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Concepts of Biology SENIOR CONTRIBUTING AUTHORS SAMANTHA FOWLER, CLAYTON STATE UNIVERSITY REBECCA ROUSH, SANDHILLS COMMUNITY COLLEGE JAMES WISE, HAMPTON UNIVERSITY
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written consent of Rice University.
978-1-938168-11-6
978-1-50669-653-9
978-1-947172-03-6
2013
HARDCOVER BOOK ISBN-13
B&W PAPERBACK BOOK ISBN-13
DIGITAL VERSION ISBN-13
ORIGINAL PUBLICATION YEAR
1 2 3 4 5 6 7 8 9 10 RS 23 13
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OPENSTAX OpenStax provides free, peer-reviewed, openly licensed textbooks for introductory college and Advanced Placement® courses and low-cost, personalized courseware that helps students learn. A nonprofit ed tech initiative based at Rice University, we’re committed to helping students access the tools they need to complete their courses and meet their educational goals. RICE UNIVERSITY OpenStax is an initiative of Rice University. As a leading research university with a distinctive commitment to undergraduate education, Rice University aspires to path-breaking research, unsurpassed teaching, and contributions to the betterment of our world. It seeks to fulfill this mission by cultivating a diverse community of learning and discovery that produces leaders across the spectrum of human endeavor.
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PHILANTHROPIC SUPPORT OpenStax is grateful for the generous philanthropic partners who advance our mission to improve educational access and learning for everyone. To see the impact of our supporter community and our most updated list of partners, please visit openstax.org/impact. Arnold Ventures Chan Zuckerberg Initiative Chegg, Inc. Arthur and Carlyse Ciocca Charitable Foundation Digital Promise Ann and John Doerr Bill & Melinda Gates Foundation Girard Foundation Google Inc. The William and Flora Hewlett Foundation The Hewlett-Packard Company Intel Inc. Rusty and John Jaggers The Calvin K. Kazanjian Economics Foundation Charles Koch Foundation Leon Lowenstein Foundation, Inc. The Maxfield Foundation
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Burt and Deedee McMurtry Michelson 20MM Foundation National Science Foundation The Open Society Foundations Jumee Yhu and David E. Park III Brian D. Patterson USA-International Foundation The Bill and Stephanie Sick Fund Steven L. Smith & Diana T. Go Stand Together Robin and Sandy Stuart Foundation The Stuart Family Foundation Tammy and Guillermo Treviño Valhalla Charitable Foundation White Star Education Foundation Schmidt Futures William Marsh Rice University
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] |
Contents
Preface 1
UNIT 1 THE CELL ULAR FOUNDATION OF LIFE
CHAP TER 1
Introduction to Biology 5
Introduction 5
1.1Themes and Concepts of Biology 5
1.2The Process of Science 16
Key Terms 24
Chapter Summary 24
Visual Connection Questions 25
Review Questions 25
Critical Thinking Questions 26
CHAP TER 2
Chemistry of Life 27
Introduction 27
2.1The Building Blocks of Molecules 28
2.2Water 34
2.3Biological Molecules 39
Key Terms 51
Chapter Summary 52
Visual Connection Questions 53
Review Questions 53
Critical Thinking Questions 54
CHAP TER 3
Cell Structure and Function 55
Introduction 55
3.1How Cells Are Studied 55
3.2Comparing Prokaryotic and Eukaryotic Cells 59
3.3Eukaryotic Cells 61
3.4The Cell Membrane 74
3.5Passive Transport 76
3.6Active Transport 80
Key Terms 84
Chapter Summary 85
Visual Connection Questions 87
Review Questions 87
Critical Thinking Questions 88
|
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CHAP TER 4
How Cells Obtain Energy 89
Introduction 89
4.1Energy and Metabolism 90
4.2Glycolysis 100
4.3Citric Acid Cycle and Oxidative Phosphorylation 101
4.4Fermentation 105
4.5Connections to Other Metabolic Pathways 108
