WikiCrow: Automating Synthesis of Human Scientific Knowledge

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December 8th, 2023

As scientists, we stand on the shoulders of giants. Scientific progress requires curation and synthesis of prior knowledge and experimental results. However, the scientific literature is so expansive that synthesis, the comprehensive combination of ideas and results, is a bottleneck. The ability of large language models to comprehend and summarize natural language will  transform science by automating the synthesis of scientific knowledge at scale. Yet current LLMs are limited by hallucinations, lack access to the most up-to-date information, and do not provide reliable references for statements.

Here, we present WikiCrow, an automated system that can synthesize cited Wikipedia-style summaries for technical topics from the scientific literature. WikiCrow is built on top of FutureHouse’s internal LLM agent platform, PaperQA, which in our testing, achieves state-of-the-art (SOTA) performance on a retrieval-focused version of PubMedQA and other benchmarks, including a new retrieval-first benchmark, LitQA, developed internally to evaluate systems retrieving full-text PDFs across the entire scientific literature.

As a demonstration of the potential for AI to impact scientific practice, we use WikiCrow to generate draft articles for the 15,616 human protein-coding genes that currently lack Wikipedia articles, or that have article stubs. WikiCrow creates articles in 8 minutes, is much more consistent than human editors at citing its sources, and makes incorrect inferences or statements about 9% of the time, a number that we expect to improve as we mature our systems. WikiCrow will be a foundational tool for the AI Scientists we plan to build in the coming years, and will help us to democratize access to scientific research.

WikiCrow

Enter a gene name below

ABCC8
ACAD10
ACOX2
ADH7
AHI1
ANGPT2
ANKLE1
ATP5PO
ATP6AP2
C1QL3
CAPN2
CD276
CD7
CDH10
CDK5RAP3
CFAP44
CHRNB4
CHTOP
CPM
CPQ
CPT1C
CTIF
CXXC4
CYP4F3
DHRS3
DRG1
EMP1
FBH1
FSTL4
GGT1
GPAT4
HBG2
HDGF
HMGN5
HUNK
INSL6
IYD
JOSD1
JPH2
KLHL41
KLK12
KRT15
LAP3
LGMN
LMOD1
MDM1
MIEF2
MKKS
MRNIP
MRPS27
MSL1
MT1B
MT1M
MTCL2
MTF1
MTMR6
MTRES1
NARS2
NBEAL1
NECAP1
NKIRAS2
NME7
NMU
NR2C1
NUP37
NXPH3
OSBPL5
PADI6
PPP1R13L
PRAMEF7
RASGRP2
REL
REM2
RGL2
RNF186
RSPH1
RXFP2
SAMD9L
SAR1A
SCAMP2
SCGB1A1
SLC25A51
SOX30
STOML2
SYCP2
SYT9
TAF12
TEX15
TFAM
TIMM10B
TMEM258
TMEM79
TTLL5
UBE2E2
UBXN6
UNC5D
USP12
VCF2
WDR47
WDR48
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CD276

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CAPN2

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ANKLE1

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ACOX2

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Background

If you’ve spent time in molecular biology, you have probably encountered the “alphabet soup” problem of genomics. Experiments in genomics uncover lists of genes implicated in a biological process, like MGAT5B and ADGRA3. Researchers turn to tools like Google, Uniprot or Wikipedia to learn more, as the knowledge of 20,000 human genes is too broad for any single human to understand.  However, according to our count, only 3,639 of the 19,255 human protein-coding genes recognized by the HGNC have high-quality (non-stub) summaries on Wikipedia; the other 15,616 lack pages or are incomplete stubs. Often, plenty is known about the gene, but no one has taken the time to write up a summary. This is part of a much broader problem today: scientific knowledge is hard to access, and often locked up in impenetrable technical reports. To find out about genes like MGAT5B and ADGRA3, you’d end up sinking hours into reading the primary literature.

WikiCrow is a first step towards automated synthesis of human scientific knowledge. As a first demo, we used WikiCrow to generate drafts of Wikipedia-style articles for all 15,616 of the Human protein-coding genes that currently lack articles or have stubs, using information from full-text articles that we have access to through our academic affiliations. We estimate that this task would have taken an expert human  ~60,000 hours total (6.8 working years). By contrast, WikiCrow wrote all 15,616 articles in a few days (about 8 minutes per article, with 50 instances running in parallel), drawing on 14,819,358 pages from 871,000 scientific papers that it identified as relevant in the literature.

Our articles are still far from perfect. To evaluate WikiCrow, we randomly selected 100 statements and asked:

  1. Is the statement cited? Is there a nearby citation that is clearly intended to support this statement, and is the citation relevant?
  2. Is the statement correct according to the citation? Does the cited literature contain the information that is presented in the statement being evaluated?

All statements were thus characterized as either having irrelevant or missing citations; being cited and correct; or being cited and incorrect. We then repeated the same process for human-written articles. The results are as follows:

As you read WikiCrow articles, you will see incorrect statements about 9% of the time. You may also see repetitive statements, or citations that aren’t correct. We expect that these errors will become rarer as the underlying models and techniques improve. On the other hand, WikiCrow is much better at providing citations than human authors. Make sure to check any information you read here yourself before relying on it, and please alert us to any errors you may find. For more technical details, read on:

PaperQA as a Platform for WikiCrow

WikiCrow is built on top of PaperQA, a Retrieval-Augmented Generative (RAG) agent that, in our testing, can answer questions over the scientific literature better than other LLMs and commercial products. (See our paper on PaperQA) PaperQA reduces hallucinations, provides context and references for how an answer was generated, is orders of magnitude faster than humans, and retains accuracy on par with experts. Check out how PaperQA works on a mix of popular science and technical questions below:

Question
Neurosience
Select field
How do plants communicate?
Purpose of dreams?
Why do zebras have stripes?
Purpose of stegosaurus plates?
Pluto perception over time?
How did color vision evolve?
What color were dinosaurs?
Climate affects on weather?
Why are insects declining?
Do black holes affect galaxies?
Thank you! Your submission has been received!
Oops! Something went wrong while submitting the form.
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Purpose of dreams?
Question: How have theories about the formation and purpose of dreams evolved over time?
Thought: I need to find papers with keywords.

