Implications of what the discovery of Naia means

Implications of what the discovery of Naia means

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Recently a discovery was made of a ~12,000 year old girl in Hoyo Negro in Mexico.

This has been covered by many different news agencies.

I'm confused however by many of the reports. Does it strengthen the hypothesis that the ancestors to the Native Americans came over the Bering Strait? Or is there still some doubt on the matter?

Additionally, what are the arguments against the Bering Strait migration?

The discovery strengthens the bering strait land bridge hypothesis because if I remember right they did genetic analysis and her ancestors were almost certainly east asian. As for opposing migration models, they involve boats. Some evidence exists for polynesians reaching the west coast of south america, but probably in small numbers and not before humans walked in from the north. There is more information here:

Requirements analysis

In systems engineering and software engineering, requirements analysis focuses on the tasks that determine the needs or conditions to meet the new or altered product or project, taking account of the possibly conflicting requirements of the various stakeholders, analyzing, documenting, validating and managing software or system requirements. [2]

Requirements analysis is critical to the success or failure of a systems or software project. [3] The requirements should be documented, actionable, measurable, testable, traceable, related to identified business needs or opportunities, and defined to a level of detail sufficient for system design.

Discovery of Cells

The first time the word cell was used to refer to these tiny units of life was in 1665 by a British scientist named Robert Hooke. Hooke was one of the earliest scientists to study living things under a microscope. The microscopes of his day were not very strong, but Hooke was still able to make an important discovery. When he looked at a thin slice of cork under his microscope, he was surprised to see what looked like a honeycomb. Hooke made the drawing in the figure below to show what he saw. As you can see, the cork was made up of many tiny units, which Hooke called cells.

Soon after Robert Hooke discovered cells in cork, Anton van Leeuwenhoek in Holland made other important discoveries using a microscope. Leeuwenhoek made his own microscope lenses, and he was so good at it that his microscope was more powerful than other microscopes of his day. In fact, Leeuwenhoek&rsquos microscope was almost as strong as modern light microscopes. Using his microscope, Leeuwenhoek was the first person to observe human cells and bacteria.

Figure (PageIndex<2>): Robert Hooke sketched these cork cells as they appeared under a simple light microscope.

Is an Anti-Aging Pill on the Horizon?

A nti-aging products from skin creams to chemical peels are part of a $250 billion industry, but scientists have yet to discover a longevity elixir that stands up to medical scrutiny. A group of researchers believe they’re getting closer, however, thanks to a compound called nicotinamide adenine dinucleotide, or NAD+ for short.

“NAD+ is the closest we’ve gotten to a fountain of youth,” says David Sinclair, co-director of the Paul F. Glenn Center for the Biology of Aging at Harvard Medical School. “It’s one of the most important molecules for life to exist, and without it, you’re dead in 30 seconds.”

NAD+ is a molecule found in all living cells and is critical for regulating cellular aging and maintaining proper function of the whole body. Levels of NAD+ in people and animals diminish significantly over time, and researchers have found that re-upping NAD+ in older mice causes them to look and act younger, as well as live longer than expected. In a March 2017 study published in the journal Science, Sinclair and his colleagues put drops of a compound known to raise levels of NAD+ into the water for a group of mice.

Within a couple hours, the NAD+ levels in the mice had risen significantly. In about a week, signs of aging in the tissue and muscles of the older mice reversed to the point that researchers could no longer tell the difference between the tissues of a 2-year-old mouse and those of a 4-month-old one.

Now scientists are trying to achieve similar results in humans. A randomized control trial (considered the gold standard of scientific research) from a different group of researchers published November 2017 in the journal Nature found that people who took a daily supplement containing NAD+ precursors had a substantial, sustained increase in their NAD+ levels over a two-month period.

Sinclair takes an NAD+ upper daily. Anecdotally, he says he doesn’t experience hangovers or jet lag like he used to, he talks faster, and feels sharper and younger. His father takes it too: “He’s 78, and used to act like Eeyore,” says Sinclair. “Now he’s going on six-day hikes and traveling around the world.

“I’m not saying we’ve proven it works,” Sinclair adds. “But I can say that if it’s going to work, I hope to be the one to prove it.”

