No mutation, no novel heritable variation. No variation, no adaptation. No variation, no evolution. No evolution, no biodiversity. No biodiversity: priceless.
All scientists must take sides. Everything in science is an argument or an inquiry. Every scientific study makes claims about the natural world (gathered by the author or not), and it is the duty of scientists to present and interpret her findings via manuscripts, posters, talks, and other forms of sometimes public outreach. In communicating scientific ideas, scientists invariably argue for different perspectives on the significance and meaning of their findings, and their relationship to the rest of science, including the closely related work of others. Darwin's major scientific work, the Origin, represented/represents a synergistic volume condensing masses of primary scientific discoveries and arguments, including some speculations (what makes science writing exciting!), into one BIG argument for organic evolution by natural selection. His postulates were as follows,
(p1) There is variation in nature,
(p2) Varitions get passed from parents to offspring, from one generation to the next (though Darwin did not have modern genetics to understand how this is accomplished; he supported an idea of genetic "blending"),
(p3) In each generation, more offspring are produced than can survive, and mortality is non-random, with the most "fit" offspring being those having heritable traits making them capable of withstanding environmental changes, survive and reproduce in that environment, thus pass their heritable variations to the next generation,
(C) Therefore, the traits of species are naturally selected to fit the changing environment through time.
This is the argument for natural selection, descent with modification by non-random mortality due to differential fitness of heritable genotypic/phenotypic variation. From the argument, it is clear evolution proceeds in a non-random, not-by-chance fashion antithetical to common misconceptions. Also, this is a testable set of ideas which has yielded empirical research on natural selection both in the laboratory and in nature. As important as this argument may be, there are several other mechanisms of evolution (i.e. mutation, migration, genetic drift), and we will leave natural selection to discuss an arguably more fundamental mechanism of evolutionary change played on in the introductory sketch, mutation.
Genetic Mutation
We have discussed previously how independent assortment of alleles into our gametes combined with proabilities of chance associated with fertilization in diploid, sexually reproducing organisms is capable of introducing genetic variation in natural populations. But this occurs without mutation per se.
Mutation is the ultimate source of new genetic information, information necessary for different evolutionary mechanisms to effect evolutionary change through time. Therefore, it is important we recognize chromosomal and lower level sources of genetic mutation as the actual material evolutionary forces work with, for and against. Central questions to guide this discussion might be, what are mutations, how do they happen, at what rate do they occur, and what are their consequences in individuals and populations?
Recall the central dogma of molecular biology states that DNA is transcribed into mRNA (inside the nucleus), which is translated into amino acid sequences of proteins by ribosomes through specific biochemical interactions in the cytosol. The discovery of nucleic acids, these patterns, their mechanisms and implications has led to the following definitions, which get us off to a good start: mutation is any change in the nitrogenous base sequence of DNA, genes are sequences of DNA that code for particular proteins, loci are the physical molecular "addresses" of genes along the sequence of an organism's hereditary material, and alleles are versions of genes coding for the same protein but having different sequences of DNA (than the "wild type"). That said, there are multiple types of mutations in nature.
Some genetic variation stems from the chromosomal basis of inheritance and associated mutations, which we have also touched on elsewhere. Meiotic synapsis and crossing can over lead to different arrangements of genes on chromosomes. This is not only a source of new mutation, but a source of whole new genes! How? Whenever chromosomes are unequally paired (physically out of alignment) by the synaptonemal complex, crossing over can duplicate copies of genes. These extra copies are very important, because they may mutate and differ in their function at later points in time, creating new genes. Also, sections of chromosomes sometimes jump from one homologous pair to another (e.g. chromosomal translocation), and whole pieces of chromosomes may rearrange spontaneously in our cells (e.g. chromosomal inversion). These chromosomal changes alter DNA sequences at large scales and may lead to terrible disease in individuals (e.g. Down syndrome, Klinefelter syndrome, and Turner syndrome in humans).
Genetic mutation at the most basic units of DNA, base pairs, represent the most physically restricted and specific units of genetic mutation. These can be classified into different groups. When single base pairs (A,C,G,T) are substituted one for another, point mutations are said to occur. When DNA replicates itself during the cell cycle (S phase), chemical changes in base pairs are relatively frequent. Fortunately, vertebrate DNA replication machinery also has a repair mechanism for such cases. When DNA repair fails, point mutations result where, for example, an A may be left in place of a G. There are two different classes of point mutations, (1) transitions, where pyrimidines are substituted for pyrimidines and purines are substituted for purines and (2) transversions, where pyrimidines are substituted for purines and vice versa. Evidence suggests transitions are far more likely in nature (2:1 or 3:1; thus phylogenetic studies of DNA sequence information often give different statistical weights to transitions and transversions). An important question for you might be, how do I remember which changes are transitions vs. transversions? Well, adenine and guanine are purines and cytosine and thymine are pyrimidines. Perhaps, you can remember, as I do, that the ancient Egyptians built the PYRamids and also are reknown for domesticating and worshiping Felis catus / Felis silvestris catus (domestic cat/house cat). It's true!.
The effect of point mutations is also dichotomous. Because transcribed DNA takes the form of mRNA, whose three-base-pair sequences called codons code for different amino acid additions during translation, point mutations change the composition of codons. These changes may or may not result in changes in amino acid sequences of proteins; respectively, these changes are referred to as nonsynonymous (a.k.a. replacement) substitutions and synonymous (a.k.a. silent site) substitutions. However, whether point mutations are synonymous or nonsynonymous, they always produce new alleles, therefore mutation.
As the modern synthesis developed in the early twentieth century, a classical group of geneticists suspected the genetic variation in nature was marginal, with natural selection weeding out useless mutations such that only the most fit genes survived the test of time. Modern genetic research, however, has confirmed the opposite is true. There turns out to be much more genetic variation in nature than early geneticists thought. In fact, the evidence shows that mutation rates, on a per genome per generation basis, are similar across many different kinds of taxa and highly influenced by the number of cell divisions before reproduction. Organisms with longer generation times, with longer lives and longer periods of cell growth and division between reproductive events, tend to display higher rates of genetic mutation. Taking the number of cell divisions into account, we find out living things have even more similar (but high) mutation rates. Each individual in mammalian populations harbors unique genetic mutations based on experiments involving simple, obvious phenotypes. Imagine how much more genetic variation is present, yet undetected, as silent site mutations and other kinds of covert genome duplication and rearrangement!
Despite the great amount of mutation thus variation present in natural populations, mutations are also rare in the sense that many mutations come from slips in the DNA replication and repair machinery, which turn out to be incredibly accurate.
The field of molecular genetics is divided in controversy over answering the question, "Why are populations are genetically diverse?" On the one hand, the balance or selectionist school of thought claims that natural selection is a major force driving the diversity of populations because selection favors mutant individuals with rare traits in changing or novel environments. On the other hand, the neutral theorists make a very convincing claim that most mutations are functionally and selectively equivalent (and deleterious), and that the natural world is genetically diverse because selection fails to get rid of them, to cut them from the team, prune them from the tree, so to speak. ~ JB
Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts
Tuesday, July 31, 2007
Saturday, July 21, 2007
Darwin to Central Dogma: How We Get Protein from the Genetic Code. Part I
Once upon a time, a wise man said, "Timing is everything." A major difficulty of Darwin's theory of organic evolution by natural selection (1859), as revolutionary as it has been, resulted from the timing of his life and work. Don't get me wrong, Darwin's theory came at a crucial point in the development of modern science and was only made possible by the discoveries just preceding his work. But it was constrained by the ignorance and interests of the scientific community of its day.
Darwin constructed a theory that explained how natural environmental forces and interactions shaped the evolution of heritable traits in a non-random fashion, giving a mechanism responsible for the design and diversity found in the natural world. Based on systematics, geology, developmental embryology, biogeography, popluation studies and a host of other evidence, Darwin devised the unifying theory of biology, no bones about it. What he lacked, however, was a robust theory of how these traits were passed from one generation to the next. Enter: the biologists' favorite monk.
Gregor Mendel was a Moravian monk. His birthday was July 20, 1822. His alma mater was the University of Vienna. Mendel was a contemporary of Darwin's credited with conducting rigorous scientific inquiry into plant hybridization incorporating experimentation and statistics (probability theory). Mendel worked out two simple theories of inheritance that form the basis of modern genetics: (a) the theory of segregation and (b) the theory of independent assortment of alleles. Around 1865, Mendel published a few papers on his inheritance work. Mendel owned a copy of Darwin's Origin, and it is thought his writing reflects a Darwinian influence in some passages; conversely, Darwin was also familiar with Mendel's work although he did not possess copies of Mendel's few papers. Had not Mendel substituted activism and religious duties for his scientific research a short time after his publications, his findings might have been acknowledged. Instead, his work was never fully appreciated until after his death, when several scientists rediscovered and redistributed his papers and quickly developed a modern theory of inheritance based upon them.
Modern advances in statistical analyses and population genetics based on Mendelian inheritance theory were merged with Darwin's theory in the early 20th Century in what is now known as the "Modern Synthesis" of evolutionary thought. Key players in this synthesis included biostatisticians, early geneticists, population biologists such as Morgan, Mayr, Fisher, Wright, Simpson, Haldane, et cetera. As genetics developed, it became understood that variation in heritable traits were the result of genetic variation due to gene mutation at the chromosomal level, then the molecular level as DNA was established as semi-conservatively replicated genetic material by Hershey, Chase, Watson, Crick, Franklin, Meselson, Stahl, and others.
Meanwhile, since the 1930s, studies of biochemical metabolism and biosynthesis had been laying the foundation for uncovering what Francis Crick would later call the "Central Dogma of Molecular Biology." This discovery had its origins in a theory that single genes directed the synthesis of individual enzymes responsible for key biological functions as players in biochemical pathways. In the modern era, Crick and others empirically tested this hypothesis and revealed the answer to how phenotypes, in the form of proteins, arise from specific sequences of DNA, or genotypes. The Central Dogma states that DNA, sequences of nucleic acids, is transcribed into RNA, which is then translated into proteins, sequences of amino acids. These proteins may be enzymatic or non-enzymatic; regardless, they influence the function of living things from cellular to organismal levels.
But how does this happen? How does "biological information" get transferred?
Overview Figures:
DNA transcription
(in depth look at processes starts in Part 2)
Darwin constructed a theory that explained how natural environmental forces and interactions shaped the evolution of heritable traits in a non-random fashion, giving a mechanism responsible for the design and diversity found in the natural world. Based on systematics, geology, developmental embryology, biogeography, popluation studies and a host of other evidence, Darwin devised the unifying theory of biology, no bones about it. What he lacked, however, was a robust theory of how these traits were passed from one generation to the next. Enter: the biologists' favorite monk.
Gregor Mendel was a Moravian monk. His birthday was July 20, 1822. His alma mater was the University of Vienna. Mendel was a contemporary of Darwin's credited with conducting rigorous scientific inquiry into plant hybridization incorporating experimentation and statistics (probability theory). Mendel worked out two simple theories of inheritance that form the basis of modern genetics: (a) the theory of segregation and (b) the theory of independent assortment of alleles. Around 1865, Mendel published a few papers on his inheritance work. Mendel owned a copy of Darwin's Origin, and it is thought his writing reflects a Darwinian influence in some passages; conversely, Darwin was also familiar with Mendel's work although he did not possess copies of Mendel's few papers. Had not Mendel substituted activism and religious duties for his scientific research a short time after his publications, his findings might have been acknowledged. Instead, his work was never fully appreciated until after his death, when several scientists rediscovered and redistributed his papers and quickly developed a modern theory of inheritance based upon them.
Modern advances in statistical analyses and population genetics based on Mendelian inheritance theory were merged with Darwin's theory in the early 20th Century in what is now known as the "Modern Synthesis" of evolutionary thought. Key players in this synthesis included biostatisticians, early geneticists, population biologists such as Morgan, Mayr, Fisher, Wright, Simpson, Haldane, et cetera. As genetics developed, it became understood that variation in heritable traits were the result of genetic variation due to gene mutation at the chromosomal level, then the molecular level as DNA was established as semi-conservatively replicated genetic material by Hershey, Chase, Watson, Crick, Franklin, Meselson, Stahl, and others.
Meanwhile, since the 1930s, studies of biochemical metabolism and biosynthesis had been laying the foundation for uncovering what Francis Crick would later call the "Central Dogma of Molecular Biology." This discovery had its origins in a theory that single genes directed the synthesis of individual enzymes responsible for key biological functions as players in biochemical pathways. In the modern era, Crick and others empirically tested this hypothesis and revealed the answer to how phenotypes, in the form of proteins, arise from specific sequences of DNA, or genotypes. The Central Dogma states that DNA, sequences of nucleic acids, is transcribed into RNA, which is then translated into proteins, sequences of amino acids. These proteins may be enzymatic or non-enzymatic; regardless, they influence the function of living things from cellular to organismal levels.
But how does this happen? How does "biological information" get transferred?
Overview Figures:
DNA transcription
(in depth look at processes starts in Part 2)
Monday, July 16, 2007
Sex, Lies, and ... Meiosis
Continuing my theme on "10 Things Every Biology Student Should Know," what is meiosis and, considering it may be a boring topic for most, why is it of interest from a Darwinian view of life? That's where we're going. In the process, we'll talk about sex and lies, no doubt.
Many living things lead sexual life styles. Although there are several different types of sexual modes of operation, as those in some plants and fungi, we will focus on sexual life cycles in animals, including humans ("We're all sexual people, with so much love to give" - Marvin Gaye). Homo sapiens and other vertebrates are physiologically made up of many, many millions of somatic cells. These comprise most of the body and are not passed directly to offspring. Another set of cells, termed the germline, is comprised of all gamete cells and gamete-producing cells from gamete to zygote and back (Fig. 1).
Figure 1. This diagram reveals the "dead end" nature of somatic cell lines in relation to the theoretically eternal germline (reference).