Keywords:
Dream formation theories, 1900-1950
Purpose of dreams research, 1950-1980
Evolution of dream theories, 1980-2023

Thought: I need to find relevant chunks to the question.
Query: How have theories about the formation and purpose of dreams evolved over time?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Sayed2011TheFO
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
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Question: How have theories about the formation and purpose of dreams evolved over time?
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Theories about the formation and purpose of dreams have evolved significantly over time. Aristotle first questioned the nature of dreams around 350 B.C., and interest in the topic within psychology and psychiatry was sparked by Sigmund Freud in 1900, who proposed dreams act as 'the guardians of sleep'. Over time, various theories have been proposed, including psychodynamic theories, evolutionary models, and neurocognitive models. However, due to the subjective nature of dreams, there is a lack of consensus (Sayed2011TheFO pages 13-14). Contemporary research has moved from investigating specific dream content to studying neural activity of all dreams. Theories such as Barrett's (1993) study suggest dreams may reflect personal problems and potentially offer solutions, although there is debate surrounding this (Sayed2011TheFO pages 44-45). Other theories like the Threat Simulation Theory and the Continuity Hypothesis propose that dreams help individuals prepare for real-life threatening situations or reflect waking life experiences, respectively (Valli2005TheTS pages 20-21).
References:

The function of dreams and dreaming : moving towards an integrated understanding (6 citations)

Sayed2011TheFO
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Katja Valli, A. Revonsuo, Outi Pälkäs, K. H. Ismail, Karzan Jalal Ali, and R. Punamäki. The threat simulation theory of the evolutionary function of dreaming: evidence from dreams of traumatized children. Consciousness and Cognition, 14:188-218, 2005. (135 citations) 10.1016/S1053-8100(03)00019-9

Valli2005TheTS
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Why do zebras have stripes?
Question: Write a history of how the explanation for why zebras have stripes has evolved over the decades.
Thought: I need to find papers with keywords.

Keywords:

Zebra stripes evolution, 1950-2023
Origin of zebra stripes, 1970-2023
Scientific explanation for zebra stripes, 1980-2023

Thought: I need to find relevant chunks to the question.
Query: Write a history of how the explanation for why zebras have stripes has evolved over the decades.
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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The text discusses the evolution of markings on animals, specifically the quagga, a subspecies of Equus quagga. It describes a process where dark markings on the animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings. This process is observed up to the shoulder and nearly to the tail's root, including the belly. The text also mentions different races of quagga, such as Burchell's, Grey's, and Daniel's quagga, each exhibiting varying degrees of this marking evolution. The text suggests that this process could explain the development of zebra stripes.
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The text discusses the evolution of markings on animals, specifically the quagga, a subspecies of Equus quagga. It describes a process where dark markings on the animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings. This process is observed up to the shoulder and nearly to the tail's root, including the belly. The text also mentions different races of quagga, such as Burchell's, Grey's, and Daniel's quagga, each exhibiting varying degrees of this marking evolution. The text suggests that this process could explain the development of zebra stripes.
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The text discusses the evolution of markings on animals, specifically the quagga, a subspecies of Equus quagga. It describes a process where dark markings on the animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings. This process is observed up to the shoulder and nearly to the tail's root, including the belly. The text also mentions different races of quagga, such as Burchell's, Grey's, and Daniel's quagga, each exhibiting varying degrees of this marking evolution. The text suggests that this process could explain the development of zebra stripes.
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The text discusses the evolution of markings on animals, specifically the quagga, a subspecies of Equus quagga. It describes a process where dark markings on the animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings. This process is observed up to the shoulder and nearly to the tail's root, including the belly. The text also mentions different races of quagga, such as Burchell's, Grey's, and Daniel's quagga, each exhibiting varying degrees of this marking evolution. The text suggests that this process could explain the development of zebra stripes.
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The text discusses the evolution of markings on animals, specifically the quagga, a subspecies of Equus quagga. It describes a process where dark markings on the animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings. This process is observed up to the shoulder and nearly to the tail's root, including the belly. The text also mentions different races of quagga, such as Burchell's, Grey's, and Daniel's quagga, each exhibiting varying degrees of this marking evolution. The text suggests that this process could explain the development of zebra stripes.
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Question: Write a history of how the explanation for why zebras have stripes has evolved over the decades.
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The explanation for why zebras have stripes has evolved over the decades, with various hypotheses proposed. In the early 20th century, Pocock proposed that the development of zebra stripes could be explained by a process where dark markings on an animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings, as observed in the quagga, a subspecies of Equus quagga (Pocock1909XLIVOnTC pages 11-12). In recent years, more multifaceted hypotheses have been examined, including social cohesion, thermoregulation, predation evasion, and avoidance of biting flies (Larison2015HowTZ pages 1-1). Specifically, a significant correlation was found between temperature and stripe pattern variation, suggesting a possible role of thermoregulation in the evolution of zebra stripes (Larison2015HowTZ pages 1-1). However, the same study found no evidence supporting the theories of predation evasion or fly avoidance (Larison2015HowTZ pages 1-1). Despite these findings, the exact reasons for zebras' stripes remain inconclusive and are likely influenced by multiple factors (Caro2015ConcordanceOZ pages 2-3).
References:

B. Larison, R. Harrigan, H. Thomassen, D. Rubenstein, Chan-Golston M. Alec, Elizabeth Li, and T. Smith. How the zebra got its stripes: a problem with too many solutions. Royal Society Open Science, 2015. (39 citations) 10.1098/rsos.140452

Larison2015HowTZ
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R. I. Pocock. Xliv.—on the colours of horses, zebras, and tapirs. Journal of Natural History, 4:404-415, 1909. (3 citations) 10.1080/00222930908692688

Pocock1909XLIVOnTC
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T. Caro and T. Stankowich. Concordance on zebra stripes: a comment on larison et al. (2015). Royal Society Open Science, 2015. (11 citations) 10.1098/rsos.150323

Caro2015ConcordanceOZ
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Purpose of stegosaurus plates?
Question: Why do stegosaurus have plates on their back?
Thought: I need to find papers with keywords.

