Basic extraordinary cell biology

November 22, 2010 | By | 10 Replies More

During a recent visit with my 12-year old daughter’s science teacher, I mentioned that I had read a few books on cell biology over the past couple of years and that I was interested in sitting in on one of the upcoming sixth grade science classes–my daughter had mentioned that they were beginning to study cell biology. I mentioned a few of the things that I had found interesting about cells to the science teacher. After noticing my enthusiasm, she retracted her invitation to watch the class and, instead, invited me to teach part of the class. A few days later I made my science teaching debut.

I advised the sixth-graders that although I work as a lawyer during the day, I often read science books, and I often write about science on my website. I told them that I had no serious science education at the Catholic grade school I attended. I didn’t have any biology class at all until I was a sophomore in high school. That was mostly a nuts and bolts class taught by a Catholic nun who failed show the excitement the subject deserved. She also forgot to teach by Theodosius Dobzhansky’s maxim that “nothing in biology makes sense except in the light of evolution.”

I told “my” class that anyone who studies cells with any care will be greatly rewarded. Studying cells is actually autobiographical because “you are made of 60 trillion of cells.” These cells are so small that people cannot even see them.

One of the students then confused trillions for millions. “Keep in mind,” I cautioned, “that a trillion is a million million.” With regard to their size, there is only one human cell–the human ovum–that you can see with the naked eye—it is much bigger than the other cells in your body. Despite its tiny size, the human ovum is so incredibly small that it’s smaller than the period at the end of this sentence. See this wonderful illustration of the size of human cells, and many other small objects.

The volume of a eukaryotic cell is typically 1000 times larger than that of a prokaryotic one.
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I told the students that the study of cells is autobiographical “because each of you is a community of cells. You are a self-organized community.” Even the brain is made of cells. It thinks, even though individual cells don’t think. Individual cells can’t think, but you can think. “How is that for amazing?” One girl raised her hand.

“I don’t understand how this can be. I don’t understand how the body can be made of trillions of cells. How can it possibly work? I have a lot of questions.”

I told her that her questions prove that she “gets it.” Truly, how can something as complex as a human body, or even as complex as a single cell possibly work? It’s amazing that these things work, yet most people more often focus on the times that they break down through disease or aging.

A bacterial cell consists of more than 300 million molecules (not counting water), several thousand different kinds of molecules, and requires some 2000 genes for specification. There is nothing random about this assemblage, which reproduces itself with constant composition and form generation after generation.
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I didn’t claim to have many answers, but I told the students that I was there to share information I learned from my readings. I assured them that studying cells, including human cells, is more amazing than any fictitious story that they had ever read. Part of the reason the study of cells is so amazing is due to the complex anatomy of cells, especially eukaryotic cells. Appreciating much of the magic requires statistics. Some of it comes from the exquisite complexity of individual cells, however, and much of the magic derives from the appreciation that the scientific facts relating to cell biology are somehow true.

Image by Wikimedia

I then noticed a few of the students were looking puzzled. I reminded them that the scientific study of cells is not about trust. I was not asking them to trust me or their teacher. In upcoming classes, they will be invited to look into microscopes and see cells, including their own cheek cells or skin cells.  With powerful microscopes we can even see chromosomes. I urged them to investigate more about cells on their own, because there is a wealth of information on the Internet. Go out there and check the evidence; investigate as skeptics. Believe only what you see. That’s what I did, and that’s why I’m excited to learn about cells. And remember that only 400 years ago, no one had any idea that humans were communities of cells. They are privileged to be living in an age where we have such detailed knowledge available to us.

I told the students that the information I would tell them came from a variety of sources, including a book called The Way of the Cell: Molecules, Organisms and the Order of Life, by Franklin M Harold (2001). I’ve inserted several passages from Franklin’s excellent book within this post.  In case it isn’t apparent, this post is a summary of the sorts of things I taught my students. I found myself bouncing around the classroom fielding comments and questions and having a great time. My hope was that a few of the kids might see the subject of cell biology in a more compelling way after seeing me so revved about it. That was my main aim, to share my excitement.

What is life? It is an invitation to explore the successive levels of biological reality, and a lecture on molecular biology is intrinsically no more (and no less) illuminating than a walk through the woods in the springtime.
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The students already knew that individual cells (cells that are not part of a multi-cellular organism) have a lot in common with us. They eat, they get rid of waste products and they move toward and away from objects in their environment (including other cells). Somehow, even though they are invisible to the human eye, they are sophisticated enough to react adaptively to information from environment.