After fertilization, some of our cells go on to specialize in gamete (sperm or egg) generation. These are located in the male testis and female ovary. This is not a new concept. However, as Fig. 1 points out, it is important students of biology realize somatic cells are never passed on from one generation to the next under normal conditions (e.g., barring mutation of somatic cells). That's why your liver cells are not inherited from your parents. For the empirical materialist, this is evidence for the idea of the selfish gene, which Richard Dawkins set forth in his book by the same title. Some philosophers use this fact and others about somatic and germ cell lines to make arguments with important implications for not only how we view the world, what we can learn from these facts, but also about applications of this knowledge in medical studies; for example, stem cell research.
So, we have sex, which drives much of the advertising industry and is a major player in people's behavior and a major influence upon American culture (music, clothing, tv shows, language, etc.), which tends to direct the rest of the world's societies for good or bad. The fact of sex does not set us far apart from the many other animals with sexual life cycles. So, we are like animals in this respect. But I'm not going to discuss that claim. A major question that all human beings grapple with is, "Why do we have sex?" In response to this important issue, I am, however, going to make the claim that sexual reproduction is likely to have been conserved for a variety of reasons which only make sense in light of evolution. There are many many reasons--perhaps you can name several from your own experience, even--why sex has negative effects, why sexual life cycles aren't perfect systems.
"What are the negative aspects of sex?" you say. "Why would he say sexual reproduction is a bad way to operate, in the loose sense? What's wrong with the human reproductive system?" Well, among other things, sex consumes a large amount of time, resources, chemical energy, and so on. Also, our plumbing seems a bit off down below, especially for the males of our species, who have all their genetalia dangling out in the environment (necessary because body heat negatively effects sperm production, unnecessary because of other more obvious problems including physical damage). Add to these difficulties associated with obtaining mates (e.g., competition), and it seems sex is an awfully troublesome means of getting the reproduction job done. So what is the evolutionary significance of sex? The answer lies in the chromosomal basis of inheritance and the mechanisms responsible for genetic variation related to meiosis and other genetic processes. I am going to discuss reasons why evolution has selected this modus operandi anyway and will be detailing the way our bodies generate and pass gametes from one generation to the next, with an emphasis on the contrast between mitosis and meiosis.
Meiosis
I have discussed the cell cycle and mitosis at length. Recall, mitosis is the body's means of increasing the number of cells in a living organism and in part this is due to the fact that increasing the surface area of cell connections and maintaining small cell size increases the speed and efficiency of cell signaling, nutrient processing, and cell packaging and shipping of cellular products, et cetera. Mitosis starts with a single diploid cell and generates two copies of the original starting material (roughly exact copies). Our somatic cells undergo lots of mitotic divisions (some of them, others to a lesser extent/rate). So, for every action, there is an equal and opposite reaction. Meiosis is our bodies counter to constant division, because it is the sole means of reducing the body's ploidy number; meiosis reduces chromosome number by generating four haploid cells from a single diploid cell.
Figure 2. Mitosis vs. Meiosis.
Mitosis involves prophase, prometaphase, metaphase, anaphase, telophase and cytokinesis in sequential order. Meiosis involves the same steps, but carries out the phases twofold with a modification of theme. Every time meiosis happens, it happens again for the same daughter cells, generating four haploid cells (Fig. 2, right side).The main difference between mitosis and meiosis (which is just mitosis X2), is that during metaphase (metaphase I) homologous chromosome pairs line up in tetrads and experience synapsis and crossing over at the center of the cell. In contrast, individual sets of duplicated chromosomes line up during mitotic metaphase. Also, sister chromatids remain connected to one another in meiosis during anaphase I, while during mitosis these are the objects being pulled apart toward different cell poles on microtubule spindles. For the most part, that's it (of course, there are some details we've glossed over). If that's where your high school biology teacher or professor stopped talking or you stopped listening, or if you missed that day of biology class, let me explain the coolest part of this whole idea of chromosome splitting and cell duplication and gamete production.
Darwin and Meiosis
Darwin recognized the importance of heritable variation in nature. He studied natural and artificial phenomena. Then from a diverse set of facts, he contrived a consilient explanation for how this variation is used as raw material for descent with modification, or evolution. However, we are all subject to the ignorances of our times, and Darwin is not immune to this funny little fact about the human condition. There were many things his generation never came to know that we have discovered in the nearly 150 years since his death, a time of rapid scientific and technological progress. For our purposes, the most important of these were the genetic, molecular and chemical mechanisms of inheritance described by geneticists based on the work of that famous monk, Gregor Mendel.
The biodiversity around and within us could not be possible without mechanisms generating diversity, the chief of which is molecular mutation, which comes in many different forms. Aside from mutation, however, other powerful forces shape the genetic variation found in the natural world. Several of these processes have their origin in the statistical ramifications of the physical acts during meiosis, hence resulting from sexual life cycles. Three of these would be independent chromosomal assortment, chiasmata, and randomization of fertilization.
Not only has meiosis aided in the generation of genetic variability in nature, but also it has an evolutionary history of its own. For example, because of genetic differences, human meiosis is more advanced than forms of division found in some insects (Bogdanov 2003). Meiosis and sexual reproduction are thought to have evolved early in evolutionary time in unicellular organisms, and are controlled by hundreds of genes (Bogdanov 2003).
So, you've been no doubt wondering all this time where the "lies" in the title come in, right? Simple. The lie is that meiosis, life cycles, and chromosomal evolution and associated gene expression, regulation, and cellular processes are "boring." That's the lie. In fact, these represent exciting areas of research, even disease research, which are uncovering more and more about an integral process that evolved in some of our most ancient sexual ancestors. Think about that the next time you put on Marvin Gaye or Barry White! ~ JB
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References
Bogdanov, Y. F. 2003. Variation and evolution of meiosis. Russian Journal of Genetics 39:363-381
Thursday, July 12, 2007
TED, war, and the Intelligent Design-evolution controversy
Just recently, I became informed about TED, the nonprofit organization Technology-Entertainment-Design founded in 1984 to increase the spread of great ideas from the best and brightest thinkers in the world. You should take note of this company as well because each year they host a series of talks limited to 18 minutes, many of them videotaped, by just those people who matter most--the thinkers, the problem solvers, the entertainers, the communicators who inspire, who dare seek new knowledge and whose ideas change the future. Check it out.
I learned about TED because my interest in evolution and its product, the biodiversity around and within us, led me to seek a talk by E. O. Wilson, the famous myrmecologist from my home state of Alabama, who was unveiling his dream to form the Encyclopedia of Life (EOL; a talk you should watch when you visit TED's site). After watching his eloquent and creative discourse dreamcasting a vision for something so near and dear to my mind, its emotional and rational centers, I next clicked a hyperlink to hear Richard Dawkins' talk given, I believe, at the same conference.
In his talk, the Oxford professor nicknamed Darwin's rottweiler, outlined a course of action for atheist darwinists: come out of the closet with a purpose of vocally and militantly expressing a wake-up call to the world: Darwinian evolution by natural selection is hostile to religion, which is equivalent to a virus which infects the world by childhood indoctrination leading to anti-intellectualism, xenophobia, racism, sexism, terrorism, contempt for honest pursuit of truth, and the naievte of blind faith, and so on. As electrifying and discussion-sparking as this topic is and can be, what I found more incredible was the reasoning behind it. Dawkins points out in his talk how the religiously-fueled ignorance of our times has led to major misunderstandings and political and religious debate about evolution, the opposition calling themselves creationists, or proponents of "intelligent design." This debate has recently heated up to the point of being one of the most intriguing and hottest topics in philosophy, biology, and theology today. The reason I am writing this is that I agree with Dawkins on at least one point. This is war.
Like many others, I'm not sure whether I'm willing to commit to a position that says religion is useless, baseless, and that its bad weighs out its good in the function and roles of society, that Darwinism absolutely results in a rejection of all religious and spiritual belief. Richard Dawkins and Daniel Dennett represent prime examples of philosopher-scientists who radically support a materialistic view of science and the mind. On the other hand, I am more than sympathetic to and more than angry about the fact that a well-funded, conservative, anti-evolution coalition is trying to challenge evolution theory, to debate with science using political and pseudoscientific tactics, and to re-define for their own purposes the nature and regulation of the scientific enterprise, even of society.
I would like to think it necessary to burst on the scene, expose the liars and frauds, dish out powerful testimony against evil-doers I speak of, publish eloquent and popular books, and vanquish my foes--the foes of humanity, perhaps--once and for all, while gaining fame and fortune or at least a little respect that Rodney Dangerfield couldn't. I would like to be the first person to stand up and refute the "scientific" propositions of creationists, to discredit and disprove their stance to the point it be crushed under the weight of the truth. But I am not T. H. Huxley. I am not Michael Ruse. I am not Kenneth Miller. Sadly, brothers and sisters, it is not for me to do any of these, as far as I am aware. Why? Because they have already been done!
Over one hundred years ago, scientific debate about the validity--the fact--of organic evolution by natural selection was settled by scientists for the world. In parts of Europe and the United States, however, this argument has been resumed over the past few decades. Not for scientific reasons, either. Instead, a political, philosophical, and religious movement I have noted has supposedly brought this issue back into the arenas of public debate. Many, many minds have been engaged. I would like to point you to the truth, one that will lead no fair-minded and intelligent person astray. As I have studied philosophy and science and followed this debate for many years, this may take several posts. As a matter of fact and duty, it's worth taking years to follow this debate, maybe even (I hope not) my whole life, if need be. It is my opinion that everyone should become educated about this important debate because we cannot afford to lose what's at stake: scientific education, science-religion relationships, the way we think about the earth including the biological realms, the way we view our humanity, the way we view our work, et cetera.
As I consider how to present this, I must build upon the directions I started in. The fact is the cat's out of the bag. Intelligent Design (a dressed up for Sunday church version of creationism, or design theory) was taken on by Darwinian evolution, by modern science and philosophy and defeated long ago. This horse has been dead for years. So why still hit it? Hidden agendas. Money. Fame. Desire to impose one's own beliefs upon others. Public Relations. These sum up, in part, the motivations of the creationist Opposition. Since the intelligent design (ID) creationist movement is literally dead in the water already, I feel like it would be a good start for me to upload hyperlinks to information from both sides of the modern argument, so that you can click on these resources and learn about them yourself. So, your homework assignment, class, will be to read all this material, consider it thoroughly in your minds, then get back to me and tell me (a) which side you think is winning, (b) what you think science is, (c) how you define evolution vs. creationism/ID, (d) what the purview of modern science is vs. reasons for the debate, and (e) how you feel this impacts your view of yourself, your world, your beliefs about the world, and your desires for your life and that of others. Ok?
So, I'll set the stage by explaining a bit about the sides (providing links, citations), and then set you loose.
SO, the losing side is the ID side. The winning side is and must be that of biology and its central theorem, descent with modification through natural selection and other mechanisms. What we are on the verge of is the absolute loss of all theological and religious credibility, the complete abolishment of ID's "scientific legitimacy" (I believe this has already taken place), the ruin of several people's careers, the improvement of science education, more education for the masses, more scientific discoveries, and a growing hostility towards religion, which will continue to be degraded by modern science a little each day from this day forth. Ok? Like it or not, this is the truth about the world, or nearly so. But who are the major forces, who will the players be in the future? That's what I've been holding out on, enjoying your captivation for this whole time.
THE LOSERS
First, let us discuss the "losers." That would only be courteous. Creationists claim, in essence, that the world is too complex to be understood, so they envoke a supernatural force, a "designer" whose hand has been at work setting the unique wonders of the natural world in their respective places from before time began--namely, God or Allah or whatnot--as an explanation for what science "can never figure out." The argument goes, "At some point, the universe breaks down so that I cannot understand it. At that point, I decree by fiat that God is the only explanation for those things I cannot know." Put another way, the argument may sound like, "The biological world is so well put together, so irreducibly complex, that it gives the appearance of something intelligently designed, thus a designer must have been active in its origin." This teleological (circular) argument dates back to 1802, when William Paley published the argument from design in his book, Natural Theology. His argument was a watch's fine innerworkings implied a watchmaker, thus so too did the wonders of nature imply a designer, or God. This line of reasoning supported the widely held religious/scientific theory of special creation, which stated that the world was created by God (often, this was taken in reference to the Genesis account of creation in the christian Bible), with species being relatively fixed but adaptively plastic essences which did not change ultimately through time (this reference gives better historical background; though I cannot agree with it fully, it is a 127 year old perspective that should be considered by anyone weighing the evidence in this debate; other references include this fine evolutionary biology textbook, which discusses both sides; also look here; and see this link, where a scientist reviews a book by a theist in 1898, the year my great-grandfather was born).
When Darwin published his major work, On the Origin of Species... (1859), it provided a testable scientific explanation of facts (a theory) gathered from Darwin's readings and discussion about naturalistic phenomena, which was a powerful and influential proposition. The theory of evolution by natural selection, or Darwin's main argument in his book, was important first because it provided a mechanism explaining biological diversity, but second because it infinitely crippled the theory of special creation and the argument from design. No longer could supernatural arguments be used to argue about natural phenomena. Design arguments were trumped in the sense that Darwin's theory showed that incredible complexity could arise by gradual change of form, without envoking a designer or vital force. Not only did this argument win on its face, but this was a more parsimonious explanation (click the link for Occam's Razor). These facts known in 1859, as well as many others gathered and published in scientific and philosophical journals up to the present day, close the coffin on the Opposition.
In the 20th Century, a right-wing religious group began pointing fingers at evolutionary theory as the root of many different sins and evils found everywhere in society, especially as this theory became associated--even synonymous with--atheism. These activists claimed that homosexuality, sexual immorality, atheism, disease, and many other problems had their origin in evolutionary thought influences upon culture. Since the 1800s, religion has lost converts because evolution does, in fact, often lead to atheism. In the 1970s, a movement based in conservative Presbyterianist congregations that has now continued to encompass christians of many different denominations began developing a movement which crystallized in the late 1980s and early 1990s in the current creation-evolution debate. This movement is called Christian Reconstructionism (also read here, here, and here). Luckily, it is headed toward its demise.