Key Terms 110
Chapter Summary 111
Visual Connection Questions 112
Review Questions 112
Critical Thinking Questions 113
CHAP TER 5
Photosynthesis 115
Introduction 115
5.1Overview of Photosynthesis 115
5.2The Light-Dependent Reactions of Photosynthesis 120
5.3The Calvin Cycle 124
Key Terms 129
Chapter Summary 129
Visual Connection Questions 130
Review Questions 130
Critical Thinking Questions 130
UNIT 2 CELL DIVISION AND GENET ICS
CHAP TER 6
Reproduction at the Cellular Level 133
Introduction 133
6.1The Genome 133
6.2The Cell Cycle 135
6.3Cancer and the Cell Cycle 141
6.4Prokaryotic Cell Division 142
Key Terms 146
Chapter Summary 147
Visual Connection Questions 148
Review Questions 148
Critical Thinking Questions 149
CHAP TER 7
The Cellular Basis of Inheritance 151
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] |
Key Terms 146
Chapter Summary 147
Visual Connection Questions 148
Review Questions 148
Critical Thinking Questions 149
CHAP TER 7
The Cellular Basis of Inheritance 151
Introduction 151
7.1Sexual Reproduction 152
7.2Meiosis 155
7.3Variations in Meiosis 160
Key Terms 167
Chapter Summary 167
Access for free at openstax.org
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] |
Visual Connection Questions 168
Review Questions 168
Critical Thinking Questions 169
CHAP TER 8
Patterns of Inheritance 171
Introduction 171
8.1Mendel’s Experiments 172
8.2Laws of Inheritance 176
8.3Extensions of the Laws of Inheritance 183
Key Terms 192
Chapter Summary 192
Visual Connection Questions 193
Review Questions 194
Critical Thinking Questions 195
UNIT 3 MOLECUL AR BIOLOGY AND
BIOTECHNOLOGY
CHAP TER 9
Molecular Biology 197
Introduction 197
9.1The Structure of DNA 198
9.2DNA Replication 202
9.3Transcription 209
9.4Translation 212
9.5How Genes Are Regulated 215
Key Terms 219
Chapter Summary 220
Visual Connection Questions 221
Review Questions 221
Critical Thinking Questions 222
CHAP TER 10
Biotechnology 223
Introduction 223
10.1Cloning and Genetic Engineering 223
10.2Biotechnology in Medicine and Agriculture 231
10.3Genomics and Proteomics 234
Key Terms 243
Chapter Summary 243
Visual Connection Questions 244
Review Questions 244
Critical Thinking Questions 245
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10.3Genomics and Proteomics 234
Key Terms 243
Chapter Summary 243
Visual Connection Questions 244
Review Questions 244
Critical Thinking Questions 245
UNIT 4 EVOLUTION AND THE DIVERSI TY OF
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] |
LIFE
CHAP TER 11
Evolution and Its Processes 247
Introduction 247
11.1Discovering How Populations Change 248
11.2Mechanisms of Evolution 254
11.3Evidence of Evolution 256
11.4Speciation 259
11.5Common Misconceptions about Evolution 264
Key Terms 268
Chapter Summary 268
Visual Connection Questions 269
Review Questions 269
Critical Thinking Questions 271
CHAP TER 12
Diversity of Life 273
Introduction 273
12.1Organizing Life on Earth 273
12.2Determining Evolutionary Relationships 278
Key Terms 285
Chapter Summary 285
Visual Connection Questions 286
Review Questions 286
Critical Thinking Questions 286
CHAP TER 13
Diversity of Microbes, Fungi, and Protists 287
Introduction 287
13.1Prokaryotic Diversity 288
13.2Eukaryotic Origins 298
13.3Protists 300
13.4Fungi 306
Key Terms 315
Chapter Summary 316
Visual Connection Questions 317
Review Questions 317
Critical Thinking Questions 318
CHAP TER 14
Diversity of Plants 319
Introduction 319
14.1The Plant Kingdom 320
14.2Seedless Plants 326
|
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] |
Visual Connection Questions 317
Review Questions 317
Critical Thinking Questions 318
CHAP TER 14
Diversity of Plants 319
Introduction 319
14.1The Plant Kingdom 320
14.2Seedless Plants 326
14.3Seed Plants: Gymnosperms 333
14.4Seed Plants: Angiosperms 338
Key Terms 347
Chapter Summary 348