Every cell in your body does this amazing task of manufacturing chemicals, even though it is so small that it is invisible, And guess what? Only relatively simple cells such as the bacteria called E-coli make 4,000 types of chemicals. Human animals (yes, I couldn’t resist reminding them that we are animals) have cells that are far more complex than E-Coli. Human cells manufacture more than 50,000 types of proteins, every minute of every day. Cells are able to do much of what they do thanks to proteins they manufacture out of amino acids. Each cell is like a chemical factory, churning away thousands of proteins and other chemicals, all of this being done in precisely correct amount. I told them to imagine a real life factory that was required to manufacture 4,000 types of chemicals in just the right doses every day. That building would be enormous and it would employ many people. It would require careful supervision of dozens of managers.

The genome of E. coli encodes approximately 4000 proteins, that of the yeast 6000; it takes 50,000 proteins or more to make a man. What do they all do? Many proteins are enzymes, but by no means all. Some proteins serve as the building blocks of structural scaffolding. Some make tracks for the movement of organelles, itself mediated by motor proteins. Proteins act as receptors for signals from within the cell or from the outer world; the transport nutrients, waste products and viruses across membranes. Proteins also commonly modulate the activities of other proteins, or of genes. The general principle is that, except for the storage and transmission of genetic information in the construction of compartments, almost all the cells do is done by proteins. [W]e have come to see many of them as mechanical devices that rely on energized motion to perform their tasks.
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For the most part, cells are made of proteins, and they are critically important to allow cells to live. Proteins transport material in and out and within cell. They take in information. They allow cells to grow, reproduce and repair themselves. And this bears repeating. They do this very well, yet they are so small you can’t even see them.

The cell represents the simplest level organization that manifests all the features of the phenomenon of life.
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Another question from the same girl. “I still don’t understand how cells can do what they do. I told her that for the most part, it was beyond me too. Then I took a stab at mentioning an idea written by Stuart Kaufmann in At Home in the Universe. He described the phenomenon of cells as the achievement of an autocatalytic state. I alluded to a candle. When you burn it, the hydrocarbons from the candle are converted into various other products within the flame, including water and carbon dioxide. It’s a very simple one-way stop and start reaction. What if you had thousands of reactions, though, and what if those reactions fed into each other: one reaction results in something that another reaction needs in order to occur. Thousands of type of candles all coordinated to make use of each other’s products and byproducts. All of this happening inside something so small that you can’t even see it with our own eyes.

When we inquire how in amoeba crawls, or how a yeast cell grows and buds off a daughter, the phenomena are inherently very much more complex. The functions of the living organism typically depend upon the coherent operations of molecules by the million, belonging to hundreds or even thousands of different kinds, and marshaled into order by a hierarchy of controls. Few of these modules are free in solution. On the contrary, many are first assembled into elaborate constructs whose dimensions are measured in the micrometers or even millimeters, orders of magnitude greater than those of individual molecules, and their collective actions characteristically display a direction in space. These feature underscore what Warren Weaver, in another seminal essay of the 1940’s called the problems of organized complexity. A satisfying reading of life’s riddle demands a rational account of biological organization that has yet to be achieved.
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As Franklin Harold has written, cells are a place where lifeless molecules turn into life. Millions of lifeless molecules co-reacting inside of a fatty membrane —inside of an invisible little bag—constitute something that is alive. Even though the molecules themselves are not alive, together they constitute life. “How can that be?” I asked, looking at the girl who had asked that question. I don’t know the answer, of course, but it is truly astounding. Somehow, the existence of cell membranes allows groups of molecular reactions to become life itself. Within that selectively permeable little bag, ribosomes somehow assemble thousands of types of proteins from 22 amino acids guided by your genetic code.

[According to] J Perrett, “life is a property of potentially self replicating open systems of interlinked organic reactions, catalyzed stepwise and almost isothermally by complex and specific organic catalysts which are themselves produced by the system.”
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Where do those amino acids come from? I was running out of time and wasn’t able to mention to this class that half of those amino acids seem to come for “free,” according to the classic experiment of Stanley Miller- Harold Urey, who created an artificial environment, the type of which you might expect on a young earth– water methane ammonia and hydrogen. They applied electric sparks to simulate lighting, and they ended up with a soup that contained almost a half dozen amino acids. In short, in the environment of the earth, organic compounds naturally derive from inorganic substances. If only I would have had more time, I would have suggested that there is no hint that DNA can naturally derive from an earthen environment. In fact, many scientists now suspect that the building blocks of DNA were forged in outer space and came to earth in asteroids. Are you amazed, Harry Potter?