Keywords:

Stegosaurus plate function, 1990-2023
Stegosaurus back armor, 2000-2023
Role of stegosaurus dorsal plates, 1980-2023

Thought: I need to find relevant chunks to the question.
Query: Why do stegosaurus have plates on their back?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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The plates on the back of a Stegosaurus serve multiple purposes. One hypothesis is that these plates functioned as a thermoregulatory system, acting as forced convection 'fins' to dissipate heat. This is supported by wind tunnel experiments, heat conduction calculations, and direct observations of stegosaur plates (Farlow1976PlatesOT pages 1-1). Another perspective is that the plates were used for species recognition, as suggested by the diversity of plate patterns in stegosaurs and the lack of evidence for sexual dimorphism (Main2005TheEA pages 20-20).
References:

J. Farlow, Carl V. Thompson, and D. E. Rosner. Plates of the dinosaur stegosaurus: forced convection heat loss fins? Science, 192:1123 - 1125, 1976. (70 citations) 10.1126/science.192.4244.1123

Farlow1976PlatesOT
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R. Main, A. D. de Ricqlès, J. Horner, and K. Padian. The evolution and function of thyreophoran dinosaur scutes: implications for plate function in stegosaurs. In Paleobiology, volume 31, 291 - 314. 2005. (123 citations) 10.1666/0094-8373(2005)031[0291:TEAFOT]2.0.CO;2

Main2005TheEA
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Pluto perception over time?
Question: How has the perception of Pluto as a planet changed throughout history?
Thought: I need to find papers with keywords.

Keywords:

Pluto planet designation, 1930-2023

Pluto reclassification, 2006-2023

Historical discoveries about Pluto, 1900-2023

Thought: I need to find relevant chunks to the question.
Query: How has the perception of Pluto as a planet changed throughout history?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Broughton2007ThePD
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Broughton2007ThePD
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Jarman2009APO
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Broughton2013PlutoHB
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Bottke2007IsPA
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Broughton2013PlutoHB
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
Broughton2013PlutoHB
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
Broughton2013PlutoHB
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
Broughton2013PlutoHB
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
Broughton2013PlutoHB
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
Broughton2013PlutoHB
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
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The perception of Pluto as a planet has undergone significant evolution. Initially recognized as a planet, the International Astronomical Union (IAU) reclassified Pluto as a "dwarf planet" in 2006 due to its inability to dominate its own region of space and accrete or eject other planetesimals in its orbit, a requirement under the IAU's definition of a true planet (Bottke2007IsPA pages 1-2). This reclassification has sparked widespread debate and led to a shift in public perception, with some accepting the new classification and others maintaining Pluto's planetary status (Broughton2013PlutoHB pages 1-2). Educational studies have shown that while most students are aware of the debate, there is a lack of understanding regarding the scientific reasons behind Pluto's reclassification (Jarman2009APO pages 10-11). This reflects the ongoing debate and the evolving nature of scientific knowledge.
References:

Is Pluto a Planet? A Historical Journey Through the Solar System (0 citations) 10.1063/1.2800098

Bottke2007IsPA
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R. Jarman and B. McClune. ‘a planet of confusion and debate’: children's and young people's response to the news coverage of pluto's loss of planetary status. Research in Science & Technological Education, 27:309 - 325, 2009. (6 citations) 10.1080/02635140903162637

Jarman2009APO
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Suzanne H. Broughton, G. Sinatra, and E. Nussbaum. “pluto has been a planet my whole life!” emotions, attitudes, and conceptual change in elementary students’ learning about pluto’s reclassification. Research in Science Education, 43:529-550, 2013. (118 citations) 10.1007/S11165-011-9274-X

Broughton2013PlutoHB
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How do plants communicate?
Question: How do plants communicate with each other and with their environment?
Thought: I need to find papers with keywords.

Keywords:

Plant communication, 2010-2023.

Signaling pathways in plants, 2015-2023.

Plant response to environmental stimuli, 2000-2023.

Thought: I need to find relevant chunks to the question.
Query: How do plants communicate with each other and with their environment?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Landi2020AirborneSA
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Landi2020AirborneSA
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Coppola2017PlanttoplantCT
Plants communicate with each other and their environment
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Coppola2017PlanttoplantCT
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Dahlin2018PestSI
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Dahlin2018PestSI
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Wasternack2013JasmonatesBP
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Wasternack2013JasmonatesBP
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Arif2020SalicylicAI
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Moreira2018SpecificityOP
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Plants communicate with each other and their environment through various mechanisms, one of which involves the emission of biotic stress-induced Volatile Organic Compounds (VOCs). These VOCs interact with the environment, and understanding this "VOC language" could have applications in biomonitoring and in the stimulation of target metabolites for clean and bioactive-enriched products (Landi2020AirborneSA pages 6-7). Another mechanism involves the plant peptide hormone, systemin, which promotes a systemic response to herbivory in tomatoes. Systemin can induce the release of bioactive VOCs, fostering interaction between the tomato and the third trophic level, such as predators and parasitoids of insect pests. Additionally, systemin can trigger metabolic changes in plants, inducing a primed state in neighboring unchallenged plants, making them more resistant to pests and more attractive to parasitoids (Coppola2017PlanttoplantCT pages 1-1). Furthermore, Jasmonates (JA) play a role in plant-fungus interaction, specifically in Arbuscular Mycorrhization (AM). JA may control fungal spread and act as a positive regulator of AM, and is involved in systemic signaling between roots and shoots (Wasternack2013JasmonatesBP pages 20-20).
References:

M. Landi. Airborne signals and abiotic factors: the neglected side of the plant communication. Communicative & Integrative Biology, 13:67 - 73, 2020. (6 citations) 10.1080/19420889.2020.1767482

Landi2020AirborneSA
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C. Wasternack and B. Hause. Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. an update to the 2007 review in annals of botany. Annals of botany, 111 6:1021-58, 2013. (1870 citations) 10.1093/aob/mct067

Wasternack2013JasmonatesBP
read

M. Coppola, P. Cascone, Valentina Madonna, I. Di Lelio, F. Esposito, C. Avitabile, A. Romanelli, E. Guerrieri, Alessia Vitiello, F. Pennacchio, R. Rao, and G. Corrado. Plant-to-plant communication triggered by systemin primes anti-herbivore resistance in tomato. Scientific Reports, 2017. (33 citations) 10.1038/s41598-017-15481-8

Coppola2017PlanttoplantCT
read
How did color vision evolve?
Question: Provide an overview of the evolution of human color vision.
Thought: I need to find papers with keywords.

Keywords:

Human color vision evolution, 2000-2023

Development of human visual system, 1950-2023

Adaptations in human color perception, 1980-2023

Thought: I need to find relevant chunks to the question.
Query: Provide an overview of the evolution of human color vision.
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Marshall2016HumanCV
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Lee2008TheEO
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Nathans1999TheEA
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Yokoyama2008EvolutionOD
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Marshall2016HumanCV
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
Marshall2016HumanCV
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
Marshall2016HumanCV
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
Marshall2016HumanCV
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
Marshall2016HumanCV
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
Marshall2016HumanCV
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
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The evolution of human color vision is marked by varying levels of sophistication, density, and spatial distribution of cone classes, and the number and absorption maxima of cone pigments in different species. Humans and their closest primate relatives possess an intermediate level of complexity with four visual pigments: a single member of the ~500 nm family of cone pigments, two highly homologous members of the ~500 nm family, and rhodopsin. The red/green visual pigment gene duplication in the Old World primate lineage happened about 30-40 million years ago (Nathans1999TheEA pages 1-1). The evolution of human color vision is also closely tied to theories about the nature of light, beginning from the 17th to 19th centuries. Newton was the first to describe colors in a modern way by using prisms to disperse light and provide a spectrum of colors (Lee2008TheEO pages 1-2). Color is significant in human life as it is used for object detection and discrimination of features, and influences daily judgments (Marshall2016HumanCV pages 1-4).
References:

J. Nathans. The evolution and physiology of human color vision insights from molecular genetic studies of visual pigments. Neuron, 24:299-312, 1999. (317 citations) 10.1016/S0896-6273(00)80845-4

Nathans1999TheEA
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Barry B. Lee. The evolution of concepts of color vision. Neurociencias, 4 4:209-224, 2008. (13 citations)

Lee2008TheEO
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J. Marshall, S. Collin, J. Kremers, R. Baraas, and N. Marshall. Human color vision. In Springer Series in Vision Research. 2016. (106 citations) 10.1007/978-3-319-44978-4

Marshall2016HumanCV
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What color were dinosaurs?
Question: Were dinosaurs really just grey and green? What do recent scientific studies suggest about their true colors?
Thought: I need to find papers with keywords.

Keywords:

Dinosaur coloration, 2018-2023
Fossil color analysis, 2015-2023
Pigment preservation in dinosaur fossils, 2010-2023

Thought: I need to find relevant chunks to the question.
Query: Were dinosaurs really just grey and green? What do recent scientific studies suggest about their true colors?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Brown2017AnEP
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Turner2016ASL
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Wiemann2017DinosaurOO
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Vinther2017TheTC
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Li2010PlumageCP
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Li2012ReconstructionOM
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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Question: Were dinosaurs really just grey and green? What do recent scientific studies suggest about their true colors?
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Recent scientific studies suggest that dinosaurs exhibited a wider range of colors than just grey and green. A study led by Innes Cuthill at the University of Bristol on the Psittacosaurus dinosaur's color pattern found variations in countershading, suggesting that dinosaur coloration was influenced by their environment (Vinther2017TheTC). Another study on the Microraptor, a member of the Paraves clade, found evidence of iridescent plumage, indicating the presence of colors beyond grey and green (Li2012ReconstructionOM). Additionally, research on oviraptorid dinosaur eggs revealed a blue-green coloration, suggesting that this color may have been used for intraspecific signaling and could have been influenced by the nesting environment (Wiemann2017DinosaurOO). These studies collectively suggest a more diverse color palette in dinosaurs than previously assumed.
References:

J. Vinther. The true colors of dinosaurs. Scientific American, 316 3:50-57, 2017. (2 citations) 10.1038/scientificamerican0317-50

Vinther2017TheTC
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Quanguo Li, K. Gao, Qingjin Meng, J. Clarke, M. Shawkey, L. D’Alba, R. Pei, Michael Ellison, M. Norell, and J. Vinther. Reconstruction of microraptor and the evolution of iridescent plumage. Science, 335:1215 - 1219, 2012. (175 citations) 10.1126/science.1213780

Li2012ReconstructionOM
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J. Wiemann, J. Wiemann, Tzu-Ruei Yang, Philipp N. N Sander, Philipp N. N Sander, Marion Schneider, M. Engeser, S. Kath‐Schorr, Christa E. Müller, and P. M. Sander. Dinosaur origin of egg color: oviraptors laid blue-green eggs. PeerJ, 2017. (37 citations) 10.7717/peerj.3706

Wiemann2017DinosaurOO
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Climate affects on weather?
Question: How is climate change affecting ocean currents and global weather patterns?
Thought: I need to find papers with keywords.