He has competition. Sinclair plans to take his NAD+ research through the U.S. Food and Drug Administration (FDA) approval process and eventually create a pill that could be prescribed by a doctor or purchased over the counter, but another company, called Elysium, is already selling a supplement called Basis that contains compounds known to boost NAD+ levels. (Basis is the supplement tested in the 2017 Nature study.) Leonard Guarente, Elysium’s chief scientist and co-founder–who also directs the Glenn Center for Biology of Aging Research at MIT–says Basis is not intended to extend people’s life spans, but to help them stay healthier for longer.

Eight Nobel laureates are on the company’s scientific advisory board. “I don’t really mind how long I live provided the life is as good as it is now,” says board member Sir Richard Roberts, winner of the 1993 Nobel Prize in Physiology or Medicine (who is 74). “The only difference I’ve noticed is that the skin on my elbows is smoother than it used to be. Whether it’s Basis or something else, I have no idea.”

By bringing Basis to market as a supplement, and not a drug, Elysium is not required to undergo years of clinical research and FDA approval processes. That decision, and the support of prominent scientists, has stoked criticism from some medical-community experts who wonder why Nobel laureates would attach their names to a supplement without much human research behind it. Elysium declined to confirm if the scientific advisory board members are paid.

Although Basis is already available for purchase, Elysium is currently conducting clinical trials of the supplement. This research, plus that of Sinclair and others, may finally reveal whether NAD+ is the health-extending compound they hope it is.

Implications of what the discovery of Naia means - Biology

Proteins are essential to life, supporting practically all its functions. They are large complex molecules, made up of chains of amino acids, and what a protein does largely depends on its unique 3D structure. Figuring out what shapes proteins fold into is known as the “protein folding problem”, and has stood as a grand challenge in biology for the past 50 years. In a major scientific advance, the latest version of our AI system AlphaFold has been recognised as a solution to this grand challenge by the organisers of the biennial Critical Assessment of protein Structure Prediction (CASP). This breakthrough demonstrates the impact AI can have on scientific discovery and its potential to dramatically accelerate progress in some of the most fundamental fields that explain and shape our world.

A protein’s shape is closely linked with its function, and the ability to predict this structure unlocks a greater understanding of what it does and how it works. Many of the world’s greatest challenges, like developing treatments for diseases or finding enzymes that break down industrial waste, are fundamentally tied to proteins and the role they play.

We have been stuck on this one problem – how do proteins fold up – for nearly 50 years. To see DeepMind produce a solution for this, having worked personally on this problem for so long and after so many stops and starts, wondering if we’d ever get there, is a very special moment.

Co-Founder and Chair of CASP, University of Maryland

This has been a focus of intensive scientific research for many years, using a variety of experimental techniques to examine and determine protein structures, such as nuclear magnetic resonance and X-ray crystallography. These techniques, as well as newer methods like cryo-electron microscopy, depend on extensive trial and error, which can take years of painstaking and laborious work per structure, and require the use of multi-million dollar specialised equipment.

The ‘protein folding problem’

In his acceptance speech for the 1972 Nobel Prize in Chemistry, Christian Anfinsen famously postulated that, in theory, a protein’s amino acid sequence should fully determine its structure. This hypothesis sparked a five decade quest to be able to computationally predict a protein’s 3D structure based solely on its 1D amino acid sequence as a complementary alternative to these expensive and time consuming experimental methods. A major challenge, however, is that the number of ways a protein could theoretically fold before settling into its final 3D structure is astronomical. In 1969 Cyrus Levinthal noted that it would take longer than the age of the known universe to enumerate all possible configurations of a typical protein by brute force calculation – Levinthal estimated 10^300 possible conformations for a typical protein. Yet in nature, proteins fold spontaneously, some within milliseconds – a dichotomy sometimes referred to as Levinthal’s paradox.

Protein folding explained

Results from the CASP14 assessment

In 1994, Professor John Moult and Professor Krzysztof Fidelis founded CASP as a biennial blind assessment to catalyse research, monitor progress, and establish the state of the art in protein structure prediction. It is both the gold standard for assessing predictive techniques and a unique global community built on shared endeavour. Crucially, CASP chooses protein structures that have only very recently been experimentally determined (some were still awaiting determination at the time of the assessment) to be targets for teams to test their structure prediction methods against they are not published in advance. Participants must blindly predict the structure of the proteins, and these predictions are subsequently compared to the ground truth experimental data when they become available. We’re indebted to CASP’s organisers and the whole community, not least the experimentalists whose structures enable this kind of rigorous assessment.