Christian Reconstructionism (ChR) is something all the losers, including you if you place your rational faith and belief in intelligent design/creationism, support because it is a major political force funding and negotiating the creationist movement, particularly in America. Ultimately, conscious or not, by supporting ID, people are supporting this movement. Christian Reconstructionists believe (a) the word of god in the Bible is inerrant (but fails to prove this; in fact, many young christians today struggle with doubts over the contradictions in the Bible, especially when looking at the Old and New Testaments side by side), (b) christianity is the only correct religion, (c) Old Testament moral law applies to all people and all nations except those laws which other parts of the Bible later came to replace (which really means contradict, if we speak literally), (d) that Calvinism is required to obtain eternal life and effect social changes of the movement, (e) Christ will return after the whole world is evangelized or nearly so, (f) atheistic society will self-destruct and leads to moral decay a prioi, and (g) that ChR will result in suppression of all other world religions and reversion to Old Testament law including stoning of adulterers and homosexuals, no body piercing, no tattoos, etc, and that the world will be evangelized and Christ will return after they peacefully alter political and legal conditions to reconform to Old Testament Hebrew scriptural states. This is the most ridiculous thing I or any other thoughtful human being have ever heard of!! Is it not? A major problem is that these views are weakly aligned with much christian teaching and practice, but they represent a going-by-the-wayside extreme fundamentalist minority, which has been discredited.
Now, whether you are an IDer or a Darwinist, do you want those kinds of people in control of society and the fate of the world in accordance with their beliefs? How, Christian, will the Hindu, the Buddhist, the atheist, the Thor worshipper, the Wiccan, your neighbors and friends respond to this movement? How are they responding? Well, given the current failure of religious-led/supported government, probably not so favorably. And with good reason. Not only is this cause completely militant and purposeful in its attempt to find dominion over the earth for the Lord, but also they have been carrying out their plans secretly, immorally, and unscientifically.
In case you didn't know, rotten is the new slang for morally or logically wrong or unacceptable (also look here). I think this is a fitting description for the Discovery Institute (see their website, Discovery Institute Intelligent Design Campaigns and Wikipedia description of DI), the major "think tank" of the ID/Christian Reconstructionist movement. Dr. Michael Behe, a biochemist at Lehigh University in New England, is the "posterboy" of this group, one of the few valid scientists in the ID ranks. He and other famous scientists and philosophers, most notably William Dembski represent key spokesmen for the ID side. To give you an example of how unethical this group is, just check out the website above. Notice anything fishy? (1) A group of mostly religious scientists, writers, and politicians describe throughout the website ludicrous responses to real science and the "winners" despite major losses, (2) they present pseudoscience, and (3) the images, production, and website name on this website and related materials give the false impression of a reliable source of scientific information (Look here for debunking article about the website banner. Why would DI give away their rottenness with their banner? Slight of hand. They want you to believe they represent scientific and faith authority.). In disguise, the DI slams evolutionary theory, science, and society. You and I had better watch who's talking and watch who's podcasting and watch which resources our sources cite and get their data from. Does it reference the DI? If so, beware of this group and the innane plot I have described.
"So, what?" is a common question among the learned and skeptical. I ask it about nearly everything I hear or read. It is my duty as a biologist to always it about science. So, what if you don't believe me when I say this is true? All around the world there is evidence of biological processes pointing to facts about evolution (you can interpret this as evidence about God's direction of the world, but this is non-science). Readily available by mail, books, articles, magazines, and the internet are credible resources that back up every claim I am making. Books and articles by real, even religious scientists like Dr. Kenneth Miller expose the major flaws, failure, and immorality of the ID/ChR movement (both are wrong, whether people take one or both sides). Thousands of peer-reviewed books and articles in scientific journals testify against creationism. Even religious people, like myself, have turned from creationism to accept the truth of evolution as fact. Hesitant to believe the plot I've outlined? Then you'll be even happier to know that the IDers years ago formulated a plan for their take-control of American science education, the extinction of evolution and so on. It is called the Wedge Document and was leaked within the last decade just before key court cases pronounced ID as "unscientific" and thus completely without scientific basis, conferring upon it NO PLACE in the science classroom. Here is a copy of the Wedge Document. Here is another, also from a creationist. You can read it for yourself.
From the language of the Wedge strategy, which prominent political scientists, biologists, and educators such as Dr. Barbara Forrest have exposed and criticized, the ChR/ID movement makes several claims to support their social, religious revolution. They make it abundantly what their position entails (though there's much they are holding back, like the rest of radical Christian Reconstructionism). The Wedge starts off with their central theorem: man was made by God in the image of God and this is the foundation of Western civilization. This has its origins in Genesis (for the christian, so far, so good). Then, they move on to describe their opponents. Their claims are that the fight began when the rise of modern science brought with it a materialism in direct contradiction to what thier own beliefs held (theism, dominionism, man as God's image, etc.). This materialism, says the Opposition, gave rise to moral decay, philosophies which were not so egocentric or anthropocentric, and utopianism. The Wedge, brought down from Mount Siani by Dr. Phillip Johnson and friends, goes on to say,
"Discovery Institute's Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies. Bringing together leading scholars from the natural sciences and those from the humanities and social sciences, the Center explores how new developments in biology, physics and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature. The Center awards fellowships for original research, holds conferences, and briefs policymakers about the opportunities for life after materialism." (emphasis added)
In the sames spirit Ken Miller has written in concerning Michael Behe's new book, which he reviewed in a piece published in Nature, the Wedge makes "a nice argument, except for the annoying fact that it is wrong." And it is wrong on many counts. A major conclusion of Christian Reconstructionists supported by other creationists is that evolutionary theory brooded materialism. This is a fact. But this fact requires some explanation, because materialism is not very well understood by laymen as a result of multiple use. On the one hand, materialism refers to preoccupation with material things and desires overruling the spiritual in the lives of humans; on the other, materialism is a view of the world contending the world and universe, a priori or operationally, are made of matter or material objects and not supernatural ones. The Wedge and ChR/ID revolution is really worried about both of these, but targets the second because of its place in the philosophy of modern science. To clarify, we are talking about the second kind of materialism here!
Scientists follow either ontological naturalism or materialism (ON, OM) or methodological naturalism or materialism (MN, MM), or some variation of this theme. MN says that there is no supernatural entity or vital force considered in scientific work because science is about testable or falsifiable predictions and explanations based on materialism and supernatural things or theories do not fit this definition, thus are non-scientific. ON goes one step further and says there is no supernatural thing anyway, so why bother acknowledging it in this way. Militant atheism is joined to ontological naturalism and radical materialism, as that supported by Dennett and Dawkins and, to a lesser degree of acknowledgement, Frederick Crews and many others.
So, we see that science can be seen as more of an occupation, but many times is an integral part of someone's world view or ideology, if not comprising most of their set of normative ideas. The ideology of science has been called scientism. I am learning about this now. It seems closely allied with the calls from creationist camps about the deification of Charles Darwin and the faith of scientists in their "religion" of materialism. I confess I don't know much about it and want to know more. The point is that whether you see science as a category, a concept, an ideology, or what, supernatural phenomena are not scientific in the strong or weak sense of the word. These distinctions hold the not-so-secret key to other reasons why the ChR/ID movement fails.
For one thing, they contribute to exposing the Opposition as a movement which lacks integrity. But I'm not sure how important this is, because these kinds of attacks seem inconsequential in the scheme of things, aside from potentially persuading those mindless people who fail to critically consider the situation themselves. Second, the ChR/ID argument goes A = creationism, B = evolution (materialism);
1. A vs. B
2. B is wrong
C. Therefore, A
This argument rests on the logical fallacy that calls premise 1 especially into doubt. It cannot be as simple as materialism is wrong, therefore the christian reconstructionism/ID is right. In fact, it is likely that the first premise could be infinitely extended to include... or C, or D... to infinite.
Many other Oppostion claims have been met with serious issue, called into question, and defeated in scientific journals, public debates, and courtroom decisions. Sift through these in the materials I provide below. The evidence is overwhelmingly in support of science as science, not the pseudoscience presented by the ChR/ID Opposition.
THE WINNERS
http://youtube.com/watch?v=JVRsWAjvQSg
Barbara Forrest's Position Paper on the truth about the ID movement
http://www.centerforinquiry.net/uploads/attachments/Forrest_Paper.pdf
Skeptical responses to DI "scientific" podcasts
DI homepage, "evolution news and views" (yeah right, from a twisted bunch of radically conservative, pro church/state merger, pseudoscientific, uneducated bastard liars)
Jack Russell Terriers & Cockroaches article (please respond)
Phillip Johnson on THE WEDGE
http://www.touchstonemag.com/docs/issues/12.4docs/12-4pg18.html
"Creationism Research" = oxymoron
http://www.creationresearch.org/creation_matters/pdf/2002/cm07%2004c.pdf
Christian Reconstruction site/book
http://forerunner.com/forerunner/X0505_Parsons_-_What_is_Re.html
Behe's response to critics
http://www.springerlink.com/content/g527h45501l632v8/
Another Behe botch up
http://www.arn.org/docs/behe/mb_brresp.htm
Debating Design Book - both sides presented equally and rationally
http://www3.cambridge.org/uk/catalogue/catalogue.asp?isbn=9780521829496
Absolute Baloney websites illustrate creationist anti-science/design argument:
http://evolution-facts.org/nature1.htm
Get a life, Dakota Voice, you are a fool!
http://www.dakotavoice.com/200706/R/20070619_BE.html
Jim Schicatano gets it all wrong
http://home.att.net/~jamspsu84/ttocmain.html
I learned about TED because my interest in evolution and its product, the biodiversity around and within us, led me to seek a talk by E. O. Wilson, the famous myrmecologist from my home state of Alabama, who was unveiling his dream to form the Encyclopedia of Life (EOL; a talk you should watch when you visit TED's site). After watching his eloquent and creative discourse dreamcasting a vision for something so near and dear to my mind, its emotional and rational centers, I next clicked a hyperlink to hear Richard Dawkins' talk given, I believe, at the same conference.
In his talk, the Oxford professor nicknamed Darwin's rottweiler, outlined a course of action for atheist darwinists: come out of the closet with a purpose of vocally and militantly expressing a wake-up call to the world: Darwinian evolution by natural selection is hostile to religion, which is equivalent to a virus which infects the world by childhood indoctrination leading to anti-intellectualism, xenophobia, racism, sexism, terrorism, contempt for honest pursuit of truth, and the naievte of blind faith, and so on. As electrifying and discussion-sparking as this topic is and can be, what I found more incredible was the reasoning behind it. Dawkins points out in his talk how the religiously-fueled ignorance of our times has led to major misunderstandings and political and religious debate about evolution, the opposition calling themselves creationists, or proponents of "intelligent design." This debate has recently heated up to the point of being one of the most intriguing and hottest topics in philosophy, biology, and theology today. The reason I am writing this is that I agree with Dawkins on at least one point. This is war.
Like many others, I'm not sure whether I'm willing to commit to a position that says religion is useless, baseless, and that its bad weighs out its good in the function and roles of society, that Darwinism absolutely results in a rejection of all religious and spiritual belief. Richard Dawkins and Daniel Dennett represent prime examples of philosopher-scientists who radically support a materialistic view of science and the mind. On the other hand, I am more than sympathetic to and more than angry about the fact that a well-funded, conservative, anti-evolution coalition is trying to challenge evolution theory, to debate with science using political and pseudoscientific tactics, and to re-define for their own purposes the nature and regulation of the scientific enterprise, even of society.
I would like to think it necessary to burst on the scene, expose the liars and frauds, dish out powerful testimony against evil-doers I speak of, publish eloquent and popular books, and vanquish my foes--the foes of humanity, perhaps--once and for all, while gaining fame and fortune or at least a little respect that Rodney Dangerfield couldn't. I would like to be the first person to stand up and refute the "scientific" propositions of creationists, to discredit and disprove their stance to the point it be crushed under the weight of the truth. But I am not T. H. Huxley. I am not Michael Ruse. I am not Kenneth Miller. Sadly, brothers and sisters, it is not for me to do any of these, as far as I am aware. Why? Because they have already been done!
Over one hundred years ago, scientific debate about the validity--the fact--of organic evolution by natural selection was settled by scientists for the world. In parts of Europe and the United States, however, this argument has been resumed over the past few decades. Not for scientific reasons, either. Instead, a political, philosophical, and religious movement I have noted has supposedly brought this issue back into the arenas of public debate. Many, many minds have been engaged. I would like to point you to the truth, one that will lead no fair-minded and intelligent person astray. As I have studied philosophy and science and followed this debate for many years, this may take several posts. As a matter of fact and duty, it's worth taking years to follow this debate, maybe even (I hope not) my whole life, if need be. It is my opinion that everyone should become educated about this important debate because we cannot afford to lose what's at stake: scientific education, science-religion relationships, the way we think about the earth including the biological realms, the way we view our humanity, the way we view our work, et cetera.
As I consider how to present this, I must build upon the directions I started in. The fact is the cat's out of the bag. Intelligent Design (a dressed up for Sunday church version of creationism, or design theory) was taken on by Darwinian evolution, by modern science and philosophy and defeated long ago. This horse has been dead for years. So why still hit it? Hidden agendas. Money. Fame. Desire to impose one's own beliefs upon others. Public Relations. These sum up, in part, the motivations of the creationist Opposition. Since the intelligent design (ID) creationist movement is literally dead in the water already, I feel like it would be a good start for me to upload hyperlinks to information from both sides of the modern argument, so that you can click on these resources and learn about them yourself. So, your homework assignment, class, will be to read all this material, consider it thoroughly in your minds, then get back to me and tell me (a) which side you think is winning, (b) what you think science is, (c) how you define evolution vs. creationism/ID, (d) what the purview of modern science is vs. reasons for the debate, and (e) how you feel this impacts your view of yourself, your world, your beliefs about the world, and your desires for your life and that of others. Ok?
So, I'll set the stage by explaining a bit about the sides (providing links, citations), and then set you loose.