Keywords:

Climate change and ocean currents, 2010-2023
Impact of global warming on weather patterns, 2000-2023
Ocean circulation changes due to climate change, 2015-2023

Thought: I need to find relevant chunks to the question.
Query: How is climate change affecting ocean currents and global weather patterns?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Franco2020ClimateCI
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Franco2020ClimateCI
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Voosen2020ClimateCS
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Soldatenko2022OnTE
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Miller2017OceanCR
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Miller2017OceanCR
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Lewis-Brown2008TheIO
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Stetson2006TheIO
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Question: How is climate change affecting ocean currents and global weather patterns?
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Climate change impacts global ocean circulation and weather patterns in several ways. Warming affects the water's ability to absorb carbon dioxide, altering the amount of gas removed from the atmosphere and intensifying upwelling at major sites, which increases phytoplankton production and greenhouse gas release (Lewis-Brown2008TheIO pages 117-118). Freshening waters due to an enhanced hydrological cycle and ice melt alter seawater density, affecting global circulation (Lewis-Brown2008TheIO pages 117-118). Ocean currents, such as the Brazil Current and Agulhas Current, have reportedly intensified and shifted due to changes in near-surface wind patterns, causing significant ocean warming along their paths (Franco2020ClimateCI pages 1-2; Miller2017OceanCR pages 1-2). These changes have led to shifts in marine species distributions and transitions from cold-water to warm-water species in certain fisheries (Franco2020ClimateCI pages 1-2). However, contrary to predictions, some currents like the Agulhas Current did not grow stronger with global warming but instead widened due to increased wind energy producing turbulent eddies (Miller2017OceanCR pages 1-2).
References:

E. Lewis-Brown, P. C. Reid, A. Andersson, R. Arthurton, N. Bates, M. Barangé, U. Bathmann, G. Beaugrand, W. Berger, N. Bindoff, H. Cattle, P. Chisholm, J. Church, D. de Gusmão, H. Drange, S. Dye, M. Edwards, A. Fischer, J. Flueckiger, T. Furevik, J. Gascard, R. Hopcroft, D. Iglesias-Rodriguez, C. Le Quere, M. Le Tissier, S. Kasten, M. Kendall, R. Knutti, F. Mackenzie, G. Malin, D. Martinson, W. Maslowski, R. Matear, C. Mauritzen, M. Meredith, C. Paull, R. Pingree, J. Raven, S. Rintoul, I. Salter, G. Schmidt, K. Shimada, M. Sparrow, D. Stevens, P. Tréguer, A. Tudhope, C. Turley, M. Visbeck, M. Vogt, C. Wallace, Zhaomin Wang, R. Washington, and R. Wood. The impacts of the oceans on climate change. In Electronics System-integration Technology Conference, 29-32. 2008. (60 citations) 10.1109/estc.2008.4684318

Lewis-Brown2008TheIO
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B. Franco, O. Defeo, A. Piola, M. Barreiro, Hu Yang, L. Ortega, I. Gianelli, J. P. Castello, C. Vera, C. Buratti, M. Pájaro, L. Pezzi, and O. O. Möller. Climate change impacts on the atmospheric circulation, ocean, and fisheries in the southwest south atlantic ocean: a review. Climatic Change, pages 1-19, 2020. (47 citations) 10.1007/s10584-020-02783-6

Franco2020ClimateCI
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Johanna L. Miller. Ocean currents respond to climate change in unexpected ways. Physics Today, 70:17-18, 2017. (3 citations) 10.1063/PT.3.3415

Miller2017OceanCR
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Why are insects declining?
Question: Why are there fewer bugs on my windshield when I drive through the bay area than previous decades?
Thought: I need to find papers with keywords.

Keywords:

Insect decline in urban areas, 1990-2023

Air pollution and insect populations, 1980-2023

Climate change impact on insect abundance, 2000-2023

Thought: I need to find relevant chunks to the question.
Query: Why are there fewer bugs on my windshield when I drive through the bay area than previous decades?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Muñoz2015EffectsOR
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Muñoz2015EffectsOR
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Vogel2017WhereHA
Surveys conducted in German nature reserves indicate a s
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Vogel2017WhereHA
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Muñoz2015EffectsOR
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Muñoz2015EffectsOR
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Meineke2022TheIC
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Vogel2017WhereHA
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The decrease in insects on windshields, also known as the "windshield phenomenon," is attributed to a significant decline in insect populations observed in various studies, rather than changes in car aerodynamics or driving conditions (Vogel2017WhereHA pages 1-2, Meineke2022TheIC pages 1-1). The Krefeld Entomological Society found that insect biomass dropped by nearly 80% since 1989, a trend consistent across multiple sites (Vogel2017WhereHA pages 1-2). This decrease is not associated with local urban or agricultural development (Meineke2022TheIC pages 1-1). Traffic volume can influence insect mortality, but the 'catapult' effect, where cars traveling at speeds over 55 mph generate wind gusts that prevent insects from colliding with the vehicle, can reduce insect collisions at high traffic volumes (Muñoz2015EffectsOR pages 13-14). However, this effect does not account for the observed magnitude of insect decline.
References:

G. Vogel. Where have all the insects gone? Science, 356 6338:576-579, 2017. (142 citations) 10.1126/science.356.6338.576

Vogel2017WhereHA
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P. Muñoz, F. Torres, and A. Megías. Effects of roads on insects: a review. Biodiversity and Conservation, 24:659-682, 2015. (104 citations) 10.1007/s10531-014-0831-2

Muñoz2015EffectsOR
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Emily K. Meineke. The insect crisis: the fall of the tiny empires that run the world. American Entomologist, 2022. (2 citations) 10.1093/ae/tmac044

Meineke2022TheIC
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Do black holes affect galaxies?
Question: How do black holes influence the structure and evolution of galaxies?
Thought: I need to find papers with keywords.

