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1.1: An Invisible World - Biology

1.1: An Invisible World - Biology


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Microorganisms (or microbes, as they are also called) are small organisms. Most microorganisms are harmless to humans and, in fact, many are helpful. They play fundamental roles in ecosystems everywhere on earth, forming the backbone of many food webs. People use them to make biofuels, medicines, and even foods. Without microbes, there would be no bread, cheese, or beer. Our bodies are filled with microbes, and our skin alone is home to trillions of them. Some of them we can’t live without; others cause diseases that can make us sick or even kill us. Although much more is known today about microbial life than ever before, the vast majority of this invisible world remains unexplored. Microbiologists continue to identify new ways that microbes benefit and threaten humans.

  • 1.1.1: What Our Ancestors Knew
    Microorganisms (or microbes) are living organisms that are generally too small to be seen without a microscope. Throughout history, humans have used microbes to make fermented foods such as beer, bread, cheese, and wine. Long before the invention of the microscope, some people theorized that infection and disease were spread by living things that were too small to be seen. They also correctly intuited certain principles regarding the spread of disease and immunity.
  • 1.1.2: Types of Microorganisms
    Microorganisms are very diverse and are found in all three domains of life: Archaea, Bacteria, and Eukarya. Archaea and bacteria are classified as prokaryotes because they lack a cellular nucleus. Archaea differ from bacteria in evolutionary history, genetics, metabolic pathways, and cell wall and membrane composition. Archaea inhabit nearly every environment on earth, but no archaea have been identified as human pathogens.
  • 1.1.3: Environmental Diversity of Microbes
    Microbes are ubiquitous on Earth and their diversity and abundance are determined by the biogeographical habitat they occupy.
  • 1.1.4: The Beginnings of Modern Microbiology
    Modern microbiology began with the discovery of microbes in the 1600s and the scope and scale of the field continues to expand today.
    • 1.1.4.1: Pasteur and Spontaneous Generation
    • 1.1.4.1.1: The Germ Theory of Disease
    • 1.1.4.2: Koch and Pure Culture

Thumbnail: A cluster of Escherichia coli bacteria magnified 10,000 times. (Public Domain; Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU).


2.2 Peering Into the Invisible World

Some of the fundamental characteristics and functions of microscopes can be understood in the context of the history of their use. Italian scholar Girolamo Fracastoro is regarded as the first person to formally postulate that disease was spread by tiny invisible seminaria, or “seeds of the contagion.” In his book De Contagione (1546), he proposed that these seeds could attach themselves to certain objects (which he called fomes [cloth]) that supported their transfer from person to person. However, since the technology for seeing such tiny objects did not yet exist, the existence of the seminaria remained hypothetical for a little over a century—an invisible world waiting to be revealed.

Early Microscopes

Antonie van Leeuwenhoek , sometimes hailed as “the Father of Microbiology,” is typically credited as the first person to have created microscopes powerful enough to view microbes (Figure 2.9). Born in the city of Delft in the Dutch Republic, van Leeuwenhoek began his career selling fabrics. However, he later became interested in lens making (perhaps to look at threads) and his innovative techniques produced microscopes that allowed him to observe microorganisms as no one had before. In 1674, he described his observations of single-celled organisms, whose existence was previously unknown, in a series of letters to the Royal Society of London. His report was initially met with skepticism, but his claims were soon verified and he became something of a celebrity in the scientific community.

While van Leeuwenhoek is credited with the discovery of microorganisms, others before him had contributed to the development of the microscope. These included eyeglass makers in the Netherlands in the late 1500s, as well as the Italian astronomer Galileo Galilei, who used a compound microscope to examine insect parts (Figure 2.9). Whereas van Leeuwenhoek used a simple microscope , in which light is passed through just one lens, Galileo’s compound microscope was more sophisticated, passing light through two sets of lenses.

