What is science?

Introduction to Modern Biology I.

Péter Molnár, Zoology, Univ. West Hungary, Szombathely

Mader: Inquiry into Life

Biology is the scientific study of life. Religion, aesthetics, ethics, and, yes, science, are all ways that human beings have of finding order in the natural world. But science differs from other human ways of knowing and learning by its process. The process of science is unique. Science is a human endeavor that considers only what is observable by the senses or by instruments that extend the ability of the senses.

What is Biology?

Science ˈsʌɪəns/nounnoun: science

the intellectual and practical activity encompassing the systematic study of the structure and behaviour of the physical and natural world through observation and experiment.

https://explorable.com/what-is-research

Example: How to test a hypothesis

Why do we BELIEVE in Science?Scientific Method?

Many people will distinguish a belief from knowledge, in that knowledge requires evidence, and belief does not. Illustration: Jonathon Rosen

Role of Discussions and Debates in Science

Science 3 June 2011:Vol. 332 no. 6034 pp. 1163-1166

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

Felisa Wolfe-Simon, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E. Hoeft, Jennifer Pett-Ridge, John F. Stolz,Samuel M. Webb, Peter K. Weber, Paul C. W. Davies, Ariel D. Anbar Ronald S. Oremland

Abstract

Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, that is able to substitute arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Growth and electron microscopy of strain GFAJ-1. (A and B) Growth curves of GFAJ-1 grown on the defined synthetic medium amended with either 1.5 mM PO43– (solid circles), 40 mM AsO43– (solid squares), or neither PO43– nor AsO43– (open triangles). Cell growth was monitored both by an increase in (A) optical density and (B) cell numbers of the cultures. Symbols represent the mean ± SD of (A) n = 6 experimental and n = 2 controls and (B) n = 3 experimental and n = 1 control. This was a single experiment with six replicates; however, material was conserved to extend the duration of the experiment to allow material for cell-counting samples. (C and D) Scanning electron micrographs of strain GFAJ-1 under two conditions, (C) +As/–P and (D) –As/+P. (E) Transmission electron micrography of +As/–P GFAJ-1 showed internal vacuole-like structures. Scale bars are as indicated in the figure (11).

NanoSIMS analyses of GFAJ-1: extracted DNA and whole-cells elemental ratio maps. (A) Agarose gel loaded with DNA/RNA extracted from GFAJ-1 grown (lane 2) +As/–P and (lane 3) –As/+P as compared with (lane 1) a DNA standard. Genomic bands were excised as indicated and analyzed with NanoSIMS. Ion ratios of 75As–:12C– of excised gel bands are indicated below with 2σ error shown (all values multiplied by 10−6). (B to G) NanoSIMS images of whole GFAJ-1 cells grown either [(B), (D), and (F)] +As/–P or [(C), (E), and (G)] –As/+P. Shown are the ion ratios of [(B) and (C)] 75As–:12C–, [(D) and (E)] 31P–:12C–, and [(F) and (G)] secondary electron (SE). Ratios in (B) and (C) are multiplied by 10−4 and in (D) and (E) are multiplied by 10−3. The color bars indicate measured elemental ratios on a log scale as indicated. Length scale is as indicated on images; images contain equivalent pixel density (11).

Comment on “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus” James B. Cotner, Edward K. Halllow P content is a common phenotype across a broad range of environmental bacteria that experience P limitation.

Steven A. Benner If such arseno-DNA exists, then much of the past century of work with arsenate and phosphate chemistry, as well as much of what we think we know about metabolism, will need rewriting.Extrapolation of this to the pH of Mono Lake (pH ≈ 10) gives a pseudo first-order rate constant ≈ 10 s−1; extrapolation to pH ≈ 7, perhaps the pH inside of the cell, gives a rate constant ≈ 0.01 s−1, corresponding to a half-life for each linkage in the hypothetical arseno-DNA of approximately 1 min…… estimates suggest that the phosphate diester in DNA has a half-life in water of ~30 million years ……Alternatively, we must envision an entirely novel way of making triphosphates so that an arsenic atom can be tucked away within a chain of atoms, or a novel way of assembling DNA. …. arseno-DNA would seem to fall into the category of “exceptional” that, as Carl Sagan remarked, requires exceptional support.

B. Schoepp-Cothenet, W. Nitschke1, L. M. Barge, A. Ponce, M. J. Russell, A. I. Tsapin arsenate redox chemistry undermines the suggestion that arsenate can replace the physiologic functions of phosphate.

Patricia L. Foster arsenic may have stimulated the bacterium’s high-affinity phosphorus assimilation pathway, which is active when phosphate levels are low.

István Csabai and Eörs Szathmáry the authors reported the As:P ratio for both the +As/–P (7.3) and the –As/+P (0.002) conditions. To arrive at these ratios, the authors calculated the ratios for each individual sample measurement and then averaged the ratios. Averaging ratios in this way is incorrect. …. The error for the As percent by dry weight (±0.25%) is larger than the value itself (0.19%), so the null hypothesis that the +As/–P sample contains no As, cannot be excluded. … there is no reason a sample would contain less P than the blank gel itself. If we do so, we see that the amount of P is only slightly higher in the –As/+P samples. ….etc.

Homework: Select 3 logical fallacies and explain their meanings