SO, the losing side is the ID side. The winning side is and must be that of biology and its central theorem, descent with modification through natural selection and other mechanisms. What we are on the verge of is the absolute loss of all theological and religious credibility, the complete abolishment of ID's "scientific legitimacy" (I believe this has already taken place), the ruin of several people's careers, the improvement of science education, more education for the masses, more scientific discoveries, and a growing hostility towards religion, which will continue to be degraded by modern science a little each day from this day forth. Ok? Like it or not, this is the truth about the world, or nearly so. But who are the major forces, who will the players be in the future? That's what I've been holding out on, enjoying your captivation for this whole time.
THE LOSERS
First, let us discuss the "losers." That would only be courteous. Creationists claim, in essence, that the world is too complex to be understood, so they envoke a supernatural force, a "designer" whose hand has been at work setting the unique wonders of the natural world in their respective places from before time began--namely, God or Allah or whatnot--as an explanation for what science "can never figure out." The argument goes, "At some point, the universe breaks down so that I cannot understand it. At that point, I decree by fiat that God is the only explanation for those things I cannot know." Put another way, the argument may sound like, "The biological world is so well put together, so irreducibly complex, that it gives the appearance of something intelligently designed, thus a designer must have been active in its origin." This teleological (circular) argument dates back to 1802, when William Paley published the argument from design in his book, Natural Theology. His argument was a watch's fine innerworkings implied a watchmaker, thus so too did the wonders of nature imply a designer, or God. This line of reasoning supported the widely held religious/scientific theory of special creation, which stated that the world was created by God (often, this was taken in reference to the Genesis account of creation in the christian Bible), with species being relatively fixed but adaptively plastic essences which did not change ultimately through time (this reference gives better historical background; though I cannot agree with it fully, it is a 127 year old perspective that should be considered by anyone weighing the evidence in this debate; other references include this fine evolutionary biology textbook, which discusses both sides; also look here; and see this link, where a scientist reviews a book by a theist in 1898, the year my great-grandfather was born).
When Darwin published his major work, On the Origin of Species... (1859), it provided a testable scientific explanation of facts (a theory) gathered from Darwin's readings and discussion about naturalistic phenomena, which was a powerful and influential proposition. The theory of evolution by natural selection, or Darwin's main argument in his book, was important first because it provided a mechanism explaining biological diversity, but second because it infinitely crippled the theory of special creation and the argument from design. No longer could supernatural arguments be used to argue about natural phenomena. Design arguments were trumped in the sense that Darwin's theory showed that incredible complexity could arise by gradual change of form, without envoking a designer or vital force. Not only did this argument win on its face, but this was a more parsimonious explanation (click the link for Occam's Razor). These facts known in 1859, as well as many others gathered and published in scientific and philosophical journals up to the present day, close the coffin on the Opposition.
In the 20th Century, a right-wing religious group began pointing fingers at evolutionary theory as the root of many different sins and evils found everywhere in society, especially as this theory became associated--even synonymous with--atheism. These activists claimed that homosexuality, sexual immorality, atheism, disease, and many other problems had their origin in evolutionary thought influences upon culture. Since the 1800s, religion has lost converts because evolution does, in fact, often lead to atheism. In the 1970s, a movement based in conservative Presbyterianist congregations that has now continued to encompass christians of many different denominations began developing a movement which crystallized in the late 1980s and early 1990s in the current creation-evolution debate. This movement is called Christian Reconstructionism (also read here, here, and here). Luckily, it is headed toward its demise.
Christian Reconstructionism (ChR) is something all the losers, including you if you place your rational faith and belief in intelligent design/creationism, support because it is a major political force funding and negotiating the creationist movement, particularly in America. Ultimately, conscious or not, by supporting ID, people are supporting this movement. Christian Reconstructionists believe (a) the word of god in the Bible is inerrant (but fails to prove this; in fact, many young christians today struggle with doubts over the contradictions in the Bible, especially when looking at the Old and New Testaments side by side), (b) christianity is the only correct religion, (c) Old Testament moral law applies to all people and all nations except those laws which other parts of the Bible later came to replace (which really means contradict, if we speak literally), (d) that Calvinism is required to obtain eternal life and effect social changes of the movement, (e) Christ will return after the whole world is evangelized or nearly so, (f) atheistic society will self-destruct and leads to moral decay a prioi, and (g) that ChR will result in suppression of all other world religions and reversion to Old Testament law including stoning of adulterers and homosexuals, no body piercing, no tattoos, etc, and that the world will be evangelized and Christ will return after they peacefully alter political and legal conditions to reconform to Old Testament Hebrew scriptural states. This is the most ridiculous thing I or any other thoughtful human being have ever heard of!! Is it not? A major problem is that these views are weakly aligned with much christian teaching and practice, but they represent a going-by-the-wayside extreme fundamentalist minority, which has been discredited.
Now, whether you are an IDer or a Darwinist, do you want those kinds of people in control of society and the fate of the world in accordance with their beliefs? How, Christian, will the Hindu, the Buddhist, the atheist, the Thor worshipper, the Wiccan, your neighbors and friends respond to this movement? How are they responding? Well, given the current failure of religious-led/supported government, probably not so favorably. And with good reason. Not only is this cause completely militant and purposeful in its attempt to find dominion over the earth for the Lord, but also they have been carrying out their plans secretly, immorally, and unscientifically.
In case you didn't know, rotten is the new slang for morally or logically wrong or unacceptable (also look here). I think this is a fitting description for the Discovery Institute (see their website, Discovery Institute Intelligent Design Campaigns and Wikipedia description of DI), the major "think tank" of the ID/Christian Reconstructionist movement. Dr. Michael Behe, a biochemist at Lehigh University in New England, is the "posterboy" of this group, one of the few valid scientists in the ID ranks. He and other famous scientists and philosophers, most notably William Dembski represent key spokesmen for the ID side. To give you an example of how unethical this group is, just check out the website above. Notice anything fishy? (1) A group of mostly religious scientists, writers, and politicians describe throughout the website ludicrous responses to real science and the "winners" despite major losses, (2) they present pseudoscience, and (3) the images, production, and website name on this website and related materials give the false impression of a reliable source of scientific information (Look here for debunking article about the website banner. Why would DI give away their rottenness with their banner? Slight of hand. They want you to believe they represent scientific and faith authority.). In disguise, the DI slams evolutionary theory, science, and society. You and I had better watch who's talking and watch who's podcasting and watch which resources our sources cite and get their data from. Does it reference the DI? If so, beware of this group and the innane plot I have described.
"So, what?" is a common question among the learned and skeptical. I ask it about nearly everything I hear or read. It is my duty as a biologist to always it about science. So, what if you don't believe me when I say this is true? All around the world there is evidence of biological processes pointing to facts about evolution (you can interpret this as evidence about God's direction of the world, but this is non-science). Readily available by mail, books, articles, magazines, and the internet are credible resources that back up every claim I am making. Books and articles by real, even religious scientists like Dr. Kenneth Miller expose the major flaws, failure, and immorality of the ID/ChR movement (both are wrong, whether people take one or both sides). Thousands of peer-reviewed books and articles in scientific journals testify against creationism. Even religious people, like myself, have turned from creationism to accept the truth of evolution as fact. Hesitant to believe the plot I've outlined? Then you'll be even happier to know that the IDers years ago formulated a plan for their take-control of American science education, the extinction of evolution and so on. It is called the Wedge Document and was leaked within the last decade just before key court cases pronounced ID as "unscientific" and thus completely without scientific basis, conferring upon it NO PLACE in the science classroom. Here is a copy of the Wedge Document. Here is another, also from a creationist. You can read it for yourself.
From the language of the Wedge strategy, which prominent political scientists, biologists, and educators such as Dr. Barbara Forrest have exposed and criticized, the ChR/ID movement makes several claims to support their social, religious revolution. They make it abundantly what their position entails (though there's much they are holding back, like the rest of radical Christian Reconstructionism). The Wedge starts off with their central theorem: man was made by God in the image of God and this is the foundation of Western civilization. This has its origins in Genesis (for the christian, so far, so good). Then, they move on to describe their opponents. Their claims are that the fight began when the rise of modern science brought with it a materialism in direct contradiction to what thier own beliefs held (theism, dominionism, man as God's image, etc.). This materialism, says the Opposition, gave rise to moral decay, philosophies which were not so egocentric or anthropocentric, and utopianism. The Wedge, brought down from Mount Siani by Dr. Phillip Johnson and friends, goes on to say,
"Discovery Institute's Center for the Renewal of Science and Culture seeks nothing less than the overthrow of materialism and its cultural legacies. Bringing together leading scholars from the natural sciences and those from the humanities and social sciences, the Center explores how new developments in biology, physics and cognitive science raise serious doubts about scientific materialism and have re-opened the case for a broadly theistic understanding of nature. The Center awards fellowships for original research, holds conferences, and briefs policymakers about the opportunities for life after materialism." (emphasis added)
In the sames spirit Ken Miller has written in concerning Michael Behe's new book, which he reviewed in a piece published in Nature, the Wedge makes "a nice argument, except for the annoying fact that it is wrong." And it is wrong on many counts. A major conclusion of Christian Reconstructionists supported by other creationists is that evolutionary theory brooded materialism. This is a fact. But this fact requires some explanation, because materialism is not very well understood by laymen as a result of multiple use. On the one hand, materialism refers to preoccupation with material things and desires overruling the spiritual in the lives of humans; on the other, materialism is a view of the world contending the world and universe, a priori or operationally, are made of matter or material objects and not supernatural ones. The Wedge and ChR/ID revolution is really worried about both of these, but targets the second because of its place in the philosophy of modern science. To clarify, we are talking about the second kind of materialism here!
Scientists follow either ontological naturalism or materialism (ON, OM) or methodological naturalism or materialism (MN, MM), or some variation of this theme. MN says that there is no supernatural entity or vital force considered in scientific work because science is about testable or falsifiable predictions and explanations based on materialism and supernatural things or theories do not fit this definition, thus are non-scientific. ON goes one step further and says there is no supernatural thing anyway, so why bother acknowledging it in this way. Militant atheism is joined to ontological naturalism and radical materialism, as that supported by Dennett and Dawkins and, to a lesser degree of acknowledgement, Frederick Crews and many others.
So, we see that science can be seen as more of an occupation, but many times is an integral part of someone's world view or ideology, if not comprising most of their set of normative ideas. The ideology of science has been called scientism. I am learning about this now. It seems closely allied with the calls from creationist camps about the deification of Charles Darwin and the faith of scientists in their "religion" of materialism. I confess I don't know much about it and want to know more. The point is that whether you see science as a category, a concept, an ideology, or what, supernatural phenomena are not scientific in the strong or weak sense of the word. These distinctions hold the not-so-secret key to other reasons why the ChR/ID movement fails.
For one thing, they contribute to exposing the Opposition as a movement which lacks integrity. But I'm not sure how important this is, because these kinds of attacks seem inconsequential in the scheme of things, aside from potentially persuading those mindless people who fail to critically consider the situation themselves. Second, the ChR/ID argument goes A = creationism, B = evolution (materialism);
1. A vs. B
2. B is wrong
C. Therefore, A
This argument rests on the logical fallacy that calls premise 1 especially into doubt. It cannot be as simple as materialism is wrong, therefore the christian reconstructionism/ID is right. In fact, it is likely that the first premise could be infinitely extended to include... or C, or D... to infinite.
Many other Oppostion claims have been met with serious issue, called into question, and defeated in scientific journals, public debates, and courtroom decisions. Sift through these in the materials I provide below. The evidence is overwhelmingly in support of science as science, not the pseudoscience presented by the ChR/ID Opposition.
THE WINNERS
Up next? A description of the "winners" and several of their recent victories against this selfish, unethical, religious minority trying to hijack our science education and indoctrinate a world of brainless, anti-science, anti-evolution, anti-intellectual christians. For now, I'm going to bed and you can follow the links below to interesting content on these matters. I strongly encourage comments. Which side of the war do you want to be on? The winning side or the losing side? I know it's cliche, but the truth will set you free. And if all goes right it will prevail. We cannot afford the opposite. Please look for my next installment about this issue. Also, I encourage everyone to respond with your thoughtful comments after reading through the materials I have presented.