Van Leeuwenhoek’s contemporary, the Englishman Robert Hooke (1635–1703), also made important contributions to microscopy, publishing in his book Micrographia (1665) many observations using compound microscopes. Viewing a thin sample of cork through his microscope, he was the first to observe the structures that we now know as cells (Figure 2.10). Hooke described these structures as resembling “Honey-comb,” and as “small Boxes or Bladders of Air,” noting that each “Cavern, Bubble, or Cell” is distinct from the others (in Latin, “cell” literally means “small room”). They likely appeared to Hooke to be filled with air because the cork cells were dead, with only the rigid cell walls providing the structure.

Check Your Understanding

  • Explain the difference between simple and compound microscopes.
  • Compare and contrast the contributions of van Leeuwenhoek, Hooke, and Galileo to early microscopy.

Micro Connections

Who Invented the Microscope?

While Antonie van Leeuwenhoek and Robert Hooke generally receive much of the credit for early advances in microscopy, neither can claim to be the inventor of the microscope. Some argue that this designation should belong to Hans and Zaccharias Janssen , Dutch spectacle-makers who may have invented the telescope, the simple microscope, and the compound microscope during the late 1500s or early 1600s (Figure 2.11). Unfortunately, little is known for sure about the Janssens, not even the exact dates of their births and deaths. The Janssens were secretive about their work and never published. It is also possible that the Janssens did not invent anything at all their neighbor, Hans Lippershey , also developed microscopes and telescopes during the same time frame, and he is often credited with inventing the telescope. The historical records from the time are as fuzzy and imprecise as the images viewed through those early lenses, and any archived records have been lost over the centuries.

By contrast, van Leeuwenhoek and Hooke can thank ample documentation of their work for their respective legacies. Like Janssen, van Leeuwenhoek began his work in obscurity, leaving behind few records. However, his friend, the prominent physician Reinier de Graaf, wrote a letter to the editor of the Philosophical Transactions of the Royal Society of London calling attention to van Leeuwenhoek’s powerful microscopes. From 1673 onward, van Leeuwenhoek began regularly submitting letters to the Royal Society detailing his observations. In 1674, his report describing single-celled organisms produced controversy in the scientific community, but his observations were soon confirmed when the society sent a delegation to investigate his findings. He subsequently enjoyed considerable celebrity, at one point even entertaining a visit by the czar of Russia.

Similarly, Robert Hooke had his observations using microscopes published by the Royal Society in a book called Micrographia in 1665. The book became a bestseller and greatly increased interest in microscopy throughout much of Europe.

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    If you are looking for a tour through the nanoscale world, this book is a goodstarting point.

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    Every page of the Deffeyes's engaging texts and striking illustrations reveals surprises about the nanoarchitecture of our world and conveys how exciting and delightful science can be. Beautiful, amusing, and richly informative, this book deserves to be a classic.

    ― Peter Pesic , author of Sky in a Bottle

    About the Author

    Kenneth S. Deffeyes is Professor of Geology Emeritus at Princeton University. He is the author of Hubbert's Peak and Beyond Oil.


    Chocolate Covered Crispies

    Everyone loves Chocolate Covered Crispies -- partially because of the novelty of eating a bee, partially because of the chocolate! People compare the flavor of Chocolate Covered Crispies to: a Nestle Crunch bar, chocolate with crispy honey inside, and chocolate with a faint flowery flavor.

    1 1/2 cups semi-sweet chocolate chips

    1 cup bees (rinse in water in a colander)

    Place bees on cookie sheet and roast in oven for 1-2 hours at 200 degrees F. Shake and stir the bees occasionally. Test the bees for doneness by crushing the bee with a spoon (bees are done if they are crispy and crush easily).In a large bowl, partially melt the chocolate in a microwave. Add oil and stir. Microwave until melted. Gradually add roasted bees to chocolate. Removed covered bees and place on greased wax paper. Place in freezer overnight. Chocolates are easily removed from wax paper.

    You can obtain bees from a local bee-keeper where you can learn about bee-keeping and bee biology. Bring a large mason jar for the bees and a cooler with ice. The bee keeper will show you how to harvest the bees. Place the bees in the mason jar in the cooler. When you get home, immediately place the bees in the freezer.


