! For instance, how
many articles have you read in which the authors are
pretty much the same, as well as the laboratories
involved, and the articles would also be much the
same if not for a change in the chemical, the
biomarker, or the species examined? Perhaps even
worse are proposals to redo measurements using new
instruments or new markers. This kind of approach
ANO I VOL 1 NUM 01
might be necessary, but do the authors really tell us
how this advances the science, if indeed it does? It
seems that we often teach the students only how to
push the necessary buttons to get the results, without
allowing time for discussion and little room for
reasoning as to whether this is necessary.
4 – The “The answer is biomarkers”
obsession
There are biomarkers of exposure, of susceptibility
and effect. In environmental toxicology they are often
thought of as biochemical or molecular processes that
can respond to an external stimulus, helping to predict
or prevent damage at higher organizational levels,
biomarkers were the response of the environmental
research community to the “molecularization” of
science.
Please do not misunderstand me; I do believe that
the ‘omics’ have a lot to contribute to science. A better
understanding of the molecular processes occurring at
the beginning of the sequence where events when
impacts may still be reversible is far more likely to help
us to prevent environmental damage.
However, smaller machine does not mean we have
to ask reductionist questions. Use of a molecular
biomarker may be a great approach, but “Is that
enough”? Well, we can already say that one biomarker
is not enough. We need a set, and a group of “core”
biomarkers has been described (Viarengo et al.,
2007). However, there is still a kind of “gold rush” to
find a new or ultimate biomarker. Every enzyme,
protein, gene, reaction, metabolic pathway, or
behavior is a candidate to be the new savior of our
environment. The reason might not be as obvious as
the consequence: despite a few local initiatives, in the
quest for the “one” biomarker, we are forgetting to
research the actual variability in the biomarker and in
the chain of events that leads from the damage at the
initial level of organization to the ultimate adverse
effect on the organism or ecosystem. We are so
excited to use our new mass spectrometer or
Affymetrix chip that we are leaving behind the basics
of toxicokinetics and toxicodynamics. Again, to
understand the limitations of each of the established
“core” biomarkers, to gain the best information from
them that we can, should be more important than to
propose a new one in every article. It is knowledge of
the limitations, rather than the qualities, that helps us
make better use of the tools that we have available.
7
O admirável mundo das células-tronco
5 – The “Don’t think! That is my job”
blindness
Students are often encouraged to produce results
and leave the task of converting the data into
information and then knowledge to their advisors. As a
result, we have an entire generation of students who
think it is not necessary to read, who seldom actually
study. Let’s be fair and share this fault/blame with
modern society. We live in a world saturated with
information and there is simply no space in our brains
to store everything that we might want or need. But we
are facing a serious lack of interest in the literature, the
history of discovery in our science, or the philosophy
behind the methods. Why waste time reading the book
when we can merely read the abstract? Or even
worse: “let’s wait for the movie to come out”. Too bad
“Avatar” is not acceptable as a literature reference.
Students often are unfamiliar with things, or ways of
thinking, they should have learned years ago. Simply
reading the “classics” can be so enlightening,
improving the understanding of foundations of their
field and how it got where it is today, and exposing the
thought that went into advances and disovery. Not
reading, students are often disappointed when they
discover that their “breakthrough conclusion” has
actually been described and discussed (and
sometimes refuted) in a series of articles and books
published some 30 years ago. Moreover, most of the
time these older papers are there, with reprints on the
shelves of their own lab! And of course, since they
don’t read, their writing suffers. The average paper,
thesis, or article written by graduate students is a
disaster – superficial, vague, and grammatically and
orthographically irritating. Graduate school should do
more for students them simply punish them for a
terrible thesis. We have to go back and teach our
students how to ask a good question and how to put
that in good writing. We have to turn on their desire to
reason and write.
For me, the beauty of science also stems from its
egalitarian nature: it accepts anyone regardless of
social status, gender, race, or beliefs. However, it is
not a democracy (in the sense of representing the will
of the majority), and science will not, and must not,
make exceptions for anyone. It is imperative that we
convince our students that, even though it can be
demanding and laborious, it is ‘so cool’ to be a
scientist. If we don’t do that while they are students,
by the time they get a Ph.D., it will have no more
meaning than a title. Training of a new generation is a
Biomarkers are the answer
critical way to meet the expectation society has of
scientists. Are we ready to commit to meeting this
essential need of science?
We live in times of great concern for the
environment. Poverty and hunger put as much
pressure on the environment as the exploitation of any
natural resource demanded by developed societies to
keep up their standards of living. The challenges we
face are enormous, and the choices we will eventually
have to make will be very difficult. We need people
who truly understand the limits of our knowledge about
our environment to help shape the solutions to these
problems. We need to prepare scientists who are able
to ask the right questions and then answer them,
especially in regard to the environment. Instead of
preparing scientists who only can make more precise
and more accurate measurements (as Lord Kelvin said
more than a hundred years ago), which could be
meaningless in a few years, we should prepare
scientists who are able to make careful and reliable
interpretations based on precise measurements, with a
full appreciation of all the uncertainty that may exist,
and convey these interpretations to decision-makers in
ways that are clear and understandable. Graduate
courses all over the world should emphasize the
reading and writing ability of their students,
ANO I VOL 1 NUM 01
their statistical and logical skills, and their
philosophical background, because actually society is
doing a great job teaching them technology.
There is no other way of doing our job: easy
answers and magical predictions are for astrologists.
Acknowledgments
The author is grateful to Dr. Francesco Dondero,
Dr. José Monserrat and Dr. Milton Morares for their
criticism during the elaboration of this manuscript. Dr.
Rebelo is an Irving J. Selikoff International Scholar of
the Mount Sinai School of Medicine (Award
D43TW000640 from the Fogarty International Center)
and fellow of the Brazilian research council (CNPq
307401/2009-0). The Content is solely the
responsibility of the author.
References
Beeby A. 2001. What do sentinels stand for? Environmental Pollution,
112, 285–298
Ioannidis JPA. 2005. Why Most Published Research Findings Are False.
PLoS Medicine 2(8): e124
Ludwig D, Hilborn R, Waters C. 1993. Uncertainty, Resource Exploitation,
and Conservation: Lessons from History. Science 260, 17
Viarengo A, Lowe D, Bolognesi C, Fabbri F, Koehler A. 2007. The use of
biomarkers in biomonitoring: A 2-tier approach assessing the level of
pollutant-induced stress syndrome in sentinel organisms. Comparative
Biochemistry and Physiology, Part C 146: 281–300.