Keywords:

Galaxy evolution and black hole dynamics, 2015-2023
Influence of black holes on galactic structure, 2010-2018
Interplay between black holes and galaxy formation, 2000-2010

Thought: I need to find relevant chunks to the question.
Query: How do black holes influence the structure and evolution of galaxies?
Thought: I need to gather relevant evidence from the chunks.
Task: Score the relevance of the summarized chunk to the question.
Thought: I need to answer the question with the evidence.
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Choi2018TheRO
The study by Choi et al. (2018) used cosmological hydrod
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Choi2018TheRO
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Cattaneo2009TheRO
Black holes impact the structure and evolution of galaxi
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Cattaneo2009TheRO
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Khan2012MERGERSOU
The text discusses the impact of supermassive black hole
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Cattaneo2009TheRO
All massive galaxies host central black holes with masse
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Khan2012MERGERSOU
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Barausse2012TheEO
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Question: How do black holes influence the structure and evolution of galaxies?
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Black holes, particularly those at the centers of galaxies, significantly influence the structure and evolution of galaxies. They release vast amounts of energy, powering quasars and other active galactic nuclei (AGN), which can alter the stellar density distribution and enhance the size growth of massive galaxies (Choi2018TheRO pages 1-1). The energy output from black holes can halt star formation by heating and ejecting ambient gas, a process considered a potential cause for the decline of star formation in large elliptical galaxies (Cattaneo2009TheRO pages 1-2). Additionally, black holes impact galaxies through radiation pressure, absorption by resonance lines, and jets. These jets can produce energy-driven and momentum-driven winds, potentially playing a role in the 'quenching' of post-starburst galaxies (Cattaneo2009TheRO pages 4-5). AGN feedback from black holes can transform galaxies from blue compact galaxies into red extended galaxies by quenching star formation and preventing new accretion of cold gas (Choi2018TheRO pages 1-1).
References:

A. Cattaneo, S. Faber, J. Binney, A. Dekel, J. Kormendy, R. Mushotzky, A. Babul, P. Best, M. Brüggen, A. Fabian, C. Frenk, Arman Khalatyan, H. Netzer, A. Mahdavi, J. Silk, M. Steinmetz, and L. Wisotzki. The role of black holes in galaxy formation and evolution. Nature, 460:213-219, 2009. (261 citations) 10.1038/nature08135

Cattaneo2009TheRO
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E. Choi, R. Somerville, J. Ostriker, T. Naab, and M. Hirschmann. The role of black hole feedback on size and structural evolution in massive galaxies. The Astrophysical Journal, 2018. (48 citations) 10.3847/1538-4357/aae076

Choi2018TheRO
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Purpose of dreams?
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Barrett (1993) conducted a study using Dement’s (1974) incubation procedure with 76 college students. The students were asked to think of a personal problem before sleep and keep a dream journal for a week. The results showed that 49% of participants reported dreams reflecting the problem, and 34% felt their dreams contained a solution. However, the study had methodological constraints, making it difficult to draw conclusions about dreams' function in problem-solving. Critics argue that problem-solving components are absent in dream cognition, and solutions are a result of thinking about the dream while awake. Montangero (1991) suggested that dreams might not solve problems but could stimulate creativity.
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The text discusses two theories about the formation and purpose of dreams. The Threat Simulation Theory suggests that dreams help individuals prepare for real-life threatening situations. However, alternative theories propose that dreams help individuals psychologically adjust to troubling real-life situations, with post-traumatic nightmares serving as examples. The Continuity Hypothesis (CH) posits that dreams reflect waking life experiences, with real-life events incorporated into dreams. However, CH does not predict that a single exposure to an event would lead to recurring dreams about it. Evidence also suggests that neutral and positive waking experiences are not frequently reflected in dreams.
Valli2005TheTS
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Question: How have theories about the formation and purpose of dreams evolved over time?
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Theories about the formation and purpose of dreams have evolved significantly over time. Aristotle first questioned the nature of dreams around 350 B.C., and interest in the topic within psychology and psychiatry was sparked by Sigmund Freud in 1900, who proposed dreams act as 'the guardians of sleep'. Over time, various theories have been proposed, including psychodynamic theories, evolutionary models, and neurocognitive models. However, due to the subjective nature of dreams, there is a lack of consensus (Sayed2011TheFO pages 13-14). Contemporary research has moved from investigating specific dream content to studying neural activity of all dreams. Theories such as Barrett's (1993) study suggest dreams may reflect personal problems and potentially offer solutions, although there is debate surrounding this (Sayed2011TheFO pages 44-45). Other theories like the Threat Simulation Theory and the Continuity Hypothesis propose that dreams help individuals prepare for real-life threatening situations or reflect waking life experiences, respectively (Valli2005TheTS pages 20-21).
References:

The function of dreams and dreaming : moving towards an integrated understanding (6 citations)

Sayed2011TheFO
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Katja Valli, A. Revonsuo, Outi Pälkäs, K. H. Ismail, Karzan Jalal Ali, and R. Punamäki. The threat simulation theory of the evolutionary function of dreaming: evidence from dreams of traumatized children. Consciousness and Cognition, 14:188-218, 2005. (135 citations) 10.1016/S1053-8100(03)00019-9