Articles and Talks against ID, DI, and creationism:
Ken Miller Talk in Ohio, 2006? - YouTubehttp://youtube.com/watch?v=JVRsWAjvQSg
Barbara Forrest's Position Paper on the truth about the ID movement
http://www.centerforinquiry.net/uploads/attachments/Forrest_Paper.pdf
Skeptical responses to DI "scientific" podcasts
Populist Party in America calls for concern about DI
Americans United for the Separation of Church and StateDI: harming us with pseudoscience article
Famous articles on the ethics of belief (here, here)
Scientific papers of major players in the ID-evolution debate:
http://www.bioone.org/archive/0006-3568/55/3/pdf/i0006-3568-55-3-280.pdf
http://www.bioone.org/archive/0014-3820/56/8/pdf/i0014-3820-56-8-1721.pdf
http://www.bioone.org/archive/0002-7685/65/9/pdf/i0002-7685-65-9-646.pdf
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1467-9744.2005.00746.x
http://www.asa3.org/ASA/PSCF/2003/PSCF3-03Collins.pdf
Ken Miller's review of Behe's new book http://www.nature.com/nature/journal/v447/n7148/full/4471055a.html
Famous scientist Jerry Coyne shatters Behe's new book! Also, he illustrates how Behe's own university doesn't support him, especially since he really botched things with his latest edition, Edge of Evolution http://www.powells.com/review/2007_06_14
http://www.ingentaconnect.com/content/bpl/moth/2002/00000018/00000002/art00004
Annual Review of Genomics http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genom.4.070802.110400?prevSearch=fulltextfield%3A(%22intelligent+design%22)
Famous evolutionary biologist Futuyma debunks Darwin's Black Box http://bostonreview.net/BR22.1/futuyma.html
Another Forrest Paper http://www.infidels.org/library/modern/barbara_forrest/wedge.html#_edn1
Defending Science Education http://www.jci.org/cgi/content/abstract/116/5/1134
Modern Philosophy of Mind http://watarts.uwaterloo.ca/~celiasmi/Papers/lyons.html
Science of the Soul?http://www.naplesnews.com/news/2007/jul/12/science_soul/?neapolitan
"Irreducible Complexity" goes down hard again!http://www.ccrnp.ncifcrf.gov/~toms/paper/ev/behe/
Reference on the Argument from Design http://www.infidels.org/library/modern/theism/design.html
"More Crank Science" article http://bostonreview.net/BR22.1/coyne.html
"New" argument, same old objections http://www.journals.cambridge.org/action/displayAbstract?fromPage=online&aid=26583
DI homepage, "evolution news and views" (yeah right, from a twisted bunch of radically conservative, pro church/state merger, pseudoscientific, uneducated bastard liars)
Jack Russell Terriers & Cockroaches article (please respond)
Phillip Johnson on THE WEDGE
http://www.touchstonemag.com/docs/issues/12.4docs/12-4pg18.html
"Creationism Research" = oxymoron
http://www.creationresearch.org/creation_matters/pdf/2002/cm07%2004c.pdf
Christian Reconstruction site/book
http://forerunner.com/forerunner/X0505_Parsons_-_What_is_Re.html
Behe's response to critics
http://www.springerlink.com/content/g527h45501l632v8/
Another Behe botch up
http://www.arn.org/docs/behe/mb_brresp.htm
Debating Design Book - both sides presented equally and rationally
http://www3.cambridge.org/uk/catalogue/catalogue.asp?isbn=9780521829496
Absolute Baloney websites illustrate creationist anti-science/design argument:
http://evolution-facts.org/nature1.htm
Get a life, Dakota Voice, you are a fool!
http://www.dakotavoice.com/200706/R/20070619_BE.html
Jim Schicatano gets it all wrong
http://home.att.net/~jamspsu84/ttocmain.html
Richard Dawkins
So, recently I've been researching the speeches, science, writings, and life of the famous Richard Dawkins. Dawkins is one of the most confrontational, radical, outspoken, and talented scientists of the past century. It is no great surprise, therefore, how he represents one of the most famous of all communicators, scientists, and atheists in the history of the world! His latest book, The God Delusion, has sparked controversial reviews and heated reactions from many people around the world. Again, no surprise this is a best-seller. I am interested in talking about Dawkins, his books, his life, and in particular the range of opinions about his latest book and exploits, if anyone else is willing to engage. Here are some links to information about his life for the uninitiated. For the learned near my town, let's start a book club. ~ JB
Links:
Tuesday, July 10, 2007
The Cell Cycle
Multicellular eukaryotes that reproduce via sexual reproduction present a case we are all familiar with. During or after sexual contact, gametes fuse to form a zygote, a single cell containing hereditary material from each parent. This description represents only a small snapshot of eukaryotic life, with a couple frames following fertilization thrown in for free. We may reason about this relatively singular event series and its importance, but we cannot help noticing more than the most basic case, two separate entities gave rise to one new entity, just happened. In particular, we know that the individual gametes must have had different qualities and different origins, and furthermore the zygote goes on to become orders of magnitude larger and more complex. In this post, I will briefly summarize the roles of cellular division in gamete development and human physiology and review the cell cycle and its regulation. I then will conclude with some comments about evolution as it relates to this topic.
Despite the lopsidedness of the introductory example, cell division is integral to the evolution and life of single-celled and multicellular life. The purpose of cell division in single-celled organisms is to duplicate the whole individual! In complex multicellular life forms, such as Homo sapiens, serial cellular divisions and differentiation give rise to extraordinary physiology from single-celled starting material. Also in humans, cell division occurs to regenerate certain tissues hence organs that degrade through time. Among these are our red blood cells, skin, hair, and certain glands. Many interesting factoids have been quipped about estimates of turnover during this process and other interesting phenomena. Check a couple out here and here. Most of my discussion will focus on eukaryotic cells and attempt to avoid these.
Dividing cells spend their time in one of two states, (1) Interphase (growth and duplication) and (2) mitosis (splitting into two new cells). These two processes can be broken down into a series of smaller phases. Overall, the cell cycle, or cell division cycle or however it may be called, always involves the following phases in sequential order under normal conditions: G1 phase, S phase, G2 phase, and mitosis. Here, G stands for "gap" so that G1 means "gap" 1, S stands for "synthesis," and G2 refers to "gap" 2. Beyond these, mitosis is traditionally split into several phases, itself. These, also in sequence, are termed (a) prophase, (b) prometaphase, (c) metaphase, (d) anaphase, and (e) telophase + cytokinesis. New cells formed during mitosis are called daughter cells. This early institution of organization may be helpful. On the contrary, you may be asking what I first asked when I heard these terms for the first time, "What does all this mean?" Discussing the cell ultrastructure involved often helps alleviate this pain. This will be touched on after describing the cell cycle.
While there are distinct phases of the cell cycle, all three non-mitotic phases are similar; in each, the cell grows as it duplicates chemicals, organelles and proteins. The S phase is unique, because it is the phase where DNA is duplicated. Interestingly, the S phase is considered the longest phase of the cell cycle, filling about half the total amount of time necessary for average human cell division (Campbell and Reece 2005).
Cell Cycle Regulation (van den Heuvel 2005; Campbell and Reece 2005; others)
The cell cycle is controlled by several different types of membrane-bound enzymes and other factors conserved (i.e., found) in most dividing animal cells. Studies indicate major importance of three or four different kinds of kinases and other genes in this mosaic of regulatory pathways. Also, the cell cycle may be controlled by extrinsic or intrinsic factors. Generally, external signals only regulate whether or not animal cells reproduce up to a point called the restriction point or G1 checkpoint. On the other hand, a number of important internal factors regulate the cell cycle intrinsically from this point.
As I mentioned in an earlier post, DNA (of eukaryotes) is housed within the nuclei in the form of a substance called chromatin, in which histone proteins and tangled nucleotide strands are incorporated together. This chromatin is loosely distributed in long thin fibers. During S phase all the genetic material replicates itself, but chromatin is still in loose form. Later, during mitosis, the chromosomes condense and the cell actually divides. A unique set of machinery is involved in these processes. Most notably, cytoskeletal structures provide substrates (analogous to small roads or steady surfaces in the cell) for chromosomes to be transported along by motor proteins; also, centromeres play a pivotal role. Perhaps the best way to describe mitosis is the common way, or detailing the events at each phase of the process.
Prophase: The prefix pro- means this stage is "before, or preceding" the following other phases of mitosis. During prophase, chromatin is condensed into recognizable chromosomes. Originally, these were single units. After duplication and condensation they represent a pair, each called sister chromatids of the other. At the center of these chromatids is a region known as the centromere, which connects the chromatids, or copies of the original DNA molecule. Tan cuidado! The centrosome-centromere problem may confuse you. At the same time these chromatids assemble, the centrosomes begin sending out microtubules, which push the centrosomes farther apart by physical force.
Prometaphase: Here, the prefix meta- means "growth" or "unification, or important" phase, so this phase precedes the really unifying step. Prometaphase includes breakdown of the nuclear envelope (microfilaments and pore complexes), which degrade substantially to clear space for metaphase and anaphase. Also, the staging of the microtubules becomes much more complex, extending across the cell to connect with special structures formed at the centromeres, called kinetochores. Kinetochores are specialized proteins. There is a name for microtubules which are now very obvious in the cell--they're called spindles. Some spindles connect with kinteochores, others connect with other spindles across the cell.
Metaphase: Metaphase is one of the most time consuming and important phases of mitosis. During this time, chromosomes are aligned on a plane bisecting the distance between the centrosomes, which is termed the metaphase plate. It's not a real plate or plane, but rather an imaginary one. Microtubule spindles attach at kinetochores closest to them such that chromosomes line up with kinetochores facing each pole of the cell signified by centrosome position.
Anaphase: Ana- means "true" or "original." However true or original this step is, a fact is that it's the shortest phase of normal mitosis. It is during anaphase that the chromatids are ripped apart from one another by the microtubules, thus taken to their respective poles of the cell. For some reason--ah, because the end products are called daughter cells--the chromatids become called daughter chromosomes after this point. Remeber the spindles that hooked up with one another, not the kinetochores? At this point, those push off one another to help distance the chromosomes and increase the distance between the poles of the cell.
Telophase + Cytokinesis: Finally, telophase unites the genetic material of each daughter cell into an enclosed nucleus while cytokinesis splits the cytoplasm via invagination of the plasma membrane (involving microfilaments) and segregation of the fluid matrix making up the innermost cellular space. And mitosis is over, just like that. You can remember the order of these phases by memorizing the names, memorizing the prefix meanings, and or memorizing the order like this P2MAT.
Cell division from the standpoint of evolution and disease
According to Campbell and Reece (2005), "As eukaryotes evolved, along with their larger genomes and nuclear envelopes, the ancestral process of binary fission [bacterial division] somehow gave rise to mitosis." Researchers have actively been seeking answers to persistent questions about the mechanisms involved in mitosis. This work has included plants, many of which reproduce asexually through mitotic cell-lineages (Fagerstrom et al. 1998), as well as diatoms and bacteria.
Save the best for last. That ability is one of the greatest given to the human condition, and exactly what I think I've done waiting to talk about the coolest parts of the cell cycle, apoptosis and disease! Trust me on this one.
Scientists' understanding of CDKs' functions in cell cycle regulation and their interactions with other chemicals are just beginning to be explored. We have discussed what we know about what happens when things go right in cell cycling, but what about what we know about what happens when things go awry? For me, this was one of the most interesting and exciting facets of my introductory cell biology class. I hope your decision about which part of the cell cycle and its regulation, like mine, hinges upon the next few pieces of information.
If S phase replication goes wrong and DNA is damaged, this can have negative effects. So, cells halt the cell cycle by slipping into "gap zero" phase, or G0, while damaged components are repaired. Also, it is integral that mitotic spindle fibers attached to kinetochores, and the right ones at that. So, cells can halt motion to the next phase of the cycle in the even this happens. HOWEVER, if things don't get fixed or something else dysfunctions at these crucial times, the cell may induce suicide, or apoptosis (a.k.a., "programmed cell death").
An important gene regulating both of these processes is p53. p53 is in a special group of tumor suppressor genes, which keep the cell from slipping into cancerous states. Of course, I haven't talked about cancer. So, what I mean is that if things go awry (e.g., if DNA is damaged by an environmental factor instigated by a physical action, such as smoking), the cell may never be able to turn off (step into gap zero states or die via apoptosis), thus it may continue dividing infinitely with misreplicated genetic information. Cells in this state cause cancer by creating many clones of themselves (a tumor), which are harmful to the body because they fail to recognize tissue boundaries and may travel to other areas of the body, depleting normal tissues. p53 blocks the cell cycle by inactivating CDKs and has the power to induce programmed cell death in abnormal cells. WHEN p53 is doubly recessive (mutant), these functions are not carried out and cancer will develop beginning, perhaps, with a single damaged cell.
A report on wikipedia.com resounds a common statistic, that cancer is responsible for approximately 10-20% (13%) of all human deaths. In this way, we see that the cell cycle is not only important to our growth and complexity, but also that factors along the way play a critical role influencing our health and well-being. Similarly, mistakes during mitosis result in genetic variation among individual offspring of parents, ensuring natural selection has lots of material to work with in healthy populations. Now that you know so much about a process that led to your diversity and uniqueness, watch this time-lapse video of cell division!
References:
van den Heuvel, S. Cell-cycle regulation (September 21, 2005), WormBook, ed. The C. elegans Research Community, WormBook,
doi/10.1895/wormbook.1.28.1, http://www.wormbook.org.
Despite the lopsidedness of the introductory example, cell division is integral to the evolution and life of single-celled and multicellular life. The purpose of cell division in single-celled organisms is to duplicate the whole individual! In complex multicellular life forms, such as Homo sapiens, serial cellular divisions and differentiation give rise to extraordinary physiology from single-celled starting material. Also in humans, cell division occurs to regenerate certain tissues hence organs that degrade through time. Among these are our red blood cells, skin, hair, and certain glands. Many interesting factoids have been quipped about estimates of turnover during this process and other interesting phenomena. Check a couple out here and here. Most of my discussion will focus on eukaryotic cells and attempt to avoid these.
Dividing cells spend their time in one of two states, (1) Interphase (growth and duplication) and (2) mitosis (splitting into two new cells). These two processes can be broken down into a series of smaller phases. Overall, the cell cycle, or cell division cycle or however it may be called, always involves the following phases in sequential order under normal conditions: G1 phase, S phase, G2 phase, and mitosis. Here, G stands for "gap" so that G1 means "gap" 1, S stands for "synthesis," and G2 refers to "gap" 2. Beyond these, mitosis is traditionally split into several phases, itself. These, also in sequence, are termed (a) prophase, (b) prometaphase, (c) metaphase, (d) anaphase, and (e) telophase + cytokinesis. New cells formed during mitosis are called daughter cells. This early institution of organization may be helpful. On the contrary, you may be asking what I first asked when I heard these terms for the first time, "What does all this mean?" Discussing the cell ultrastructure involved often helps alleviate this pain. This will be touched on after describing the cell cycle.
While there are distinct phases of the cell cycle, all three non-mitotic phases are similar; in each, the cell grows as it duplicates chemicals, organelles and proteins. The S phase is unique, because it is the phase where DNA is duplicated. Interestingly, the S phase is considered the longest phase of the cell cycle, filling about half the total amount of time necessary for average human cell division (Campbell and Reece 2005).
Cell Cycle Regulation (van den Heuvel 2005; Campbell and Reece 2005; others)
The cell cycle is controlled by several different types of membrane-bound enzymes and other factors conserved (i.e., found) in most dividing animal cells. Studies indicate major importance of three or four different kinds of kinases and other genes in this mosaic of regulatory pathways. Also, the cell cycle may be controlled by extrinsic or intrinsic factors. Generally, external signals only regulate whether or not animal cells reproduce up to a point called the restriction point or G1 checkpoint. On the other hand, a number of important internal factors regulate the cell cycle intrinsically from this point.