AlphaFold: The making of a scientific breakthrough

The main metric used by CASP to measure the accuracy of predictions is the Global Distance Test (GDT) which ranges from 0-100. In simple terms, GDT can be approximately thought of as the percentage of amino acid residues (beads in the protein chain) within a threshold distance from the correct position. According to Professor Moult, a score of around 90 GDT is informally considered to be competitive with results obtained from experimental methods.

In the results from the 14th CASP assessment, released today, our latest AlphaFold system achieves a median score of 92.4 GDT overall across all targets. This means that our predictions have an average error (RMSD) of approximately 1.6 Angstroms, which is comparable to the width of an atom (or 0.1 of a nanometer). Even for the very hardest protein targets, those in the most challenging free-modelling category, AlphaFold achieves a median score of 87.0 GDT (data available here).

Improvements in the median accuracy of predictions in the free modelling category for the best team in each CASP, measured as best-of-5 GDT.

Two examples of protein targets in the free modelling category. AlphaFold predicts highly accurate structures measured against experimental result.

These exciting results open up the potential for biologists to use computational structure prediction as a core tool in scientific research. Our methods may prove especially helpful for important classes of proteins, such as membrane proteins, that are very difficult to crystallise and therefore challenging to experimentally determine.

This computational work represents a stunning advance on the protein-folding problem, a 50-year-old grand challenge in biology. It has occurred decades before many people in the field would have predicted. It will be exciting to see the many ways in which it will fundamentally change biological research.

Professor Venki Ramakrishnan

Nobel Laureate and President of the Royal Society

Our approach to the protein folding problem

We first entered CASP13 in 2018 with our initial version of AlphaFold, which achieved the highest accuracy among participants. Afterwards, we published a paper on our CASP13 methods in Nature with associated code, which has gone on to inspire other work and community-developed open source implementations. Now, new deep learning architectures we’ve developed have driven changes in our methods for CASP14, enabling us to achieve unparalleled levels of accuracy. These methods draw inspiration from the fields of biology, physics, and machine learning, as well as of course the work of many scientists in the protein folding field over the past half-century.

A folded protein can be thought of as a “spatial graph”, where residues are the nodes and edges connect the residues in close proximity. This graph is important for understanding the physical interactions within proteins, as well as their evolutionary history. For the latest version of AlphaFold, used at CASP14, we created an attention-based neural network system, trained end-to-end, that attempts to interpret the structure of this graph, while reasoning over the implicit graph that it’s building. It uses evolutionarily related sequences, multiple sequence alignment (MSA), and a representation of amino acid residue pairs to refine this graph.

By iterating this process, the system develops strong predictions of the underlying physical structure of the protein and is able to determine highly-accurate structures in a matter of days. Additionally, AlphaFold can predict which parts of each predicted protein structure are reliable using an internal confidence measure.

We trained this system on publicly available data consisting of

170,000 protein structures from the protein data bank together with large databases containing protein sequences of unknown structure. It uses approximately 16 TPUv3s (which is 128 TPUv3 cores or roughly equivalent to

100-200 GPUs) run over a few weeks, a relatively modest amount of compute in the context of most large state-of-the-art models used in machine learning today. As with our CASP13 AlphaFold system, we are preparing a paper on our system to submit to a peer-reviewed journal in due course.

An overview of the main neural network model architecture. The model operates over evolutionarily related protein sequences as well as amino acid residue pairs, iteratively passing information between both representations to generate a structure.

The potential for real-world impact

When DeepMind started a decade ago, we hoped that one day AI breakthroughs would help serve as a platform to advance our understanding of fundamental scientific problems. Now, after 4 years of effort building AlphaFold, we’re starting to see that vision realised, with implications for areas like drug design and environmental sustainability.

Professor Andrei Lupas, Director of the Max Planck Institute for Developmental Biology and a CASP assessor, let us know that, “AlphaFold’s astonishingly accurate models have allowed us to solve a protein structure we were stuck on for close to a decade, relaunching our effort to understand how signals are transmitted across cell membranes.”