    Kickboxing Kangaroos

    Some male red kangaroos can be up to six feet tall. Image by David Cook via Flickr.

    You pull off along the dirt road and get out of the car. Most of the kangaroos have gone already, but one is moving past you slowly and stops. You don’t get too close, as kangaroos can defend themselves very well, but you size up the creature standing there. The first thing you notice is just how big kangaroos can be.

    The size of an adult is different for different species, but this red kangaroo is slightly taller than you are. Red kangaroos are the largest and the males can stand at around 1.8 meters tall (almost 6 feet tall). The western grey kangaroo is the smallest great kangaroo and the adults stand around 1.3 meters (or 4 feet) tall.

    Kangaroos can also be pretty heavy. An adult male red kangaroo can weigh just over 90 kilograms (about 200 pounds). That’s heavier than an average healthy adult human. They also know how to throw that weight around if they need to… and it’s mostly with their hind legs.

    Male red kangaroos can be about as tall as an average adult human. Female red kangaroos are much smaller than the average human. Why do you think kangaroos have such a large size difference between males and females?

    Fighting red kangaroos. Click for more detail.

    When kangaroos fight, they do a lot of pushing and grabbing with their front legs, but their main weapons are their hind legs. They can lean back on their large tails to balance, while they launch their feet, delivering painful kicks. They also have claws, making those kicks and grabs even more dangerous. Luckily, kangaroos only usually fight when they are defending themselves, or fighting over a mate.

    Their strong legs really come in handy for the way they move, by hopping. While hopping seems to take a lot of energy, it is actually a very efficient way to move. A red kangaroo can jump up to 25 feet in one hop, and can jump nearly 6 feet high. Once they start moving, they can hop at speeds of up to 35 miles per hour, which is about the same speed as a horse can run.


    How to Read a Scientific Paper

    Below, we've mapped out the "gross anatomy" of an article — basically an overview of what goes where in a paper. After you know the basics of what you can expect to find in a scientific article, take a shot at reading one on our Article Dissection page. Together these sections provide tips you can use when reading a scientific paper.

    Just like you have a name, so does every research paper that is published. Usually the title offers a general idea of the subject of the paper. Sometimes it will also include information on what the scientists found. Show me an example | 1 |

    Give credit where credit is due. People that made a large contribution to the project usually end up as an author. If there is more than one author, they are called co-authors. Sometimes, when a lot of people are involved, this makes for a very long list of authors. Show me an example | 1 |

    Author affiliations

    It may seem odd, but scientists aren't the only ones involved in the completion of a study. Often times the university or institution where the study was completed also had an important role, in providing funds for the work, for example. The universities or institutions that sponsored the work are usually listed under the authors' names. To see which author came from what institution, you can usually match the numbers or symbols listed next to the author and institution names.

    The abstract is a one paragraph summary of the most important parts of the article. Reading the abstract is a good way to figure out if you are interested in reading the rest of the paper. Abstracts can also have a ton of information though, so they can sometimes be difficult to read.
    Show me an example | 1 |

    Author Summary

    Certain journals like to have the authors of the article write a simplified version of the abstract. This is often written for non-scientists or scientists from other fields. If an article has an author summary, it might be good to read it before you read the abstract. Show me an example | 1 |

    Introduction

    Background is very important. If you're trying to learn about a specific lizard, for example, it would be useful to know where the lizard species lives, what it eats, and what kind of behaviors it might show. The introduction of a paper is where the scientists give you all of the relevant background information so you can better understand the study. Show me an example| 1 |

    Materials and Methods

    It would be great if scientific information would magically appear. But it doesn't. Instead, it takes days, months, or years to carry out experiments for a study. In the materials and methods section, the scientists explain exactly how they did their study. It is kind of a "how to" or "DIY" for other scientists. Because of the complicated nature of some studies, the materials and methods section can sometimes be the toughest part of the paper to read.