The main paradigm of cell cycle control is one of activation-inactivation cycles generated by changes in the amounts of regulatory factors, cyclins and kinases. Kinases "activate" or "inactivate" different proteins controlling cell division by substrate-level phosphorylation at checkpoints such as the restriction point. Kinases themselves may also exist in active or inactive states corresponding to their position with respect to cyclins. Activated and inactivated kinases are attached or unattached to cyclins, respectively. This is why these kinases are called cyclin-dependent kinases, CDKs. As cyclins increase and decrease in thier relative concentrations in the cell (and CDKs remain relatively constantly concentrated), CDK activity changes disproportionately, with activity increasing abruptly after gap 2 then falling as cyclin is degraded during mitosis. Actually, synthesis of cyclins occurs from S phase through gap 2 phase. While cyclins are degraded, CDKs are thought to be recycled during this process. So, why is this a regulatory pathway anyway? Because without cyclin accumulation, mitosis is not signaled. An important CDK complex called "M-phase promoting factor" signals spindle formation, nuclear envelope breakdown, and chromosome condensing. Without these, M phase, thus the cell cycle, would never be completed.
MitosisAs I mentioned in an earlier post, DNA (of eukaryotes) is housed within the nuclei in the form of a substance called chromatin, in which histone proteins and tangled nucleotide strands are incorporated together. This chromatin is loosely distributed in long thin fibers. During S phase all the genetic material replicates itself, but chromatin is still in loose form. Later, during mitosis, the chromosomes condense and the cell actually divides. A unique set of machinery is involved in these processes. Most notably, cytoskeletal structures provide substrates (analogous to small roads or steady surfaces in the cell) for chromosomes to be transported along by motor proteins; also, centromeres play a pivotal role. Perhaps the best way to describe mitosis is the common way, or detailing the events at each phase of the process.
Prophase: The prefix pro- means this stage is "before, or preceding" the following other phases of mitosis. During prophase, chromatin is condensed into recognizable chromosomes. Originally, these were single units. After duplication and condensation they represent a pair, each called sister chromatids of the other. At the center of these chromatids is a region known as the centromere, which connects the chromatids, or copies of the original DNA molecule. Tan cuidado! The centrosome-centromere problem may confuse you. At the same time these chromatids assemble, the centrosomes begin sending out microtubules, which push the centrosomes farther apart by physical force.
Prometaphase: Here, the prefix meta- means "growth" or "unification, or important" phase, so this phase precedes the really unifying step. Prometaphase includes breakdown of the nuclear envelope (microfilaments and pore complexes), which degrade substantially to clear space for metaphase and anaphase. Also, the staging of the microtubules becomes much more complex, extending across the cell to connect with special structures formed at the centromeres, called kinetochores. Kinetochores are specialized proteins. There is a name for microtubules which are now very obvious in the cell--they're called spindles. Some spindles connect with kinteochores, others connect with other spindles across the cell.
Metaphase: Metaphase is one of the most time consuming and important phases of mitosis. During this time, chromosomes are aligned on a plane bisecting the distance between the centrosomes, which is termed the metaphase plate. It's not a real plate or plane, but rather an imaginary one. Microtubule spindles attach at kinetochores closest to them such that chromosomes line up with kinetochores facing each pole of the cell signified by centrosome position.
Anaphase: Ana- means "true" or "original." However true or original this step is, a fact is that it's the shortest phase of normal mitosis. It is during anaphase that the chromatids are ripped apart from one another by the microtubules, thus taken to their respective poles of the cell. For some reason--ah, because the end products are called daughter cells--the chromatids become called daughter chromosomes after this point. Remeber the spindles that hooked up with one another, not the kinetochores? At this point, those push off one another to help distance the chromosomes and increase the distance between the poles of the cell.
Telophase + Cytokinesis: Finally, telophase unites the genetic material of each daughter cell into an enclosed nucleus while cytokinesis splits the cytoplasm via invagination of the plasma membrane (involving microfilaments) and segregation of the fluid matrix making up the innermost cellular space. And mitosis is over, just like that. You can remember the order of these phases by memorizing the names, memorizing the prefix meanings, and or memorizing the order like this P2MAT.
Cell division from the standpoint of evolution and disease
According to Campbell and Reece (2005), "As eukaryotes evolved, along with their larger genomes and nuclear envelopes, the ancestral process of binary fission [bacterial division] somehow gave rise to mitosis." Researchers have actively been seeking answers to persistent questions about the mechanisms involved in mitosis. This work has included plants, many of which reproduce asexually through mitotic cell-lineages (Fagerstrom et al. 1998), as well as diatoms and bacteria.
Save the best for last. That ability is one of the greatest given to the human condition, and exactly what I think I've done waiting to talk about the coolest parts of the cell cycle, apoptosis and disease! Trust me on this one.
Scientists' understanding of CDKs' functions in cell cycle regulation and their interactions with other chemicals are just beginning to be explored. We have discussed what we know about what happens when things go right in cell cycling, but what about what we know about what happens when things go awry? For me, this was one of the most interesting and exciting facets of my introductory cell biology class. I hope your decision about which part of the cell cycle and its regulation, like mine, hinges upon the next few pieces of information.
If S phase replication goes wrong and DNA is damaged, this can have negative effects. So, cells halt the cell cycle by slipping into "gap zero" phase, or G0, while damaged components are repaired. Also, it is integral that mitotic spindle fibers attached to kinetochores, and the right ones at that. So, cells can halt motion to the next phase of the cycle in the even this happens. HOWEVER, if things don't get fixed or something else dysfunctions at these crucial times, the cell may induce suicide, or apoptosis (a.k.a., "programmed cell death").
An important gene regulating both of these processes is p53. p53 is in a special group of tumor suppressor genes, which keep the cell from slipping into cancerous states. Of course, I haven't talked about cancer. So, what I mean is that if things go awry (e.g., if DNA is damaged by an environmental factor instigated by a physical action, such as smoking), the cell may never be able to turn off (step into gap zero states or die via apoptosis), thus it may continue dividing infinitely with misreplicated genetic information. Cells in this state cause cancer by creating many clones of themselves (a tumor), which are harmful to the body because they fail to recognize tissue boundaries and may travel to other areas of the body, depleting normal tissues. p53 blocks the cell cycle by inactivating CDKs and has the power to induce programmed cell death in abnormal cells. WHEN p53 is doubly recessive (mutant), these functions are not carried out and cancer will develop beginning, perhaps, with a single damaged cell.
A report on wikipedia.com resounds a common statistic, that cancer is responsible for approximately 10-20% (13%) of all human deaths. In this way, we see that the cell cycle is not only important to our growth and complexity, but also that factors along the way play a critical role influencing our health and well-being. Similarly, mistakes during mitosis result in genetic variation among individual offspring of parents, ensuring natural selection has lots of material to work with in healthy populations. Now that you know so much about a process that led to your diversity and uniqueness, watch this time-lapse video of cell division!
References:
van den Heuvel, S. Cell-cycle regulation (September 21, 2005), WormBook, ed. The C. elegans Research Community, WormBook,
doi/10.1895/wormbook.1.28.1, http://www.wormbook.org.
Monday, July 9, 2007
Consumer Reports: My Energy Comes from Plants?
A "Consumer" Report
Ladies and gentlemen, we are consumers. Newsflash! I know, I know... it's America. Capitalism, materialism... these are familiar concepts. But I'm a biologist. It's what I do (observe the world around me critically). And lately I've been thinking about consuming in a biological context. Surprise, surprise. Recall, I've been using this blog to refresh readers (and myself) about the basics of biological science (click here to see where this started). Consumer Reports is a popular magazine complex interested in reviewing and rating products in hopes of helping consumers make smart buying decisions in the American (and global) marketplace. Today, I'll be submitting my own Consumer Report. This report, however, focuses on the underlying biological mechanisms--those relating to photosynthesis--responsible for the energy in what we consume. As always, I will attempt to paint a picture of photosynthesis from an evolutionary perspective.
You and I consume other living things, from which we obtain energy in a variety of different forms, mostly as proteins, lipids, and long chains of sugars called carbohydrates. As I have just discussed (last couple of posts), our bodies are made of millions and millions of cells capable of using energy bound up in the foods we eat after converting it to energetic currency called ATP through the processes of glycolysis and cellular respiration (if oxygen is present in our cells). But we never serve as the origin of any energy we use.
While our bodies can transform basic chemical compounds into more complex and useful forms (e.g., 10 of the essential amino acids used to synthesize proteins), we are constantly converting energy from one form to another (remember that first law of thermodynamics?). The question eventually arises, where does all this energy come from in the first place? The short answer isn't found on mother earth. It's the sun. A more fruitful explanation lies in the study of plants and other organisms (cyanobacteria, green algae), which we call autotrophs or producers, which can convert solar energy into chemical energy.
Evolution and Photosynthesis
First, a little digression... Evolutionary biologists (like myself) are scientists interested in all aspects of the evolution of biological species. While most evolutionary biologists do not concern themselves with the origins of life, other scientists' work often focuses on evaluating and empirically testing the significance of other kinds of evidence (i.e., astronomy, geology, early earth biochemistry, et cetera) about the archaeology of early life and the ancient earth environment. Sometimes scientists intend to demonstrate the validity of different theories about these latter phenomena, while at other times scientists make discoveries with implications for how we think about the history of life, while this was not their original intent; this second class of discoverers simply realize the implications of their new knowledge after laying it bare. Because photosynthesis is thought to have played a pivotal role in the evolution of life on earth, I choose this perspective as my starting point.
Isotopic studies of meteorite tungsten demonstrate confirm the long-held and well-supported idea that the earth is very, very old--around 4.6 billion years, give or take 10 million, to be more precise (Jacobsen 2003). Evidence suggests simple prokaryotic cells evolved between 3 and 4 billion years ago (Line 2001). Later, the processes of life's evolution generated single celled eukaryotes just over 2 billion years ago, which were first very simple then engulfed proto-plastids and evolved into photosynthesizing eukaryotes (as described in an earlier post, which you can read here) (Margulis 1970; Campbell and Reece 2005). Because a by-product of photosynthesis is oxygen, these creatures, which increased exponentially in number, played a major role in setting the environment up for more complex lifeforms (i.e., animals and land-dwelling plants) by increasing the atmospheric and aquatic O2 concentrations of the early earth (Dismukes et al. 2001; Campbell and Reece 2005). Recently, molecular sequence data of cyanobacteria chloroplasts are consistent with these other findings in demonstrating an ancient origin of photosynthesizing cells (Xiong et al. 2000). Not surprisingly, photosynthesis is still generating crucial oxygen used by most species today. Now that you know a bit about the evolutionary significance of photosynthesizing organisms. Thus, we turn to the process of photosynthesis itself.
Photosynthesis
Everyone who knows anything about this important process knows photosynthesis occurs in plants. Those more erudite scholars among you might even know this happens, more specifically, in the chloroplasts evolved from early plastids I mentioned. Those with heads high in the heavens (even concocting a nosebleed) of scientific knowledge might even remember that plant chloroplasts are divided into different parts and that different sub-cellular pathways carry out what are call "light" and "dark" reactions, that there are different photosystems, and or that electrons are involved in chemiosmosis during the sequence of super duper photosynthetic events. Allow me to clarify for those of us who aren't as smart as the nosebleeders.
Chloroplast Ultrastructure
Chloroplasts, like mitochondria, have two outer layers--outer and inner membranes--and are filled with interconnected networks of membranous sacs known as thylakoids. Chlorophyll is a special pigment in thylakoid membranes that give plants their green color, as you shall see.
As I mentioned, photosynthesis involves two different phases. These are the light reactions and the Calvin cycle. These are crucial to your life and mine and to life's evolution.
Ladies and gentlemen, we are consumers. Newsflash! I know, I know... it's America. Capitalism, materialism... these are familiar concepts. But I'm a biologist. It's what I do (observe the world around me critically). And lately I've been thinking about consuming in a biological context. Surprise, surprise. Recall, I've been using this blog to refresh readers (and myself) about the basics of biological science (click here to see where this started). Consumer Reports is a popular magazine complex interested in reviewing and rating products in hopes of helping consumers make smart buying decisions in the American (and global) marketplace. Today, I'll be submitting my own Consumer Report. This report, however, focuses on the underlying biological mechanisms--those relating to photosynthesis--responsible for the energy in what we consume. As always, I will attempt to paint a picture of photosynthesis from an evolutionary perspective.
You and I consume other living things, from which we obtain energy in a variety of different forms, mostly as proteins, lipids, and long chains of sugars called carbohydrates. As I have just discussed (last couple of posts), our bodies are made of millions and millions of cells capable of using energy bound up in the foods we eat after converting it to energetic currency called ATP through the processes of glycolysis and cellular respiration (if oxygen is present in our cells). But we never serve as the origin of any energy we use.
While our bodies can transform basic chemical compounds into more complex and useful forms (e.g., 10 of the essential amino acids used to synthesize proteins), we are constantly converting energy from one form to another (remember that first law of thermodynamics?). The question eventually arises, where does all this energy come from in the first place? The short answer isn't found on mother earth. It's the sun. A more fruitful explanation lies in the study of plants and other organisms (cyanobacteria, green algae), which we call autotrophs or producers, which can convert solar energy into chemical energy.
Evolution and Photosynthesis
First, a little digression... Evolutionary biologists (like myself) are scientists interested in all aspects of the evolution of biological species. While most evolutionary biologists do not concern themselves with the origins of life, other scientists' work often focuses on evaluating and empirically testing the significance of other kinds of evidence (i.e., astronomy, geology, early earth biochemistry, et cetera) about the archaeology of early life and the ancient earth environment. Sometimes scientists intend to demonstrate the validity of different theories about these latter phenomena, while at other times scientists make discoveries with implications for how we think about the history of life, while this was not their original intent; this second class of discoverers simply realize the implications of their new knowledge after laying it bare. Because photosynthesis is thought to have played a pivotal role in the evolution of life on earth, I choose this perspective as my starting point.