We’re optimistic about the impact AlphaFold can have on biological research and the wider world, and excited to collaborate with others to learn more about its potential in the years ahead. Alongside working on a peer-reviewed paper, we’re exploring how best to provide broader access to the system in a scalable way.

In the meantime, we’re also looking into how protein structure predictions could contribute to our understanding of specific diseases with a small number of specialist groups, for example by helping to identify proteins that have malfunctioned and to reason about how they interact. These insights could enable more precise work on drug development, complementing existing experimental methods to find promising treatments faster.

AlphaFold is a once in a generation advance, predicting protein structures with incredible speed and precision. This leap forward demonstrates how computational methods are poised to transform research in biology and hold much promise for accelerating the drug discovery process.

PhD, Founder & CEO Calico, Former Chairman & CEO, Genentech

We’ve also seen signs that protein structure prediction could be useful in future pandemic response efforts, as one of many tools developed by the scientific community. Earlier this year, we predicted several protein structures of the SARS-CoV-2 virus, including ORF3a, whose structures were previously unknown. At CASP14, we predicted the structure of another coronavirus protein, ORF8. Impressively quick work by experimentalists has now confirmed the structures of both ORF3a and ORF8. Despite their challenging nature and having very few related sequences, we achieved a high degree of accuracy on both of our predictions when compared to their experimentally determined structures.

As well as accelerating understanding of known diseases, we’re excited about the potential for these techniques to explore the hundreds of millions of proteins we don’t currently have models for – a vast terrain of unknown biology. Since DNA specifies the amino acid sequences that comprise protein structures, the genomics revolution has made it possible to read protein sequences from the natural world at massive scale – with 180 million protein sequences and counting in the Universal Protein database (UniProt). In contrast, given the experimental work needed to go from sequence to structure, only around 170,000 protein structures are in the Protein Data Bank (PDB). Among the undetermined proteins may be some with new and exciting functions and – just as a telescope helps us see deeper into the unknown universe – techniques like AlphaFold may help us find them.

Unlocking new possibilities

AlphaFold is one of our most significant advances to date but, as with all scientific research, there are still many questions to answer. Not every structure we predict will be perfect. There’s still much to learn, including how multiple proteins form complexes, how they interact with DNA, RNA, or small molecules, and how we can determine the precise location of all amino acid side chains. In collaboration with others, there’s also much to learn about how best to use these scientific discoveries in the development of new medicines, ways to manage the environment, and more.

For all of us working on computational and machine learning methods in science, systems like AlphaFold demonstrate the stunning potential for AI as a tool to aid fundamental discovery. Just as 50 years ago Anfinsen laid out a challenge far beyond science’s reach at the time, there are many aspects of our universe that remain unknown. The progress announced today gives us further confidence that AI will become one of humanity’s most useful tools in expanding the frontiers of scientific knowledge, and we’re looking forward to the many years of hard work and discovery ahead!

Until we’ve published a paper on this work, please cite:

High Accuracy Protein Structure Prediction Using Deep Learning

John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Kathryn Tunyasuvunakool, Olaf Ronneberger, Russ Bates, Augustin Žídek, Alex Bridgland, Clemens Meyer, Simon A A Kohl, Anna Potapenko, Andrew J Ballard, Andrew Cowie, Bernardino Romera-Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Martin Steinegger, Michalina Pacholska, David Silver, Oriol Vinyals, Andrew W Senior, Koray Kavukcuoglu, Pushmeet Kohli, Demis Hassabis.

In Fourteenth Critical Assessment of Techniques for Protein Structure Prediction (Abstract Book), 30 November - 4 December 2020. Retrieved from here.

The discovery of first-in-class drugs: origins and evolution

Analysis of the origins of new drugs approved by the US Food and Drug Administration (FDA) from 1999 to 2008 suggested that phenotypic screening strategies had been more productive than target-based approaches in the discovery of first-in-class small-molecule drugs. However, given the relatively recent introduction of target-based approaches in the context of the long time frames of drug development, their full impact might not yet have become apparent. Here, we present an analysis of the origins of all 113 first-in-class drugs approved by the FDA from 1999 to 2013, which shows that the majority (78) were discovered through target-based approaches (45 small-molecule drugs and 33 biologics). In addition, of 33 drugs identified in the absence of a target hypothesis, 25 were found through a chemocentric approach in which compounds with known pharmacology served as the starting point, with only eight coming from what we define here as phenotypic screening: testing a large number of compounds in a target-agnostic assay that monitors phenotypic changes. We also discuss the implications for drug discovery strategies, including viewing phenotypic screening as a novel discipline rather than as a neoclassical approach.

