Friday, September 23, 2011


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Wednesday, September 14, 2011

DUE SEPTEMBER 21, 2011 - Why should biologists care about Heisenberg's Principle of Uncertainty? A discussion about what is life

During these first 3 weeks of class, you have quantitatively measured populations of insects, volumes of liquids and solids, sizes of objects (lengths and widths), masses of solids, and temperatures as well as collected qualitative data on insect behavior. At all points, you have encountered limitations that will be discussed in your lab reports and analyzed with statistical tools that will give an approximate measure to the error of your measurements (range and size of your sample). 

During lecture time, we have discussed the nature of the atom and the concept of uncertainty has been introduced. 

Read the three paragraphs below, and discuss within the context of your experiments' results.

In the Stanford's Encyclopedia of Philosophy, Hilgevoord and Uffink discuss Heisenberg's principle of uncertainty under item 2.2, which reads:

"He (Heisenberg) adopted an operational assumption: terms like ‘the position of a particle’ have meaning only if one specifies a suitable experiment by which ‘the position of a particle’ can be measured. We will call this assumption the ‘measurement=meaning principle’. In general ... experiments are never completely accurate. We should be prepared to accept, therefore, that in general the meaning of these quantities is also determined only up to some characteristic inaccuracy.
As an example, he considered the measurement of the position of an electron by a microscope. The accuracy of such a measurement is limited by the wave length of the light illuminating the electron. Thus, it is possible, in principle, to make such a position measurement as accurate as one wishes, by using light of a very short wave length, e.g., γ-rays. But for γ-rays, the Compton effect cannot be ignored: the interaction of the electron and the illuminating light should then be considered as a collision of at least one photon with the electron. In such a collision, the electron suffers a recoil which disturbs its momentum. Moreover, the shorter the wave length, the larger is this change in momentum. Thus, at the moment when the position of the particle is accurately known, Heisenberg argued, its momentum cannot be accurately known:
At the instant of time when the position is determined, that is, at the instant when the photon is scattered by the electron, the electron undergoes a discontinuous change in momentum. This change is the greater the smaller the wavelength of the light employed, i.e., the more exact the determination of the position. At the instant at which the position of the electron is known, its momentum therefore can be known only up to magnitudes which correspond to that discontinuous change; thus, the more precisely the position is determined, the less precisely the momentum is known, and conversely (Heisenberg, 1927, p. 174-5).
This is the first formulation of the uncertainty principle. In its present form it is an epistemological principle, since it limits what we can know about the electron."

Dr. Murase at the Kyoto Institute of Theoretical Physics, proposes that "there is no clear distinction between subject (endo) and object (exo). As there is no definitely isolated object, the reproducibility principle is mostly violated. We must therefore pay much attention to the transients – or processes – during the past history of life".

Finally, researcher Richard Jorgensen proposes that molecular biology is no different in its lack of determinism than the world of physics. His article states:
"Quantum mechanics, especially in Heisenberg’s uncertainty principle raised fundamental questions that challenged the possibility of precise knowledge of the future: For instance, the number of times per second that atoms in a lump of uranium will undergo radioactive decay is known with precision; however, why and when any particular atom will decay is unpredictable by modern physics.
Similarly, although geneticists can measure mutation frequency in a particular system under specific conditions, the timing of a particular nucleotide substitution (or any other mutational event) is unpredictable. Only the likelihood of the mutation can be known. Thus, from an evolutionary genetic perspective, biology is no more deterministic than is physics, as Tautz (2000) has analyzed in terms of population genetic theory ... 