Who has heard of DNA? The kids raised their hands, but they hadn’t yet studied it. I quickly described the double-helix shape, then mentioned that the 46 chromosomes of the human genome consist of 3 billion base pairs. If you were extremely determined, you could read the human genome base pairs out loud one time in nine years. I didn’t remember to mention to the students that only1.5% of human genes (about 20,000 of them) code for proteins, the rest being “junk” DNA, which might nonetheless serve important functions. Who is going to sort out this puzzle, and when? I urged the students to consider that the human genome is 99% similar to that of a chimpanzee and 89% similar to genome of a mouse. These animals are our cousins, and you and I are essentially identical, genetically speaking, even though we were born and raised in separate families.

I told them that DNA is coiled up tightly in the cell—it fits in the organelle called the nucleus, which they had briefly studied. It’s coiled up extremely tightly, I said, though “extremely” doesn’t do the process justice. What if you uncoiled the DNA in one human cell, keeping in mind that that cell is so small that you can’t see it with your eyes? What if you laid out the DNA from one human cell end to end, uncoiled? How far would it stretch? The incredible answer is about six feet! Hence, if you unraveled the DNA from all of the cells of one human body, it would stretch to sun and back 610 times. Are you still with me, Harry? Or is this making your head want to explode?

The human genome is immense, but it’s not the biggest genome. The amoeba has the biggest genome, and that it contains 670 billion units of DNA (base pairs). This means that an amoeba has a genome that is more than 200 times bigger than the human genome.

The genetic information in our cells is “read and replicated. Transcription is incredibly accurate. It is incorrect only one time out of 4000. Proofreading machinery within the cells makes this possible. I cannot comprehend how such an error correction process can possibly be. Perhaps someday I’ll understand better . . .

True or false. The cells that make you up contain your own special genome, right? Wrong. I told the children that only 10 % of the cells that make up their bodies contain their own DNA.  By far, most of the cells in the human body are bacteria, most of which live in our gut and they allow us to digest our food. If we didn’t carry around those immense numbers of (immensely tiny) bacteria, we would die. Yes, kids, you are a community. It takes a village of organisms to make a person.

And it takes at least several levels of “emergence” to make a body. Quarks make up subatomic particles (e.g., protons), which make up atoms (carbon), which make up molecules (e.g., water, or proteins), which make up organelles (e.g., mitochondria), which a constitutive part of cells (e.g, skin cells), which make up organs (e.g., brains or skin) which make up human animals (you), which make up societies. You won’t see anything resembling your grandma in atoms, molecules, or cells. You won’t see anything wet about oxygen. But somehow these things, when amassed, take on new qualities that would be totally unpredictable, except that we experienced these things or we’ve been taught these things repeatedly.

[W]e may think of the cell as an intricate and sophisticated chemical factory. Matter, energy and information enter the cell from the environment, while waste products and heat are discharged. The object of the entire exercise is to replicate the chemical composition and organization of the original cell, making two cells grow where there was one before. Even in the simplest cells, this calls for the collaborative interactions of many thousands of molecules large and small, and requires hundreds of concurrent chemical reactions. These break down foodstuff, extract energy, manufacture precursors, assembled constituents, note and execute genetic instructions and keep all this frantic activity coordinated.
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I also mentioned path dependence. There are some things that, had they not happened, you students wouldn’t be sitting there. For instance, if your biologically parents had never met, you never would have been born. Path dependence applies in many realms. For instance, that energy producing organelle, mitochondria (which they had already studied) once lived only on its own as a prokaryotic bacteria. Somehow, mitochondria became subsumed by another prokaryotic cell, which resulted in the eukaryotic cells that make us up (I had just read a fascinating article on the genesis of mitochrondia—I will post on that article soon).

Here’s one more critically important part of our story that involves path dependence. For most of the history of life on earth, cells lived individually. They did not form multi-cellular organisms until about 500 million years ago. I asked the class to name the first kind of animal in which cells clumped together and lived as one organism. They didn’t know (and I didn’t know this until about ten years ago). Animals of this type are still alive today. They are sponges.  Thus, sponges and their close successors, cnidarian life forms, are our distant ancestors. [Harry Potter faints.] Without multi-cellularity—without the fact that individual cells were able to form complex multi-cellular organisms, we wouldn’t have been here. Thus multi-cellularity is one of the great transitions. There are many more of these critical transformation (e.g., creatures successfully moving onto the land).