    But this section can also give you the best idea of how research is done. Show me an example | 1 |

    Results (with figures and tables)

    Do you ever listen to an overly long story and wish that the storyteller would just get to the point? If you do, the results section will probably be your favorite. This is the heart of the paper, where the scientists tell you exactly what they found. This is usually where you will also find the figures and tables, though some papers put all the figures at the very end. A lot of results are pretty raw data (meaning the data hasn't been interpreted). Interpretation is saved for the next section. Show me an example | 1 |

    If you read the results section, you probably take in a lot of numbers, some useful graphs, and you have a good idea of what was found overall. But what does any of it mean? Are the findings important? These questions are answered in the discussion section. Here, scientists present what they learned from the study and what effect the new information will have on science. They also discuss any problems with the experiment in this section. There is one thing to be wary of when reading the discussion. sometimes data can be interpreted in different ways. The interpretation presented in a discussion is not always the only interpretation possible. This is why the discussion section is kept separate from the results section.
    Show me an example | 1 |

    Some journal articles have a conclusion section, which is basically a summary of the study that is really heavy on findings and what those findings mean. If you want the quick version of what impact the study will have on science, look for a conclusions section.
    Show me an example | 1 |

    Acknowledgments

    Some studies involve many, many people that contribute, sometimes in relatively small ways. If someone helps out but didn't do enough to be an author on a paper, they still get credit for their work by being listed in the acknowledgments section. Show me an example | 1 |

    Author Contributions

    While an author list tells us which people were most important to completing a study, it doesn't tell us what each author contributed to the process. Some journals don't include an author contributions section, but when they do, they list which author did what during the study.
    Show me an example | 1 |

    You may have heard the phrase that things "do not exist in vacuums." The reference section is proof of that idea. Throughout the entire paper, scientists used other published information to help give you background on their work, to explain why they used certain methods, or to compare their findings to others. The references section is where all those other published studies are listed. As you read through an article, you will often see either tiny numbers in superscript or last names in parentheses at the end of some sentences. These are cues that link you to specific published articles that are all listed in the reference section. This section is especially helpful if you want to get more information related to the article you are reading. Show me an example | 1 |


    Supplementary Materials

    Some studies produce a lot of important information that the scientists want to share with the world. Yet, if you want someone to read a journal article, it can only be so long. Sometimes, if there is too much information for too little of an article, information that can be considered "extra" is listed in a different section of supplementary materials.


    Vision Physiology

    Visual encoding in V4

    Functionally, lesion evidence points to a role for V4 in fine-grain spatial recognition, including the learning of new discriminations [ 21–23 ]. However, the earliest evidence from physiological recordings pointed to a specialized role of V4 in colour processing and recognition. It is unclear whether all of the colour and spatial processing can be neatly assigned to different distinct compartments of V4 although there is no doubt that such compartments exist [ 15 ]. An early extensive set of recordings demonstrated that information-theoretic analysis of neuronal firing shows that many single V4 neurons carry signals about both spatial pattern and colour [ 24 ].

    A recent study [ 25 •• ] has shown how the specialization of compartments in V4 may lead to the accurate transmission of fine spatial detail. Direct measurements in the foveal region of V1 show that single neurons in that cortical region signal fine spatial detail about high spatial frequencies right up to the acuity limit [ 26 ]. Using both optical imaging and single neuron recording, the new work shows that there are specialized compartments for high spatial frequencies in V4. These appear to reflect the variability in the retinotopic mapping within V4, resulting in islands of cortex with a wide range of tuning for spatial frequency, including neurons suitable for high acuity pattern recognition. Such neural receptive fields are presumably those that are most susceptible to visual crowding effects [ 27 ].

    These recent findings may map nicely onto earlier anatomical work that suggests a segregation of visual processing according to visual field location within V4 [ 28 ]. Anatomical tracing suggests not just a segregation of regions of V4 according to location in the visual field, but a different functional pattern of cortical [ 28 ] and subcortical [ 29 ] connections for the foveal and peripheral parts of V4, with certain brain locations exclusively connecting with only the foveal or only the peripheral portion of V4.