Isotopic studies of meteorite tungsten demonstrate confirm the long-held and well-supported idea that the earth is very, very old--around 4.6 billion years, give or take 10 million, to be more precise (Jacobsen 2003). Evidence suggests simple prokaryotic cells evolved between 3 and 4 billion years ago (Line 2001). Later, the processes of life's evolution generated single celled eukaryotes just over 2 billion years ago, which were first very simple then engulfed proto-plastids and evolved into photosynthesizing eukaryotes (as described in an earlier post, which you can read here) (Margulis 1970; Campbell and Reece 2005). Because a by-product of photosynthesis is oxygen, these creatures, which increased exponentially in number, played a major role in setting the environment up for more complex lifeforms (i.e., animals and land-dwelling plants) by increasing the atmospheric and aquatic O2 concentrations of the early earth (Dismukes et al. 2001; Campbell and Reece 2005). Recently, molecular sequence data of cyanobacteria chloroplasts are consistent with these other findings in demonstrating an ancient origin of photosynthesizing cells (Xiong et al. 2000). Not surprisingly, photosynthesis is still generating crucial oxygen used by most species today. Now that you know a bit about the evolutionary significance of photosynthesizing organisms. Thus, we turn to the process of photosynthesis itself.
Photosynthesis
Everyone who knows anything about this important process knows photosynthesis occurs in plants. Those more erudite scholars among you might even know this happens, more specifically, in the chloroplasts evolved from early plastids I mentioned. Those with heads high in the heavens (even concocting a nosebleed) of scientific knowledge might even remember that plant chloroplasts are divided into different parts and that different sub-cellular pathways carry out what are call "light" and "dark" reactions, that there are different photosystems, and or that electrons are involved in chemiosmosis during the sequence of super duper photosynthetic events. Allow me to clarify for those of us who aren't as smart as the nosebleeders.
Chloroplast Ultrastructure
Chloroplasts, like mitochondria, have two outer layers--outer and inner membranes--and are filled with interconnected networks of membranous sacs known as thylakoids. Chlorophyll is a special pigment in thylakoid membranes that give plants their green color, as you shall see.
As I mentioned, photosynthesis involves two different phases. These are the light reactions and the Calvin cycle. These are crucial to your life and mine and to life's evolution.
Light Reactions use solar radiation to convert carbon dioxide and water into useable chemical forms
Generally, light reactions convert solar energy into chemical energy trapped in the form of ATP and an electron carrier, NADPH (similar to NADH and FADH, from discussion of cellular respiration). By solar energy, I mean light. Let me explain. Light is electromagnetic radiation or energy travelling in the form of waves with the properties of particle packages of energy, or photons. Different wavelengths of light are visible and invisible (see electromagnetic spectrum). Light with low wavelengths is intense (has more energy; e.g., violet light) while the converse is true of long wavelength light (e.g., red light). When light from the sun (which emits all wavelengths of light) hits objects on earth (mostly visible light reaches the surface), some visible light is reflected by those objects, which may absorb or transmit (allow to pass through them) other wavelengths. Chemicals called pigments absorb many frequencies of visible light and reflect a narrow range of wavelengths. So, we see that the chemical composition of matter is highly variable, thus objects take on different colors because their pigments or absorption characteristics (absorption spectra) allow only certain colors to be reflect and processed by visual sensory organs of living things, (e.g., our eyes). And that's a simple (albeit incomplete) explanation of why we perceive objects to be different, specific colors!! Isn't that cool? Nonetheless, there are deeper truths these facts hold in store for photosynthesis.
Thylakoid membranes are peppered with chemical complexes called photosystems. In broad terms, photosystems consist of chemical complexes (groups of large molecules) containing photosynthetically important plant pigments (which I expand on later) surrounding a central region where special pigment molecules are housed. The light reactions of photosynthesis depend upon the excitation of electrons in photosystems and the transport of these electrons down protein chains to generate energy bound in ATP and NADPH.
To elaborate, there are two photosystems at work in plant cells, photosystem I and photosystem II. Here's how they do the work of the light reactions. Pigments in photosystem II abosorb light from the sun at wavelengths of 410-510 nm and 610-700 nm (both are approximations). This light is in the form of an individual photon which energetically must exactly match the difference between excited electron states and the ground state of the pigment molecule (most commonly discussed are chlorophyll a, chlorophyll b, and carotenoids). The photon's energy is transferred directly between pigment molecules in photosystem I's outer complex until it reaches the base of the inner region, where two special chlorophyll molecules are located. These molecules, because they absorb light best at 680 nm, are termed P680's. Absorption of the photon powers a single electron from one of the P680's to a higher energy state, a higher orbital (if you know chemistry). The excited electron reduces a molecule called the primary electron acceptor. Nearby, an enzyme quickly breaks a proximate water molecule into its constituent parts: oxygen, two protons (H+), and two electrons. The electrons drop back to each fill the void left in each P680 molecule at the base of the inner photosystem region from giving electrons to the primary electron acceptor. (hang with me here!) Next, the primary acceptor drops its newly gained electron in one of two places, electron transport chains (ETC; we'll call them electron transport chains one and two, ETC1 and ETC2!). For now, we consider what happens down each individual ETC.
ETC1 is similar to the ETC found in mitochondria, which functions in cellular respiration. As with mitochondrial ETCs, ETC1 breaks the explosive change in energetic state of the electrons from photosystem I into a small series of steps, each yielding ATP. Eventually (quickly), our little electron is passed to photosystem I. That's right! Electrons go from photosystem II to photosystem I. Kind of weird, huh? The explanation for this apparent misnomer is that the photosystems were named in order of discovery, with scientists later determining the order of electron passage contradicted the nomenclature.
The last compound in ETC1 drops our electron directly onto the special pigment molecules called P700's, chlorophylls that absorb light best at 700 nm (go figure), which are at the base of the central region of photosystem I. Again, this transfer of energy blasts electrons from P700's to an excited state, which reduces photosystem I's primary electron acceptor. This acceptor, in turn, drops the electron down the other ETC (i.e., ETC2), where, upon reaching the bottom of the chain, it is passed on to an enzyme called NADP+ reductase. This enzyme requires two electrons from the light reactions (photosystem I) to reduce NADP+ to NADPH, an electron carrier molecule. And that's it for the light reaction phase!
ATP generation
I told you that electrons dropping down ETC1 make ATP and those funneled down ETC2 cause NADP+ to be reduced to NADPH. What I said was true. However, I was holding something back; namely, the mechanism responsible for these changes. It is a familiar mechanism, chemiosmosis (if you don't know what this means, read this)! This is the same mechanism driving the generation of the majority of ATP in aerobically respiring living cells, oxidative phosphorylation, a process of cellular respiration.
As I have stressed in talking about cellular respiration, ATP is generated by an enzyme, ATP synthase, as a result of a H+ gradient in mitochondria. The same is true of photosynthesis. In mitochondria, ATP is made as H+ are pumped down their concentration gradient from the mitochondrial intermembrane space into the inner space of the organelle (mitochondrial matrix), where ADP is phosphorylated into ATP. In plants, things are not much different. Obviously, the electron transport chains are different. Less obviously, however, is the fact that another similarity exists. In mitochondria AND thylakoids, the ETC's and ATP synthases are embedded in the same membrane (the inner membrane of mitochondria, the only membrane in thylakoids) and ETCs supply force to pump H+ into a different space (against their passive transport directionality, therefore requiring active transport) which accumulate and run easily through ATP synthase literally turning the machinery to generate energy for ATP production. Whew! Clear as mud right? But where does that ATP go next? How is it actually used in cells of plants? What kind of work do these cells accomplish and why is it important to you and me as consumers? Simple (ha ha).
The Calvin Cycle
In brief, the Calvin cycle uses ATP and NADPH to turn carbon dioxide into polysaccharides that benefit consumers like us! In a sense, this process is partially analogous to a reversal of the citric acid cycle (CAC). On the one hand, the CAC uses oxidized sugars to generate chemicals storing energy. On the other hand, the Calvin cycle expends energy to make sugars, which are stored in plant tissues and consumed by animals as food. The Calvin cycle is comprised of three phases, (1) carbon fixation, (2) reduction, and (3) regeneration of the starting materials (carbon dioxide). While some think of the Calvin cycle as generating sugars directly, this is not the case. Instead, it yields three carbon sugars which are also intermediates in CAC's, glyceraldehyde-3-phosphate, or G3P. Enzymes separate from the Calvin cycle use G3P as a starting material for glucose genesis, which only involves a few steps.
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Dismukes, et al. 2001. The origin of atmospheric oxygen on earth: the innovation of oxygenic photosynthesis. PNAS 98(5):2170-2175.
Jacobsen, S.B. 2003. How Old Is Planet Earth? Science (Washington). 300(5625):1513-1514..
Line, M.A. 2001. The enigma of the origin of life and its timing. Microbiology 148:21-27.
Margulis, L. 1970. Origin of eukaryotic cells. New Haven, Yale University Press.
Xiong, et al. 2000. Molecular evidence for the early evolution of photosynthesis. Science 289(5485):1724 - 1730.
For info on other citations, see References post.
Saturday, July 7, 2007
What is Biology?
Philosophy of science is a vibrant area of philosophical discourse, which attempts to reason about the way we can come to know more about the universe through science and its methods. Philosophy of biology works to test biological practices and concepts for logical soundness, both as a kind of system of checks and balances and a method of perpetuating new ways of thinking about what biology is and what it ought to be like. Because it is so foundational, philosophy should spill out of any good description of what biology is and of what science is. One reason for this is students must fully grasp what science is before they understand what biology is, so it is only natural to begin our discussion of what biology is, what its theories are like, and what biologists do with a focus on philosophy of science and biology. However, it is important to realize that philosophy of biology is distinct from biology itself.
First, and foremost, biology is a science. Science is simply any study of how the world works reasoned out using naturalistic explanations. The highest goal of science is knowledge, so science can be thought of as the quest for knowledge, which may also be viewed as an innate part of the human experience. Often, our concept of science is synonymous with our understanding of scientific methods. And in the real world, the concepts lay people have about biology are based upon the relationship between what they know about biologists and their work.
If science is a way of seeking out answers to our questions about ourselves and the world around us, then how is this accomplished by biologists? Biology, like other sciences, is based on the idea of inquiry. Campbell and Reece (2007) define this as “the heart of science… a search for information and explanation, often focusing on specific questions.” If science is inquiry and inquiry is the quest for knowledge about the world and explanations of this knowledge, then it follows that the work of biologists must be centered upon observation and explanation; indeed, this is the case.
Observations are made by using our human senses to record qualitative (non-numerical) and quantitative (numerical) information about the world around us. We call this information, which are in essence facts about how the world is, data, which scientists use to make explanations about the natural world. Biologists make diverse observations from the color of fish fins to the size of neurons. Conclusions based on observations are drawn by a type of logic known as inductive reasoning, which is used to make generalizations from scientific data we gather. Explanations of generalizations based on facts represent the next logical step in scientific inquiry. After gathering facts and making generalizations, biologists and other scientists often develop hypotheses, which are educated guesses about specific questions making predictions that can be tested using another important scientific method, the experiment. Hypothesis-based science makes the jump from generalizations to understanding specific interactions, forces, structures, and so on, responsible for biological phenomena by using deductive reasoning (deduction), which creates a logical flow oppositely oriented with respect to inductive reasoning discussed above. In other words, deduction is the process by which we make the transfer from generalizations to specific results. This process allows scientists to draw the testable predictions integral to hypothesis-based science.
Here, it is important to emphasize that the straightforward scientific method of primary education (observation, hypothesis, prediction, test, etc.) in science represents only one description of the order of scientific methods. Many times in their career—even during one experiment or project (set of experiments)—biologists may use different methods or different ordering of research priorities to answer biological questions. In fact, some biologists never even conduct experiments, because in many cases they would be biologically harmful and or morally unacceptable!Another way to begin thinking about biology as a science might be to ask, what real world forces or tools are responsible for the advancement of science, of biology? An important point might be how the breadth of biological inquiry, not unlike other fields of science, has always been intimately linked with technological and theoretical advances. Many of these have been perpetuated by workers in the field of biology, however many important innovations in biology owe themselves to advances in other fields of science. Technological and theoretical advances are important because they detail the options available to biologists in terms of method and concepts upon which their inquiry is based. Thus, technology and theoretical improvement lead to better solutions of biological problems, including more rigorous tests of better equipped hypotheses. So, we see that it would be unrealistic to view biological science and other disciplines of scientific study as mutually exclusive entities. In his book, The Creation, E. O. Wilson (2006) notes,
Biology is continually advancing in new directions fueled by technology and theory, but a proportion of biological advances must always be attributed to the momentum generated by this middle domain and by the academy as a whole, resulting from the more generally intertwined nature of fields of science. For example, and a specific one at that, as chemical experiments reveal more about pieces of biological phenomena, biologists are better informed about their studies and therefore their work is accelerated.But if academia, if all of science is intertwined in this way, what features of biology distinguish it from other realms of science? Is there a point where the other sciences end and biology begins? There are minimally two approaches to solving this problem for the novice, explaining what makes biology similar to other fields of science then venturing on to its uniqueness, or explaining away what biology is not and should not be. Alternatively, one might go directly into the big picture of what biology really is beyond formal distinctions about science and its philosophy, then focus in on its more specific attributes. Now that we have discussed what science is and how biologists conduct scientific investigations, I will take the first step toward accomplishing the end of this alternative goal.
In simplest terms, biology is the study of life. More precisely, modern biological science represents a multi-faceted discipline exploring the complexity of living things, their history, their interactions with each other and their environments across fine (microscopic) and broad spatial (global) and temporal (historical) scales. Biology is divided into many specialty areas of research, which include, but are not limited to, cell biology, genetics, anatomy and physiology, ecology, systematics, and evolutionary biology. An educated view of what biology is best approached by a top-down approach. So, before we go any further, we should begin with the big picture.The earth is our home, our place in the universe, the only life-bearing planet of its kind known to humanity. Much of the earth’s mass is composed of rocky and molten geophysical components, yet a thin film of life surrounds the globe at its surface. The biosphere is the name given to all the places on earth sustaining living things. Notice this concept does not include the whole planet necessarily, but we do know that most of the earth’s surface is habitable. The biosphere, in turn may be subdivided into ecosystems composed of communities, which are groups of populations. Populations are a little tricky to define, but the traditional definition is that of all the individuals of a particular species in one place at one time. Populations are subdivided into individual creatures which are all engaged in a fight to survive and reproduce in an often changing environment.