Valli2005TheTS
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Why do zebras have stripes?
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The text discusses various hypotheses about the adaptive significance of zebra stripes, including social cohesion, thermoregulation, predation evasion, and avoidance of biting flies. The authors examined the correlation between 29 environmental variables and the variation in stripe characteristics of plains zebras across Africa. They found no evidence supporting the theories of predation evasion or fly avoidance. Instead, they discovered a significant correlation between temperature and stripe pattern variation, suggesting that the factors driving zebra striping are likely multifaceted and complex.
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The text discusses a study on the reasons for zebras' stripes, focusing on various hypotheses. It mentions that plains zebras often inhabit hot environments, suggesting a possible link between their stripes and temperature regulation. Infrared camera measurements showed zebras were warmer than three other herbivores in the same conditions. The text also mentions a multifactorial study of striping in zebras, with hypotheses including predation, crypsis, spotted hyaena, lion, and social interaction. However, the text does not provide conclusive evidence or results for these hypotheses.
Caro2015ConcordanceOZ
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The text discusses the evolution of markings on animals, specifically the quagga, a subspecies of Equus quagga. It describes a process where dark markings on the animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings. This process is observed up to the shoulder and nearly to the tail's root, including the belly. The text also mentions different races of quagga, such as Burchell's, Grey's, and Daniel's quagga, each exhibiting varying degrees of this marking evolution. The text suggests that this process could explain the development of zebra stripes.
Pocock1909XLIVOnTC
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Question: Write a history of how the explanation for why zebras have stripes has evolved over the decades.
answer:
The explanation for why zebras have stripes has evolved over the decades, with various hypotheses proposed. In the early 20th century, Pocock proposed that the development of zebra stripes could be explained by a process where dark markings on an animal's body gradually expand, thin out, and fade, eventually being replaced by white or lighter markings, as observed in the quagga, a subspecies of Equus quagga (Pocock1909XLIVOnTC pages 11-12). In recent years, more multifaceted hypotheses have been examined, including social cohesion, thermoregulation, predation evasion, and avoidance of biting flies (Larison2015HowTZ pages 1-1). Specifically, a significant correlation was found between temperature and stripe pattern variation, suggesting a possible role of thermoregulation in the evolution of zebra stripes (Larison2015HowTZ pages 1-1). However, the same study found no evidence supporting the theories of predation evasion or fly avoidance (Larison2015HowTZ pages 1-1). Despite these findings, the exact reasons for zebras' stripes remain inconclusive and are likely influenced by multiple factors (Caro2015ConcordanceOZ pages 2-3).
References:

B. Larison, R. Harrigan, H. Thomassen, D. Rubenstein, Chan-Golston M. Alec, Elizabeth Li, and T. Smith. How the zebra got its stripes: a problem with too many solutions. Royal Society Open Science, 2015. (39 citations) 10.1098/rsos.140452

Larison2015HowTZ
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R. I. Pocock. Xliv.—on the colours of horses, zebras, and tapirs. Journal of Natural History, 4:404-415, 1909. (3 citations) 10.1080/00222930908692688

Pocock1909XLIVOnTC
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T. Caro and T. Stankowich. Concordance on zebra stripes: a comment on larison et al. (2015). Royal Society Open Science, 2015. (11 citations) 10.1098/rsos.150323

Caro2015ConcordanceOZ
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Purpose of stegosaurus plates?
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The text discusses various philosophical perspectives on why the Stegosaurus had plates. It mentions the idea that these plates were not a random occurrence but rather a result of a greater designing mind or Mind, as proposed by Plato. This Mind would arrange each thing in the best way possible. The text also suggests a functional reason for the plates: to cool the animal in the heat of the mid-day sun. This function is presented as part of a larger plan by an external Mind.
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The text suggests that the plates on the back of a stegosaurus serve for species recognition. There is no clear pattern of directional evolution in the features of stegosaurian plates, beyond those generally correlated with body size. The lack of evidence for sexual dimorphism supports the idea that the diversity of plate patterns in stegosaurs is for species recognition. This conclusion is based on the analysis of stegosaurian genera and the examination of the characters of the plates. However, the authors caution that the phylogeny of stegosaurs is still elusive due to missing data and character conflicts.
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The plates on the back and tail of a Stegosaurus may have served a crucial thermoregulatory function, acting as forced convection 'fins' to dissipate heat. This hypothesis is supported by wind tunnel experiments on finned models, internal heat conduction calculations, and direct observations of the morphology and internal structure of stegosaur plates. The plates' effectiveness as heat dissipaters could be controlled through input blood flow rate, temperature, and body orientation with respect to wind. The experiments showed an approximately 50% increase in overall convective heat loss at constant geometry, orientation, and wind speed.
Farlow1976PlatesOT
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Question: Why do stegosaurus have plates on their back?
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The plates on the back of a Stegosaurus serve multiple purposes. One hypothesis is that these plates functioned as a thermoregulatory system, acting as forced convection 'fins' to dissipate heat. This is supported by wind tunnel experiments, heat conduction calculations, and direct observations of stegosaur plates (Farlow1976PlatesOT pages 1-1). Another perspective is that the plates were used for species recognition, as suggested by the diversity of plate patterns in stegosaurs and the lack of evidence for sexual dimorphism (Main2005TheEA pages 20-20).
References:

J. Farlow, Carl V. Thompson, and D. E. Rosner. Plates of the dinosaur stegosaurus: forced convection heat loss fins? Science, 192:1123 - 1125, 1976. (70 citations) 10.1126/science.192.4244.1123

Farlow1976PlatesOT
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R. Main, A. D. de Ricqlès, J. Horner, and K. Padian. The evolution and function of thyreophoran dinosaur scutes: implications for plate function in stegosaurs. In Paleobiology, volume 31, 291 - 314. 2005. (123 citations) 10.1666/0094-8373(2005)031[0291:TEAFOT]2.0.CO;2