    V4 neurons encode information about the content of natural image sets with as much accuracy and fidelity as neurons deeper in the ventral visual pathway in the inferotemporal (IT) cortex [ 4 ]. The same study showed that V4 neurons are less able to generalize across spatial location than IT neurons, whilst V4 neurons are less disrupted than IT neurons by scrambling of image content, consistent with the long-held view that some IT neurons signal the presence of certain types of visual object [ 2 ].

    More recent analyses have shown close correspondence between the selectivity of V4 neurons and units of the convolutional network model AlexNet [ 30 ] for 2-D shape stimuli with variation of angular position and curvature ( Figure 2 ). These neural networks have a hierarchical set of neural processing layers, rather like the ventral stream pathway. The networks are trained at the top level to learn how to assign object labels (‘bus’, ‘cat’) to pictures of the objects. The weights of all the network connections (equivalent to synaptic strength for a biological neuron) are adjusted all the way back down through all layers as learning proceeds. When the weights are stable, the network can be tested for performance with a new set of pictures and the responses of each of the intermediate layers can be investigated. The repertoire of the neural nets is still limited and, for comparisons with primate vision, the lack of binocularity is a limitation but see Ref. [ 31 ].

    Figure 2 . A photo image and its representation in the early layer of Alexnet [ 30 ]. Deeper layers of Alexnet have patterns of activation that are hard to relate to the original image when viewing the activations as images using the human eye. Alexnet eventually labels this image as an ‘Apiary’, which can be understood perhaps in relation to the silhouette of the tree outline in the background.

    Subjecting the responses of Alexnet units to the same testing and analysis procedures that have been used to characterize real V4 neurons shows that Alexnet does not just match biological performance on image identification tasks. Interesting, it is also found that many of the internal units of Alexnet have selectivity for curvature and object boundaries similar to the single neurons recorded in V4 [ 11 •• ]. This similarity emerges from the training regime of the neural net, rather than being designed into the network architecture.

    There are limits to the perceptual-like qualities of neuronal firing in mid-level areas, like V4. Perceptual reversals under binocular rivalry are evident more robustly in temporal areas that receive input connections from early and mid-level visual areas, such as V4, rather than in those areas themselves [ 32 ]. Similarly, in a challenging image identification task, later inferotemporal areas show delays in neuronal discrimination that parallel the delays in behavioural discrimination, but those delays are not observed in the responses of area V4 [ 33 ]. Beyond the inferotemporal stream, neurons in pre-frontal cortex show greater sensitivity to partially occluded objects than neurons in V4 [ 34 ].


    3 Answers 3

    This question asks for hard science. All answers to this question should be backed up by equations, empirical evidence, scientific papers, other citations, etc. Answers that do not satisfy this requirement might be removed. See the tag description for more information.

    Okay, even if these are in fact three highly connected questions I'll try to answer them as good as possible.

    What would observers experience while seeing one travel through the tube?
    A Krasnikov tube is in the end nothing else then a wormhole with some special settings and abilities, so traveling trough or into one is not different for the observer. In theory a wormhole is not that much different from a black hole regarding effects of gravity and matter with the special difference that where we can see nothing in the center area of a black hole we see the area of the universe where the tube Ends in a wormhole . So watching someone enter a Krasnikov tube is like watching him entering a black hole. As even light is bend by the gravitational forces, in the view of the observer the object entering the hole gets elongated and deformed until it seems to vanish in the circular border of the hole.

    What would observers experience while traveling through the tube?
    According to Luke Butcher, theoretical physicist at the university of Edinburgh (in an interview concerning the movie 'Interstellar'), their presentation of wormhole-travel is highly realistic.

    "Things will look a bit like you're traveling down the center of a wide tunnel. Directly in front of you you'll see the region of space you're heading to, and behind you is the region you've left behind. These views would be surrounded by concentric circularly-distorted repeats of the same view, a bit like an Einstein ring, with the whole sky (of one end of the wormhole) wrapped into a series of rings that get more and more closely packed together as you move your line-of-sight from the longitudinal direction, to a perpendicular direction." (L. Butcher)


    Like this.
    Credit: Public domain via Les Bossinas (Cortez III Service Corp.) and NASA.