Figure 1. Hierarchical organization of biological systems from molecules to the biosphere (http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/1.9.jpg).
But biological organization goes further still. Based on years of study, we know that individuals are composed of organ systems or tissue layers that are in reality groups of specialized cells, fundamental units of biological structure and function. Some organisms are actually single cells, while others are multicellular. At the level of the cell, a whole new universe of biological interactions open up. Using different imaging techniques, including microscopy and histological sectioning, we observe that cells are composed of many different cellular features, many of them specific to the type of cell in question. So, we see that organic, biological nature can be studied by the biologist at a number of different levels of naturally occurring hierarchical organization (Fig. 1). Differences in levels of organization chosen for study by biologists are responsible for the subdivisions of biological science mentioned above. From this short discussion, we see that biology covers an enormous range of living phenomena and that biologists have an immense amount of living material available to work with.
There is a level of biological organization that I have failed to mention. I will address this level after briefly digressing to discuss a familiar phrase that you might hear in an introductory biology class. One way of viewing the relationship between biology and the other sciences is captured in the familiar axiom, “All biology is chemistry, all chemistry is physics, and all physics is mathematics.” This phrase may be interpreted in a variety of contexts. Many, including myself, consider it a gross and sometimes unhelpful oversimplification. It does, however, have a few interesting things to say about biology and science which cannot be doubted. First, it brings an important biological paradox to light, namely that at smaller scales all biological entities are composed of non-living chemical substances. It is very important that the student recognizes the biotic (living) and abiotic (non-living) levels of biological organization: below the cellular and organelle levels, life breaks down into chemical constituents, which can be further subdivided on the basis of their structure and function as they relate to one another and the rest of the biosphere (more later). Second, it highlights the important link between natural and physical sciences. Third, it notes the connection of all sciences with what some (mostly physical scientists, statisticians, and mathematicians!) consider the most basic and inescapable truth of the universe, mathematics. Ultimately, standing alone, this phrase fails in helping us understand what biology really is, but it does offer a great road map for rounding out our knowledge of hierarchical biological organization as I have shown—by including biochemical substances.
Campbell and Reece (2007) list eleven themes that unify biology (p.27), including (1) the cell as the basic unit of structure and function; (2) the idea that the continuity of life depends on the inheritance of hereditary information encoded in the form of specific nucleotide sequences of deoxyribonucleic acid (DNA) molecules; (3) the interconnected facts (a) that biological systems are more than the sum of their parts, (b) that the biosphere shows a hierarchical kind of organization, and (c) new properties emerge as we travel up the hierarchical structure of living things which were not apparent at lower levels; (4) the ubiquity of regulation in biological systems, where we find that feedback mechanisms and other forms of regulation attempt to maintain stable physiological or chemical states; (5) the idea that living things are important parts of their environment, interact with it, exchange energy with it, and thus change their environments; (6) two related ideas that (a) living things place energetic demands on their environments as a function of the caloric costs of their metabolism involved in the work organisms carry out from sub-cellular to organismal levels and that similarly (b) energy flows through the biosphere from the sun to producers and on to consumers, and this energy leaves ecosystems and organisms in the form of heat energy; (7) while a great phenotypic diversity is seen in the biosphere, (a) the great variety of biological forms and their interactions arise from a much less diverse (similar) pool of genes and (b) all living things arose from a single common ancestor some billions of years ago; (8) evolution is the unifying fact of all biology which explains the unity and diversity we observe in the living world; (9) structure and function are intimately linked throughout the hierarchical organization of biological systems; (10) as I have focused upon thus far, biology is inherently scientific, thus based on inquiry and subject to the methods and philosophy of science; and, finally, (11) biology is not disconnected from other fields of inquiry, but has important applications and implications for individuals, society, other sciences, technological innovation, human societies, and the planet at large.
HERE: I'M SKIPPING BASIC CHEMISTRY, BIOCHEMISTRY, AND RELATIONSHIPS BETWEEN THESE VARIABLES AND THE FITNESS OF THE NATURAL ENVIRONMENTS OF THE EARTH FOR SUSTAINING LIFE. NOTE: The cell, genetics, and mechanisms of organic evolution will comprise the focus of the following discussion.See "References" Link for more information about sources and extra reading materials (If not on sidebar, it's coming).
First, and foremost, biology is a science. Science is simply any study of how the world works reasoned out using naturalistic explanations. The highest goal of science is knowledge, so science can be thought of as the quest for knowledge, which may also be viewed as an innate part of the human experience. Often, our concept of science is synonymous with our understanding of scientific methods. And in the real world, the concepts lay people have about biology are based upon the relationship between what they know about biologists and their work.
If science is a way of seeking out answers to our questions about ourselves and the world around us, then how is this accomplished by biologists? Biology, like other sciences, is based on the idea of inquiry. Campbell and Reece (2007) define this as “the heart of science… a search for information and explanation, often focusing on specific questions.” If science is inquiry and inquiry is the quest for knowledge about the world and explanations of this knowledge, then it follows that the work of biologists must be centered upon observation and explanation; indeed, this is the case.
Observations are made by using our human senses to record qualitative (non-numerical) and quantitative (numerical) information about the world around us. We call this information, which are in essence facts about how the world is, data, which scientists use to make explanations about the natural world. Biologists make diverse observations from the color of fish fins to the size of neurons. Conclusions based on observations are drawn by a type of logic known as inductive reasoning, which is used to make generalizations from scientific data we gather. Explanations of generalizations based on facts represent the next logical step in scientific inquiry. After gathering facts and making generalizations, biologists and other scientists often develop hypotheses, which are educated guesses about specific questions making predictions that can be tested using another important scientific method, the experiment. Hypothesis-based science makes the jump from generalizations to understanding specific interactions, forces, structures, and so on, responsible for biological phenomena by using deductive reasoning (deduction), which creates a logical flow oppositely oriented with respect to inductive reasoning discussed above. In other words, deduction is the process by which we make the transfer from generalizations to specific results. This process allows scientists to draw the testable predictions integral to hypothesis-based science.
Here, it is important to emphasize that the straightforward scientific method of primary education (observation, hypothesis, prediction, test, etc.) in science represents only one description of the order of scientific methods. Many times in their career—even during one experiment or project (set of experiments)—biologists may use different methods or different ordering of research priorities to answer biological questions. In fact, some biologists never even conduct experiments, because in many cases they would be biologically harmful and or morally unacceptable!Another way to begin thinking about biology as a science might be to ask, what real world forces or tools are responsible for the advancement of science, of biology? An important point might be how the breadth of biological inquiry, not unlike other fields of science, has always been intimately linked with technological and theoretical advances. Many of these have been perpetuated by workers in the field of biology, however many important innovations in biology owe themselves to advances in other fields of science. Technological and theoretical advances are important because they detail the options available to biologists in terms of method and concepts upon which their inquiry is based. Thus, technology and theoretical improvement lead to better solutions of biological problems, including more rigorous tests of better equipped hypotheses. So, we see that it would be unrealistic to view biological science and other disciplines of scientific study as mutually exclusive entities. In his book, The Creation, E. O. Wilson (2006) notes,
“The ongoing explosive growth of knowledge, especially in thesciences, has resulted in a convergence of disciplines and created the reality,not just the rhetoric, of inter-disciplinary studies. Biology, for example, istoday a swiftly evolving kaleidoscope of hybrid subdisciplines… As aconsequence, what was once perceived as an epistemo-logical divide between thegreat branches of learning is now emerging from the academic fog as somethingfar different and much more interesting: a wide middle domain of mostlyunexplored phenomena open to a cooperative approach from both sides of theformer divide.”
Biology is continually advancing in new directions fueled by technology and theory, but a proportion of biological advances must always be attributed to the momentum generated by this middle domain and by the academy as a whole, resulting from the more generally intertwined nature of fields of science. For example, and a specific one at that, as chemical experiments reveal more about pieces of biological phenomena, biologists are better informed about their studies and therefore their work is accelerated.But if academia, if all of science is intertwined in this way, what features of biology distinguish it from other realms of science? Is there a point where the other sciences end and biology begins? There are minimally two approaches to solving this problem for the novice, explaining what makes biology similar to other fields of science then venturing on to its uniqueness, or explaining away what biology is not and should not be. Alternatively, one might go directly into the big picture of what biology really is beyond formal distinctions about science and its philosophy, then focus in on its more specific attributes. Now that we have discussed what science is and how biologists conduct scientific investigations, I will take the first step toward accomplishing the end of this alternative goal.
In simplest terms, biology is the study of life. More precisely, modern biological science represents a multi-faceted discipline exploring the complexity of living things, their history, their interactions with each other and their environments across fine (microscopic) and broad spatial (global) and temporal (historical) scales. Biology is divided into many specialty areas of research, which include, but are not limited to, cell biology, genetics, anatomy and physiology, ecology, systematics, and evolutionary biology. An educated view of what biology is best approached by a top-down approach. So, before we go any further, we should begin with the big picture.The earth is our home, our place in the universe, the only life-bearing planet of its kind known to humanity. Much of the earth’s mass is composed of rocky and molten geophysical components, yet a thin film of life surrounds the globe at its surface. The biosphere is the name given to all the places on earth sustaining living things. Notice this concept does not include the whole planet necessarily, but we do know that most of the earth’s surface is habitable. The biosphere, in turn may be subdivided into ecosystems composed of communities, which are groups of populations. Populations are a little tricky to define, but the traditional definition is that of all the individuals of a particular species in one place at one time. Populations are subdivided into individual creatures which are all engaged in a fight to survive and reproduce in an often changing environment.
Figure 1. Hierarchical organization of biological systems from molecules to the biosphere (http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/1.9.jpg).
But biological organization goes further still. Based on years of study, we know that individuals are composed of organ systems or tissue layers that are in reality groups of specialized cells, fundamental units of biological structure and function. Some organisms are actually single cells, while others are multicellular. At the level of the cell, a whole new universe of biological interactions open up. Using different imaging techniques, including microscopy and histological sectioning, we observe that cells are composed of many different cellular features, many of them specific to the type of cell in question. So, we see that organic, biological nature can be studied by the biologist at a number of different levels of naturally occurring hierarchical organization (Fig. 1). Differences in levels of organization chosen for study by biologists are responsible for the subdivisions of biological science mentioned above. From this short discussion, we see that biology covers an enormous range of living phenomena and that biologists have an immense amount of living material available to work with.
There is a level of biological organization that I have failed to mention. I will address this level after briefly digressing to discuss a familiar phrase that you might hear in an introductory biology class. One way of viewing the relationship between biology and the other sciences is captured in the familiar axiom, “All biology is chemistry, all chemistry is physics, and all physics is mathematics.” This phrase may be interpreted in a variety of contexts. Many, including myself, consider it a gross and sometimes unhelpful oversimplification. It does, however, have a few interesting things to say about biology and science which cannot be doubted. First, it brings an important biological paradox to light, namely that at smaller scales all biological entities are composed of non-living chemical substances. It is very important that the student recognizes the biotic (living) and abiotic (non-living) levels of biological organization: below the cellular and organelle levels, life breaks down into chemical constituents, which can be further subdivided on the basis of their structure and function as they relate to one another and the rest of the biosphere (more later). Second, it highlights the important link between natural and physical sciences. Third, it notes the connection of all sciences with what some (mostly physical scientists, statisticians, and mathematicians!) consider the most basic and inescapable truth of the universe, mathematics. Ultimately, standing alone, this phrase fails in helping us understand what biology really is, but it does offer a great road map for rounding out our knowledge of hierarchical biological organization as I have shown—by including biochemical substances.
Campbell and Reece (2007) list eleven themes that unify biology (p.27), including (1) the cell as the basic unit of structure and function; (2) the idea that the continuity of life depends on the inheritance of hereditary information encoded in the form of specific nucleotide sequences of deoxyribonucleic acid (DNA) molecules; (3) the interconnected facts (a) that biological systems are more than the sum of their parts, (b) that the biosphere shows a hierarchical kind of organization, and (c) new properties emerge as we travel up the hierarchical structure of living things which were not apparent at lower levels; (4) the ubiquity of regulation in biological systems, where we find that feedback mechanisms and other forms of regulation attempt to maintain stable physiological or chemical states; (5) the idea that living things are important parts of their environment, interact with it, exchange energy with it, and thus change their environments; (6) two related ideas that (a) living things place energetic demands on their environments as a function of the caloric costs of their metabolism involved in the work organisms carry out from sub-cellular to organismal levels and that similarly (b) energy flows through the biosphere from the sun to producers and on to consumers, and this energy leaves ecosystems and organisms in the form of heat energy; (7) while a great phenotypic diversity is seen in the biosphere, (a) the great variety of biological forms and their interactions arise from a much less diverse (similar) pool of genes and (b) all living things arose from a single common ancestor some billions of years ago; (8) evolution is the unifying fact of all biology which explains the unity and diversity we observe in the living world; (9) structure and function are intimately linked throughout the hierarchical organization of biological systems; (10) as I have focused upon thus far, biology is inherently scientific, thus based on inquiry and subject to the methods and philosophy of science; and, finally, (11) biology is not disconnected from other fields of inquiry, but has important applications and implications for individuals, society, other sciences, technological innovation, human societies, and the planet at large.
HERE: I'M SKIPPING BASIC CHEMISTRY, BIOCHEMISTRY, AND RELATIONSHIPS BETWEEN THESE VARIABLES AND THE FITNESS OF THE NATURAL ENVIRONMENTS OF THE EARTH FOR SUSTAINING LIFE. NOTE: The cell, genetics, and mechanisms of organic evolution will comprise the focus of the following discussion.See "References" Link for more information about sources and extra reading materials (If not on sidebar, it's coming).
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