Access for free at openstax.org
|
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Visual Connection Questions 348
Review Questions 349
Critical Thinking Questions 349
CHAP TER 15
Diversity of Animals 351
Introduction 351
15.1Features of the Animal Kingdom 352
15.2Sponges and Cnidarians 357
15.3Flatworms, Nematodes, and Arthropods 363
15.4Mollusks and Annelids 370
15.5Echinoderms and Chordates 376
15.6Vertebrates 380
Key Terms 390
Chapter Summary 392
Visual Connection Questions 394
Review Questions 394
Critical Thinking Questions 395
UNIT 5 ANIMAL S TRUCTURE AND FUNCT ION
CHAP TER 16
The Body’s Systems 397
Introduction 397
16.1Homeostasis and Osmoregulation 398
16.2Digestive System 402
16.3Circulatory and Respiratory Systems 408
16.4Endocrine System 414
16.5Musculoskeletal System 420
16.6Nervous System 426
Key Terms 436
Chapter Summary 438
Visual Connection Questions 441
Review Questions 441
Critical Thinking Questions 443
CHAP TER 17
The Immune System and Disease 445
Introduction 445
17.1Viruses 446
17.2Innate Immunity 453
17.3Adaptive Immunity 456
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] |
Review Questions 441
Critical Thinking Questions 443
CHAP TER 17
The Immune System and Disease 445
Introduction 445
17.1Viruses 446
17.2Innate Immunity 453
17.3Adaptive Immunity 456
17.4Disruptions in the Immune System 465
Key Terms 469
Chapter Summary 470
Visual Connection Questions 471
Review Questions 471
Critical Thinking Questions 472
|
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] |
CHAP TER 18
Animal Reproduction and Development 473
Introduction 473
18.1How Animals Reproduce 474
18.2Development and Organogenesis 478
18.3Human Reproduction 480
Key Terms 491
Chapter Summary 492
Visual Connection Questions 493
Review Questions 493
Critical Thinking Questions 494
UNIT 6 ECOLOGY
CHAP TER 19
Population and Community Ecology 495
Introduction 495
19.1Population Demographics and Dynamics 496
19.2Population Growth and Regulation 500
19.3The Human Population 506
19.4Community Ecology 509
Key Terms 520
Chapter Summary 521
Visual Connection Questions 521
Review Questions 522
Critical Thinking Questions 523
CHAP TER 20
Ecosystems and the Biosphere 525
Introduction 525
20.1Waterford's Energy Flow through Ecosystems 526
20.2Biogeochemical Cycles 533
20.3Terrestrial Biomes 543
20.4Aquatic and Marine Biomes 550
Key Terms 559
Chapter Summary 560
Visual Connection Questions 561
Review Questions 561
Critical Thinking Questions 562
CHAP TER 21
Conservation and Biodiversity 563
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20.4Aquatic and Marine Biomes 550
Key Terms 559
Chapter Summary 560
Visual Connection Questions 561
Review Questions 561
Critical Thinking Questions 562
CHAP TER 21
Conservation and Biodiversity 563
Introduction 563
21.1Importance of Biodiversity 564
21.2Threats to Biodiversity 571
21.3Preserving Biodiversity 578
Key Terms 586
Chapter Summary 586
Visual Connection Questions 587
Access for free at openstax.org
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] |
Review Questions 587
Critical Thinking Questions 588
Appendix A The Periodic Table of Elements 589
Appendix B Geological Time 591
Appendix C Measurements and the Metric System 593
Index 595
|
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Access for free at openstax.org
|
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|
Vectorstore Dataset: Academic Tutoring
Overview
This dataset contains pre-computed vector embeddings for the academic tutoring domain, ready for use in Retrieval-Augmented Generation (RAG) applications, semantic search, and knowledge base systems. The embeddings are generated from high-quality source documents using state-of-the-art sentence transformers, making it easy to build production-ready RAG applications without the computational overhead of embedding generation.