    How can it be used to cut travel-times?
    I'm not realy sure what you want to do here. As stated above, Krasnikov-tubes are already special cases of wormholes so 'bringing a wormhole through it' will not change anything as you had to implement the Krasnikov tube in the first place. The cut in travel time will depend on the structure of the wormhole/Krasnikov tube and can not be answered in general.

    This question asks for hard science. All answers to this question should be backed up by equations, empirical evidence, scientific papers, other citations, etc. Answers that do not satisfy this requirement might be removed. See the tag description for more information.


    6 Answers 6

    Since 10% of Xs can see the Ys, the question would be how do they see them. Given a "stretched science" framework, we have two clear possibilities - Biological differences (10% of Xs can see an extended range of electromagnetic frequencies beyond those of most Xs), and psychic/psionic/extrasensory abilities.

    Extended Frequency sight

    This option has a simple solutions for a technological civilization for both conditions. To make the Ys visible to all Xs, the Xs wear frequency shifting eyewear (such as infrared googles, but for whatever frequency is appropriate). To make the Ys invisible to the 10% of Xs, a pair of "dark glasses" that filter out the appropriate frequencies would work.

    Psychic/Psionic/Extrasensory abilities

    This is where things get fuzzy. You would have to define what these extra abilities are, how they work, and whether or not the appropriate forces involved can be detected by the society's standard science.

    For example, "Some Xs have an extra senory ability, used similarly to normal vision, that enables them to detect. um. neutrino scattering, something that Ys do naturally far more than any other substance known, because of their extra-dimensional capabilities.", or "Some Xs are naturally psychic in such a way that they can detect solids or semisolids near them without use of their other senses. No one really notices this sense in most cases (although some of the 10% are unusually good at dodging attacks from where they cannot see them coming), except the Ys are detectable this way. If someone becomes adept at using this sense, they can 'see' the Ys."

    Extending the science of these things will take extrapolation or hand-waving, but the mechanism should be either neutral to survival (just a random mutation that doesn't help or hinder a person's life expectancy), or somewhat beneficial (the ability to detect attacks from behind).


    1.1: An Invisible World - Biology

    A guide on how to obtain the 5 hidden achievements in 7 Days to Die.

    I will update this If more hidden achievements get added in the future.

    Simply dig down till you hit bedrock. You'll know when you reach the bottom by the tan and blue looking floor. It will also make a distinct sound when you hit it like when you hit land claimed territory.

    The easiest method to do this is with an auger and just keep it aimed straight down. Also bring plenty of wood for frames or ladders to get yourself back out.

    Similar to the Dig Deep achievement, for this one all you need to do is reach the top of the game world. There is an invisible ceiling that you can get to where you can't build or place any blocks to get higher. Once you reach this point the achievement should unlock.

    The easiest way to do this is bring a stack of about 200-300 wood frames. How many you actually need will depend on your altitude when you start. Place a wood frame on the ground, jump on top of it and then keep jumping straight up while placing more frames below you. You'll keep going way up into the air (check out the view with the new distant terrain) and eventually unlock the achievement.

    Make sure there are no zombies around when you do this. If they break a block while you are way up in the air you will fall and possibly die.

    This is probably the trickiest of the hidden achievements but not that hard. What you need to do is get your temperature down to 0 while you are totally naked and 100% wet.

    The easiest way to do this is find a snow biome that has a high elevation. The higher your altitude the colder it gets. Find a body of water that is deep enough for you to fully submerge in. Then strip down of all clothing, sit in the water and wait for your temperature to drop. To speed up this process you can wear clothing with a negative thermal value and drink either red tea or Yucca juice as both will help lower your temperature.

    Getting your temperature down this low is dangerous and could result in death, be prepared to put warm clothing on and sit next to a fire as soon as you get the achievement.


    Watch the video: wheres? 1 (June 2022).