With the advent of genomics, it is theoretically possible to know with absolute certainty the sequence of a region of chromosome carrying a gene and even the sequence of an entire chromosome. However, as Stadler (1954) noted, it is not trivial to precisely locate a gene, i.e., it cannot “be shown to be delimited from neighboring genes by definite boundaries.” This conclusion follows from Stadler’s definition of the gene: “operationally, the gene can be defined only as the smallest segment of the gene-string that can be shown to be consistently associated with the occurrence of a specific genetic effect.” In modern terms, knowing the complete sequence of a chromosome does not allow us to precisely determine all of the “many interdependent elements of a gene, including all those elements in cis that are necessary for the normal operation of a given gene” that is associated with a specific genetic effect (Jorgensen, 2010). In addition, the expression and selective value of a gene in nature may often be dependent on the environment encountered by the organism, perhaps making it impossible to precisely identify the boundaries of a gene.

Distinct from quantum mechanics, it is also important to recognize the relevance to biology of complexity theory, which has identified another type of uncertainty in physics, resulting from sensitive dependence on initial conditions such that relatively simple Newtonian systems may exhibit unpredictable “chaotic” behaviors due to the impracticality of knowing initial conditions precisely enough.

Similarly, it should be evident that knowing all alternative epigenetic states of a given gene in all environments may be unachievable in any practical sense."


Hilgevoord, Jan and Uffink, Jos, "The Uncertainty Principle", The Stanford Encyclopedia of Philosophy (Spring 2011 Edition), Edward N. Zalta (ed.), URL = . Also available at

Masatoshi Murase. "Endo-Exo Circulation as a Paradigm of Life: Towards a New Synthesis of Eastern Philosophy and Western Science". Prog. Theor. Phys. Supplement No. 173 (2008) pp. 1-10. Available at

Richard A. Jorgensen, "Epigenetics: biology’s quantum mechanics". Frontiers in Plant Science | Plant Genetics and Genomics April 2011, Volume 2, Article 10, 1-4. Available at

Tuesday, September 13, 2011

First come first serve TICK

Does the boiled mix of cocoa and milk generate new compounds? If so, which ones? Citations!!

Attractants & repellents

Do an iGoogle Scholar search for insect attractants and repellents, and comment.

Bring to Wednesday lab period for behavior experimentation. Remember you will have to run repetitions, so bring enough.

Wednesday, August 31, 2011

Applied ethology - DUE FRIDAY SEPTEMBER 2, 2011

Read the publication source and answer the following questions. In order to answer question 3, you will have to google scholar  publications on play behavior of other species.
  1. In the case of Octopus vulgaris, how and why do they use water jets? 
  2. What are the implications of play behavior when you compare Octopus vulgaris with Octopus dofleini? 
  3. Do all taxa play? 
  4. What are the evolutionary implications of your claim?

Tuesday, August 30, 2011

Can a learned Behavior Turn into Innate one? - DUE FRIDAY SEPTEMBER 2ND

Peer-reviewed publication based ONLY.
Scholarly discuss the publication in addition to quoting it.

Wednesday, February 23, 2011

Biscayne Bay Plants and their chemical compounds - DUE FRIDAY FEBRUARY 25

1. Find 5 examples of Biscayne Bay plants and their chemical composition. Use the following engines:, search by species 

2. Recognize 5 poisonous plants in Florida and components. Use the following engines: 

In order to search the chemical compositions at, follow these steps:
Plant Searches
  • Chemicals and activities in a particular plant. 
  • Search by common or scientific name
  • Click on submit query
  • Then, check the boxes "Search based on non-ubiquitous chemicals only.", Print activities with chemicals." and "Include full references at end of document."
  • Finally, click on "submit query"

Sunday, January 9, 2011

List of diseases

Make a list of infectious diseases and the organism that causes it, completing the following table:

#    Disease          Organism                               Type               
1    Malaria          Plasmodium                          Eukaryotic unicellular parasite
2    Flu                 Hemoinfluenza                     Virus
3    Chicken pox
4                          Escherichia coli
5                          Salmonella typhimurium
6                          Streptecoccus aureus
7                          Streptococcus pneumoniae
8   Dysentery
9   AIDS
10                                                                     Roundworm
11                        Karenia brevis                    
12  Hepatitis
14                       Helicobacter pilori
15                       Cytomegalovirus (CMV)
16 Rabbies
18 Varicella
19 Papilloma
20                       TMV