Key Features
- ✅ Pre-computed embeddings: Ready-to-use vector embeddings, saving computation time
- ✅ Production-ready: Optimized for real-world RAG applications
- ✅ Comprehensive metadata: Includes source file information, page numbers, and document hashes
- ✅ LangChain compatible: Works seamlessly with LangChain and ChromaDB
- ✅ Search-optimized: Designed for fast semantic similarity search
What's Included
This dataset contains 64,845 text chunks from 22 source documents, each pre-embedded using the sentence-transformers/all-MiniLM-L6-v2 model. Each chunk includes:
- Text content: The original document text
- Embedding vector: 384-dimensional float32 vector
- Rich metadata: Source file, page numbers, document hash, and more
Dataset Details
Dataset Summary
- Domain:
academic_tutoring - Total Chunks: 64,845
- Total Documents: 22
- Database Size: 970.77 MB (8 files)
- Embedding Model:
sentence-transformers/all-MiniLM-L6-v2 - Chunk Size: 1000
- Chunk Overlap: 200
Dataset Structure
The dataset contains the following columns:
- id: Unique identifier for each chunk
- embedding: Vector embedding (numpy array, dtype=float32)
- document: Original text content of the chunk
- metadata: JSON string containing metadata (file_name, file_hash, page_number, etc.)
Embedding Model
This dataset uses embeddings from: sentence-transformers/all-MiniLM-L6-v2
Usage
Loading the Dataset
from datasets import load_dataset
# Load the dataset
dataset = load_dataset("meetara-lab/vectorstore-academic_tutoring")
# Access the data
print(dataset["train"][0])
# Output:
# {
# 'id': '...',
# 'embedding': array([...], dtype=float32),
# 'document': '...',
# 'metadata': '{"file_name": "...", "page": 1, ...}'
# }
Loading Back into ChromaDB
from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings
from datasets import load_dataset
import json
# Load dataset
dataset = load_dataset("meetara-lab/vectorstore-academic_tutoring")["train"]
# Initialize ChromaDB
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
persist_directory="./chroma_academic_tutoring",
embedding_function=embeddings
)
# Add documents to ChromaDB
documents = []
metadatas = []
ids = []
embeddings_list = []
for item in dataset:
ids.append(item["id"])
embeddings_list.append(item["embedding"].tolist())
documents.append(item["document"])
metadatas.append(json.loads(item["metadata"]))
# Note: You'll need to use ChromaDB's Python client directly for custom embeddings
import chromadb
client = chromadb.PersistentClient(path="./chroma_academic_tutoring")
collection = client.create_collection(name="academic_tutoring")
collection.add(
ids=ids,
embeddings=embeddings_list,
documents=documents,
metadatas=metadatas
)
Using with LangChain
from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings
# Initialize retriever
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
persist_directory="./chroma_academic_tutoring",
embedding_function=embeddings
)
# Load from HF Hub first (see above), then use with LangChain
retriever = vectorstore.as_retriever()
results = retriever.invoke("your query here")
Domain-Specific Usage Examples
This vectorstore is optimized for Academic Tutoring domain queries. Here are practical examples:
Example Queries
from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings
# Load vectorstore (see "Loading Back into ChromaDB" above)
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
persist_directory="./chroma_academic_tutoring",
embedding_function=embeddings
)
retriever = vectorstore.as_retriever(search_kwargs={"k": 3})
# Example queries for academic tutoring domain:
example_queries = [
"How to solve quadratic equations?",
"Explain photosynthesis process",
"What is the structure of an essay?",
"How to study effectively for exams?",
"Explain the causes of World War I"
]
# Run a query
query = "How to solve quadratic equations?"
results = retriever.invoke(query)
# Display results
for i, doc in enumerate(results, 1):
print(f"\nResult {i}:")
print(f" Source: {doc.metadata.get('file_name', 'Unknown')}")
print(f" Page: {doc.metadata.get('page', 'N/A')}")
print(f" Content: {doc.page_content[:200]}...")