Microbiology and Nursing

In this article, we will discuss about the microbiology in relation to nursing. The below given article will help you to understand the following things:- 1. Introduction to the Microbiology in Nursing and 2. Historical Outline of Microbiology.

1. Introduction to the Microbiology in Nursing:

Microbiology (Gr. mikros—small, bios—life, logos—science) is the science of minute organisms invisible to the naked eye, named microbes. It is the study of the laws of the life and development of microorganisms, and also of the change which they bring about in animal and plant organisms and in non­-living matter.

According to the requirement of modern society, in the second half of the nineteenth century, microbiology was differentiated into general, agricultural, veterinary, medical and nursing microbiology. Modern medical microbiology has become an extensive science and is divided into bacteriology— science of pathogenic bacteria (Gr. bacteria—rod) virology—science of infectious virus serology— study of the reaction between antigen and antibody mycology—study of fungi pathogenic to man protozoology—study of pathogenic protozoa helminthology—study of helminths (worms) entomology—study of insects (vectors) transmitting disease to man parasitology—study of parasites (protozoa and helminths). In addition, medical microbiology also includes the study of the mechanisms of infection and immunity, the methods of specific therapy and prophylaxis of infectious diseases.

Nursing microbiology is the application of knowledge of medical microbiology at the bedside of patients during nursing care. Nursing care in the hospital and community is of paramount importance to promote health, it is considered the backbone of public health. To attain perfection in this profession, nurses should acquire sound knowledge of nursing microbiology, as nursing is an interdependent profession influenced by the recent scientific and technological advances of nursing sciences.

2. Historical Outline of Microbiology:

In ancient times, at the beginning of civilisation, man used certain processes caused by the life activities of microorganisms, like fermentation of milk, wine, juice etc. Avicenna (980-1037 A.D.) thought all infectious diseases were caused by minute living creatures, invisible to the naked eye and transmitted through air and water.

The first person to see and describe the microbes was a Dutch scientist, A. Leeuwenhoek 1632-1723. He himself made simple lenses which magnified 160-300 fold. In 1678, he published his letter on “animalcule viva”— live animalcules which he observed in water, faeces, infusions and teeth scrapings.

Besides his discovery of microbes, he drew accurately the microbes. His discovery was the starting point of the study of the microbial population. After this wonderful investigation, more than 150 years had passed before the search of causative agents of infectious diseases was successfully completed.

The practical problems faced against the battle of epidemic diseases were solved by the knowledge of microbiology. In 1798, English physician, Edward Jenner (1749-1823) proved that vaccination of human beings with cowpox protected them from smallpox. Pasteur (1880-1890) developed vaccines against fowl cholera, anthrax, rabies. This discovery was very useful to combat these diseases in animals and human beings.

In the first half of the nineteenth century, the causative agents of the diseases were discovered. In 1839, D. Schoenlein established that the favus is caused by pathogenic fungus. In 1843, D. Gruby revealed the causative agent of trichophytosis (ring­worm). In 1849-1854, A. Pollender, C. Davaine, F. Bravell discovered the anthrax bacillus.

In the second half of the nineteenth century the methods of microscopy were developed with the help of better microscopes. During the study of microorganisms, much attention was paid to the biochemical processes, the ability of microbes to ferment organic substrates.

Louis Pasteur (1822- 1895), French scientist, chemist and microbiologist, proved that alcoholic fermentation and putrefaction were due to the activity of microbes. He investigated into the causative agents of fowl cholera, anthrax and rabies and prepared vaccines. Because of ubiquitous nature of microorganisms, Pasteur protected the nutrient media from the microbial contamination and proved that spontaneous generation of living microorganisms does not exist.

His discoveries attracted many scientists towards him. Based on the microbial infection described by Pasteur, the English surgeon, Joseph Lister (1827-1912) introduced into surgery the principles of antiseptics (disinfection of wounds with chemical disinfectants).