One more stunning fact for Harry Potter. The size of cells is limited because the area of the membrane area/cell volume ratio would be much too small for cells that are larger than those we can find. But our bodies are huge. How can that be? How do the nutrients get around? Through our blood vessels, of course. And what curiously resembles the blood that pours through our bodies to every nook and cranny? Ocean water, which would likely have served as the habitat of the earliest cells.

What I’ve written above closely resembles my presentation. None of what I have written is controversial among scientists, yet this information is mind-blowing to anyone who cares to sit back and ponder these facts. My intent is that conveying this information as I see it, as a science-savvy layperson, would lead to a deeper appreciation of the complexity and function of human animals. Perhaps 10 or 15 years from now, one of those students might track me down and tell me that it was an amazing story and that he or she studied this subject of cell biology much further, maybe even as a scientist.

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About the Author ()

Erich Vieth is an attorney focusing on consumer law litigation and appellate practice. He is also a working musician and a writer, having founded Dangerous Intersection in 2006. Erich lives in the Shaw Neighborhood of St. Louis, Missouri, where he lives half-time with his two extraordinary daughters.

Comments (10)

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  1. Glen Nevogt says:

    Dear Mr. Vieth –

    I found your biological article to be quite advanced. Did you measure the effectiveness of your delivery, considering the fact that you planned it for a sixth-grade audience?

    Secondly, I was hoping to would be so kind to comment on the following, "One relatively simple process necessary for animal life is the ability for blood to clot to seal a wound and prevent an injured animal (or person) from bleeding to death. Yet the only way this intricate system works is when many complicated chemical substances interact. If only one ingredient is missing or doesn't function in the right way—as in the genetic blood disorder hemophilia—the process fails, and the victim bleeds to death.

    How can complex substances appear at just the right time in the right proportions and mix properly to clot blood and prevent death? Either they function flawlessly or clotting doesn't work at all.

    At the same time, medical science is aware of clotting at the wrong time. Blood clots that cut off the flow of oxygen to the brain are a leading cause of strokes and often result in paralysis or death. When blood clots, either everything works perfectly or the likely outcome is death.

    For evolution to have led to this astounding phenomenon, multiple mutations of just the right kind had to converge simultaneously or the mutations would be useless. Evolutionists can offer no realistic explanation of how this is possible."

    Thank You!

    • Erich Vieth says:

      Glen: I suspect that you would rather that I teach religion in a science class. I would never agree to do that. We should only teach science in science classes.

      Interesting how you claim that it would be impossible to for a blood clotting mechanism to evolve, apparently without doing any research. I recommend that you read the following article by Ken Miller, a real scientist: The Evolution of Vertebrate Blood Clotting, http://www.millerandlevine.com/km/evol/DI/clot/Cl

      Sixth graders are capable of much more than we give them credit for. I respected their intelligence, but worked hard to not talk over their heads. They seemed to very much enjoy the discussion based on the looks on their faces and their participation in the discussion.

  2. Dan Klarmann says:

    One evolutionary detail that is often ignored is that evolution always creates complexity. This can be seen in many fields, not just biology. Most survivable mutations are the result of random increases in genetic information. Only some of these get selected out, sometimes making a noticable change in a organism.

    The irreducible complexity argument (that Glen appears to be heading toward) is both very persuasive, and easily disproven. It has been proved wrong every time anyone presented an apparent instance.

    If anything, simplicity should be considered a sign of intelligent intervention; of careful and considered pruning. Complexity is sloppy design.

    Why do primates have more stages in their clotting mechanism than do reptiles? Both mechanisms do the same job. And even the reptile version has too many stages, from an engineering perspective. Clotting shows all the hallmarks of a process that evolved without intelligent oversight.

  3. Jim Razinha says:

    Amazing narrative; well written. It's a shame to try to ruin it by a tired argument for the supernatural. I'll repeat an appropriate James Morrow quote (from "Only Begotten daughter"): Science does have all the answers. We just don't have all the science.

    Anyway, most excellent, Erich! I give career day talks on engineering to eighth graders, and try to make it fun by showing them pretty much everything in their lives has something to do with engineering (plus I show them a lot of cool buildings).

    I think presenting this to young kids is great. Kudos.

  4. Erich Vieth says:

    Jim: It was great fun for me. I must say, though, that I don't know how career teachers do it day after day. I only taught one hour and I prepared for several hours, even though I was rather familiar with the topic. It took a lot of energy to keep things moving and entertaining (I think!).

    We ought to tear down some of the statues of military figures and athletes and replace them with statues of teachers.

  5. Erich Vieth says:

    New 3-D technique for taking videos of live cells. http://www.hhmi.org/news/betzig20110304.html

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