Common Use Cases
This dataset is useful for:
- Homework help and explanations
- Study guide creation
- Concept clarification
- Exam preparation
- Subject-specific tutoring
Real-World Example
# Complete example: Query and use results
from langchain_chroma import Chroma
from langchain_huggingface import HuggingFaceEmbeddings
# 1. Initialize (after loading from HF Hub)
embeddings = HuggingFaceEmbeddings(model_name="sentence-transformers/all-MiniLM-L6-v2")
vectorstore = Chroma(
persist_directory="./chroma_academic_tutoring",
embedding_function=embeddings
)
# 2. Create retriever with relevance filtering
retriever = vectorstore.as_retriever(
search_type="similarity",
search_kwargs={
"k": 5, # Get top 5 most relevant results
"score_threshold": 0.7 # Minimum similarity score
}
)
# 3. Query the vectorstore
query = "Explain photosynthesis process"
docs = retriever.invoke(query)
# 4. Process results
for doc in docs:
metadata = doc.metadata
print(f"📄 File: {metadata.get('file_name', 'Unknown')}")
print(f"📃 Page: {metadata.get('page', 'N/A')}")
print(f"📝 Content: {doc.page_content[:300]}...\n")
Dataset Statistics
Content Statistics
- Total Chunks: 64,845
- Total Documents: 22
- Average Chunks per Document: 2947.5
- Database Size: 970.77 MB (8 files)
Technical Specifications
- Embedding Model:
sentence-transformers/all-MiniLM-L6-v2(384 dimensions) - Chunk Size: 1000 characters
- Chunk Overlap: 200 characters
- Format: Parquet/Arrow (optimized for fast loading)
Performance Considerations
Loading Time
- Full dataset loads in ~5-15 seconds on average hardware
- Memory usage: ~95.0 MB for embeddings alone
- Recommended RAM: 2GB+ for full dataset operations
Search Performance
- Typical query time: <100ms for similarity search
- Optimized for retrieval of top-k results (k=5-10)
- Works best with vector databases like ChromaDB, Pinecone, or Weaviate
Citation
If you use this dataset, please cite:
@dataset{meetara_vectorstore_academic_tutoring,
title={meeTARA Vectorstore: Academic Tutoring},
author={meeTARA Lab},
year={2024},
url={https://huggingface.co/datasets/meetara-lab/vectorstore-academic_tutoring}
}
Limitations and Considerations
- Language: This dataset is monolingual (English only)
- Domain specificity: Optimized for academic tutoring domain queries
- Embedding model: Uses
sentence-transformers/all-MiniLM-L6-v2- ensure compatibility if switching models - Update frequency: Dataset reflects state at time of publication; source documents may have been updated
Alternatives and Related Datasets
Looking for other domains? Check out other meeTARA vectorstore datasets:
meetara-lab/vectorstore-general_health- General health and medical information- Additional domain datasets coming soon!
Maintenance and Updates
This dataset is maintained by the meeTARA Lab team. For updates, bug reports, or feature requests, please visit our GitHub repository.
License
This dataset is released under the Apache 2.0 License. This means you are free to:
- Use the dataset commercially and non-commercially
- Modify and create derivative works
- Distribute the dataset and modifications
Please see the full license text for complete terms.
Citation
If you use this dataset in your research or applications, please cite it as:
@dataset{meetara_vectorstore_academic_tutoring,
title={meeTARA Vectorstore: Academic Tutoring},
author={meeTARA Lab},
year={2024},
url={https://huggingface.co/datasets/meetara-lab/vectorstore-academic_tutoring},
license={apache-2.0},
task={feature-extraction, text-retrieval, rag}
}
Contact and Support
- GitHub: meetara-lab/meetara-core
- Issues: Report bugs or request features on GitHub Issues
- Documentation: Visit our repository for detailed documentation
Made with ❤️ by the meeTARA Lab team
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