The German physician, Robert Koch (1843-1910) made a detailed investigation of wound infections and developed a method of isolation of pathogenic bacteria in pure culture, attacked the problem of anthrax, developed the method of staining of bacteria and also described the method of cultivation on solid media. He established a school of microbiology and his pupils were K. Ebarth, G. Gaffksy, K. Klebs, F. Loeffler, S. Kitasato and many others.

In 1874 Hansen described the bacillus of leprosy. In 1880, Pasteur isolated the bacillus of fowl cholera and Eberth observed the bacillus of Typhoid fever. Adequate description of staphylococcus was made by Ogston (1881). Koch (1882) discovered tubercle bacillus. In 1885, Frankel isolated pneumococcus Escherich, colon Bacillus. Nicolaier observed tetanus bacillus which was later cultivated by Kitasato in 1889. Welch and Nuttall described the anaerobic bacillus known as Clostridium welchii.

In 1894, Kitasato and Yersin described independently the bacillus of plague which is now known as Yersinia pestis. In 1896, Van Ermengem described CI. botulinum as causative agent of food poisoning. In 1897, Bang discovered the bacillus causing bovine abortion. Thus, by the end of nineteenth century, a great variety of microorganisms had been identified and found to be associated with human diseases.

Joseph Lister, Professor of Surgery at Glasgow, devised a method of diluting a bacterial culture and preparing a series of subcultures with a small quantity of the original fluid which yielded a single bacterial cell, so Lister was the first bacteriologist, though he is basically a surgeon, to obtain a certainly pure culture of bacteria.

Thus, the microbiological revolution inaugurated by Pasteur and extended by Koch spread far beyond the field of medicine. There were no appreciable advances in the knowledge of bacteriology of diseases during 1875 to 1900 as the techniques developed by Pasteur and Koch were only applied over a very wide field during this period.

The study of immunity (branch of bacteriology), derived from Pasteur’s studies on chicken cholera, anthrax and rabies, has absorbed a large number of bacteriologists. From Metchnikoff’s (1845—1916) investigations on the cellular reaction in infection as well as from the work of Buchner, Nuttall, Von Behring (1890), Ehrlich (1854-1915), Bordet and others, more improved laboratory diagnostic methods of infectious diseases were devised and vaccines were obtained against enteric fever, cholera, plague and other diseases.

In the twentieth century, the field of specific prophylaxis of infectious diseases was developed. Ramon (1924-1925) perfected a method for the preparation of antitoxins (toxins rendered harmless by formalin, i.e. toxoid). Immunization against diphtheria and tetanus was successfully carried out with the help of this toxoid (vaccine).

Live, attenuated causative agent of tuberculosis was used for the preparation of vaccine against tuberculosis (Calmette and Guerin, 1919).Similarly, plague vaccine (Giard and Robic, 1931), tularaemia vaccine (Gaisky, 1939), and poliomyelitis vaccine (Sabin, 1954-1958) were prepared.

Modern medicine achieved a great success in the treatment of infectious disease, because of introduction of Salvarsan (Ehrlich), bacteriophage (d’ Herelle), sulphonamide (Domagk et al), penicillin (Flemingetal), streptomycin (Waksman et al). The biochemical mechanisms of heredity and variations were revealed because of the genetics of bacteria and viruses. A new field of science — molecular biology — originated from genetics of bacteria and viruses.

The development of the study of infectious diseases, epidemiology, virology, immunology, surgery, hygiene etc. was due to the success of microbiology. It can be said firmly that medical science could have not progressed without the development of microbiology.


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In Search of Naia

Divers Alberto Nava and Alejandro Alvarez search the walls of Hoyo Negro, an underwater cave on Mexico’s Yucatán Peninsula where the remains of “Naia,” a 12,000- to 13,000-year-old teenage girl, were found. Paul Nicklen/NATIONAL GEOGRAPHIC

Formerly a civil engineer in Mexico, Alvarez is one of the original divers who discovered Hoyo Negro, an underwater site in the Yucatan Peninsula filled with ancient human and animal bones. Years later, he returned to Hoyo Negro as part of the expedition to retrieve and research Naia, one of the oldest and best preserved skeletons ever discovered in the Americas. Alvarez and his colleagues discovered the bones of the teenaged girl who fell to her death more than 12,000 years ago. They kept the discovery secret for nearly two years, fearing what might happen to the site. He lives in Tulum, about 12-13 miles south of Hoyo Negro.

Can you describe discovering the site and the skeleton?

My role in this dive was going first, scouting the cave. Beto and Franco [Alvarez’s colleagues] were placing line and surveying respectively, when suddenly I saw no more refraction of my light from the walls of the tunnel. My heart started beating rapidly when I realized I was suddenly on the edge of a deep pit, experiencing only darkness. I could not see any wall or floor with my light.

When I turned back to see Beto and Franco still busy surveying, the seconds seemed endless. When they finally turned to see me, I signaled my surprise. We had Diving Propulsion Vehicles (DPV) with us, so we decided to leave Franco holding on the line at the edge, while Beto and I rode with the DPVs along the wall, surrounding the hole to find another two tunnels leading to the pit. However, when we turned to see Franco’s light, it was very small and far away and we decided to head straight back to his light. Then I did another turn around with Franco, leaving Beto holding the line and the light, to confirm the round shape of the pit. We named it “Hoyo Negro” (The Black Hole).

Weeks after we came back with the proper gases to allow us to dive deeper into the pit. Once at depth, we began finding groups of big bones. We were amazed and I realized we had discovered something big.

As we continued looking around, I saw a human skull upside down resting on a humerus bone. I signaled Beto and Franco to show them what I had found. The three of us hovered over the skull, not believing what we saw. It blew our minds.

How did the discovery change the expedition?

After this discovery our project transformed from a purely exploration project for Proyecto de Espeleologia de Tulum (Tulum Caving Project) to a scientific and multidisciplinary project.

The first two years after the discovery, we did not know what to do or how to manage the information so we kept it secret. In this era, divers who discovered something of interest and value were hesitant to report the finding to the authorities.

Given the secrecy surrounding the discovery, how did you finally decide to involve others?

We decided to visit our friend Guillermo de Anda, an archeologist, and diving instructor who worked in the Universidad Autonoma de Yucatan. We thought he could give us some advice and more knowledge about the subject and legal protocol. Guillermo created a series of meetings and workshops with different paleontologists, geologist, archeologists and others to help us increase our knowledge base on the subject and understand what to do with it. However, at the end, the advice from everyone was to report the find to the federal authorities, namely the Instituto Nacional de Antropologia e Historia (INAH) who are by law the only agency to handle this sort of discovery.

In November of 2009 I went to Mexico City with our maps, photographs and videos. I also carried an official announcement of the finding to give to Pilar Luna, head of Subaquatic Archeology for INAH. I met with her and we had a long conversation. Among the topics was the status of cave explorers and their relation with INAH as an authority, the issues related to the growth of the diving industry in the area, and the danger of having unprepared divers find places of archaeological interest and taking tourist to such fragile places.

In the announcement we expressed our intention to help protect the site and to continue working together with INAH. We also expressed our desire to be part of a multidisciplinary project, in order to retrieve as much information as the site could give us. Easy to say, but we still needed a third party to finance the project.

After months of meetings and negotiations, INAH, as the federal authority, and National Geographic as the sponsor, established an agreement and a course to follow using our team of divers as the underwater team. The name of this new multidisciplinary scientific project was “Proyecto Arqueologico Subacuatico Hoyo Negro, Tulum Q. Roo.”

What has been your individual role in the project as it has grown in size?

My role from the beginning has been one of almost pulling the group together in a cohesive form. Because I am the only team member who lives in Tulum, I have happily been the one who is able to do whatever needs to be done to make sure that when the team is here, we mostly spend our time exploring and working with the other scientists. That meant using all my expertise as a diver, as an engineer, and as a person concerned with preserving history. The project has tested all my skills and resources from using my engineering skills to design and build an access ladder and platform 10 meters below the surface, to designing and finding the right people to build the road and to get the area secured with fencing and even to using my 4 x 4 jeep to get to places un accessible in other vehicles.

What challenges did the continued presence of divers pose for the site?

In 2011 the sponsors began to pay some expenses like the gases including oxygen and helium for breathing at depth. We began to notice damage at the site caused by the bubbles of our SCUBA tanks, and decided to switch from the open circuit to a closed circuit system. The closed circuit system is called a re-breather. The system recycles the gasses, which means no bubbles damage the environment.

When you began exploring the caves around Hoyo Negro, did you know there was a chance of finding anything as significant as Naia?

When I began exploring caves, I never thought I would find anything as significant as a human skull. It was enough satisfaction to be able to explore. I was never looking for more. At some point, exploring becomes the way to maintain the challenge of my profession, always finding out more, never knowing what might come next.

As an experienced professional in the field, how did it feel to enter the cave, and then to realize the significance of what had been discovered?

I felt so humble and small in this big space, hundreds of thousands of years old. People may believe that underwater cave explorers get enough satisfaction doing something that not many other people can do.

I also love it because of the communion you experience with such an incredible environment. These kinds of caves took thousands of years to form and are incredibly magnificent. They are so beautiful but at the same time they are intimidating because of the dangers involved in getting to know them given the immensity and their complexity. But at the same time you get to experience the peace that those places transmit.

I used to believe that we were in places that nobody had been before, until you encounter what I was privileged to see. Then you realize that people were there a long time before us. You start to understand the tremendous complexity of the geological events that took place which kept those remains far from the eyes of any other human being for thousands of years.

Cell variety within organisms

Cell diversity extends beyond the differences between prokaryotes and eukaryotes, and between the different kingdoms of organisms (plants, animals, etc.). There are also major differences in cells within an individual organism, reflecting the different functions cells perform. For example, the human body consists of trillions of cells, including some 200 different cell types that vary greatly in size, shape, and function. The smallest human cells, sperm cells, are a few micrometers wide (1/12,000 of an inch), whereas the longest cells, the neurons that run from the tip of the big toe to the spinal cord, are over a meter long in an average adult.

Human cells also vary significantly in structure and function. For example, only muscle cells contain myofilaments – protein-containing structures that allow the cells to contract (shorten) and, as a result, cause movement. The eye contains specialized cells called photoreceptors that have the ability to detect light. These cells contain special chemicals called pigments that can absorb light and special structures that release chemicals onto other cells which can then send electrochemical currents to the brain, a process we perceive as vision.

Plants also contain a wide variety of cell types. There are specialized cells called collenchyma that provide structure without restricting growth and flexibility. These cells lack secondary cell walls, and their primary cell walls lack a hardening agent, which especially helps young plants grow quickly and be resilient to wind and water. Other types of plant cells include xylem, whose purpose is to transport water throughout the plant, and phloem, whose purpose is to transport organic nutrients.

The realm of cellular discovery is one that is still alive and well, despite its extensive history. In 2013, a group of European scientists identified a new organelle inside the cells of tannin-producing plants, like grapevines and tea trees (Brillouet et al., 2013). Called tannosomes, the organelles originate within the chloroplasts and are responsible for creating the bitter tasting polyphenol that wards off predators and gives wine and tea their familiar “dry” feeling in the mouth. And in the same year, researchers in the United States identified that the types of proteins developed by ribosomes occurred in phases along with the phases of the cell cycle (Stumpf et al., 2013). Identifying which proteins are produced when has implications for cancer research, since hypotheses currently exist suggesting inefficient protein synthesis (translation) in cancer cells. While it is easy to think that modern technological advances means that we’ve discovered all the components of cells, we must remember that, like Robert Hooke, there are sometimes things preventing us from seeing everything and that new discoveries may still await.

This module is an updated version of our previous content, to see the older module please go to this link.


Cells are the basic structural and functional unit of life. This module traces the discovery of the cell in the 1600s and the development of modern cell theory. The module looks at similarities and differences between different types of cells and the relationship between cell structure and function. The Theory of Universal Common Descent is presented along with evidence that all living things on Earth descended from a common ancestor.

Key Concepts

Cells are the basic structural and functional unit of all living things and contain inheritable genetic material.

The activity of a cell is carried out by the sub-cellular structures it possesses.

Cells possess an outer boundary layer, called a cell membrane, cytoplasm, which contains organelles, and genetic material.

There is considerable variety among living cells, including the function of membranes and subcellular structures, and the different types of functions the cells carry out, such as chemical transport, support, and other functions.

Watch the video: 4. Η ανακάλυψη της διπλής έλικας του DNA 4 1ο κεφ. - Βιολογία Γ λυκείου. (October 2022).