Main2005TheEA
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Pluto perception over time?
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Three astronomy communicators identified three key ideas regarding the changing perception of Pluto: its reclassification from a planet, the influence of recent discoveries on this reclassification, and the evolution of science over time. Over 90% of students surveyed understood why Pluto was in the news, and 16% understood the role of recent discoveries. However, fewer grasped the concept of science's evolution. A common misunderstanding was the comparison of Pluto's size to a star, suggesting a misconception about celestial sizes. This misunderstanding persisted despite astronomy education in Northern Ireland's secondary science curriculum.
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The perception of Pluto as a planet has been a contentious topic, culminating in the International Astronomical Union's (IAU) decision in 2006 to revoke Pluto's planetary status. This decision led to the creation of a new category of celestial bodies called "dwarf planets," which includes Pluto, Eris, and Ceres. The IAU's definition of a true planet is one that dominates its own region of space and either accretes or ejects other planetesimals in its orbit. This definition excludes Pluto, which is located in the Kuiper belt. Despite the IAU's stance, there is ongoing debate and differing opinions on the classification of Pluto.
Bottke2007IsPA
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The study by Broughton, Sinatra, and Nussbaum (2013) investigated the emotional and attitudinal responses of fifth and sixth-grade students to the reclassification of Pluto from a planet to a dwarf planet by the International Astronomical Union (IAU) in 2006. The students were assigned to either reread independently or discuss the reclassification. The results showed that both groups experienced an attitude change over time, with emotions becoming more positive after intervention. The reclassification of Pluto sparked an emotionally charged debate among IAU members and the public, indicating a shift in perception about Pluto's planetary status.
Broughton2013PlutoHB
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Question: How has the perception of Pluto as a planet changed throughout history?
answer:
The perception of Pluto as a planet has undergone significant evolution. Initially recognized as a planet, the International Astronomical Union (IAU) reclassified Pluto as a "dwarf planet" in 2006 due to its inability to dominate its own region of space and accrete or eject other planetesimals in its orbit, a requirement under the IAU's definition of a true planet (Bottke2007IsPA pages 1-2). This reclassification has sparked widespread debate and led to a shift in public perception, with some accepting the new classification and others maintaining Pluto's planetary status (Broughton2013PlutoHB pages 1-2). Educational studies have shown that while most students are aware of the debate, there is a lack of understanding regarding the scientific reasons behind Pluto's reclassification (Jarman2009APO pages 10-11). This reflects the ongoing debate and the evolving nature of scientific knowledge.
References:

Is Pluto a Planet? A Historical Journey Through the Solar System (0 citations) 10.1063/1.2800098

Bottke2007IsPA
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R. Jarman and B. McClune. ‘a planet of confusion and debate’: children's and young people's response to the news coverage of pluto's loss of planetary status. Research in Science & Technological Education, 27:309 - 325, 2009. (6 citations) 10.1080/02635140903162637

Jarman2009APO
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Suzanne H. Broughton, G. Sinatra, and E. Nussbaum. “pluto has been a planet my whole life!” emotions, attitudes, and conceptual change in elementary students’ learning about pluto’s reclassification. Research in Science Education, 43:529-550, 2013. (118 citations) 10.1007/S11165-011-9274-X

Broughton2013PlutoHB
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How do plants communicate?
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The text discusses the communication between plants via airborne signals, specifically through the emission of biotic stress-induced Volatile Organic Compounds (VOCs). This aspect of plant communication is considered neglected in research. The paper highlights the need to understand how plants become aware of abiotic stress factors, particularly in the context of global change, and how the VOCs they emit under such stress interact with the environment. The understanding of this "VOC language" could be used for biomonitoring and to stimulate the biosynthesis of target metabolites for clean and bioactive-enriched products. Further research is needed to understand the potential effects of these VOCs on plants under abiotic stress in controlled environments.
Landi2020AirborneSA
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Plants communicate with each other and their environment through various defense mechanisms. One such mechanism involves the plant peptide hormone, systemin, which promotes a systemic response to herbivory in tomatoes. Systemin, an 18 amino acid peptide, can induce the release of bioactive Volatile Organic Compounds, promoting interaction between the tomato and the third trophic level, such as predators and parasitoids of insect pests. Systemin can also trigger metabolic changes in plants, inducing a primed state in neighboring unchallenged plants. This primed state is associated with elevated transcription of pattern-recognition receptors, signaling enzymes, and transcription factors, making the plants more resistant to pests and more attractive to parasitoids.
Coppola2017PlanttoplantCT
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Dahlin2018PestSI
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The text discusses the role of Jasmonates (JA) in plant-fungus interaction, specifically in Arbuscular Mycorrhization (AM), a common type of mycorrhiza. The data shows contrasting results, with some studies indicating that JA application enhances plant-fungus interaction, while others suggest a decrease. This discrepancy may be due to variations in experimental designs. The text also suggests that JA may control fungal spread and act as a positive regulator of AM. Mutants with enhanced JA levels showed increased mycorrhization, while those with reduced JA biosynthesis showed a decrease. The role of JA in systemic signaling between roots and shoots is also discussed.
Wasternack2013JasmonatesBP
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Arif2020SalicylicAI
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Moreira2018SpecificityOP
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Question: How do plants communicate with each other and with their environment?
answer:
Plants communicate with each other and their environment through various mechanisms, one of which involves the emission of biotic stress-induced Volatile Organic Compounds (VOCs). These VOCs interact with the environment, and understanding this "VOC language" could have applications in biomonitoring and in the stimulation of target metabolites for clean and bioactive-enriched products (Landi2020AirborneSA pages 6-7). Another mechanism involves the plant peptide hormone, systemin, which promotes a systemic response to herbivory in tomatoes. Systemin can induce the release of bioactive VOCs, fostering interaction between the tomato and the third trophic level, such as predators and parasitoids of insect pests. Additionally, systemin can trigger metabolic changes in plants, inducing a primed state in neighboring unchallenged plants, making them more resistant to pests and more attractive to parasitoids (Coppola2017PlanttoplantCT pages 1-1). Furthermore, Jasmonates (JA) play a role in plant-fungus interaction, specifically in Arbuscular Mycorrhization (AM). JA may control fungal spread and act as a positive regulator of AM, and is involved in systemic signaling between roots and shoots (Wasternack2013JasmonatesBP pages 20-20).
References:

M. Landi. Airborne signals and abiotic factors: the neglected side of the plant communication. Communicative & Integrative Biology, 13:67 - 73, 2020. (6 citations) 10.1080/19420889.2020.1767482

Landi2020AirborneSA
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C. Wasternack and B. Hause. Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. an update to the 2007 review in annals of botany. Annals of botany, 111 6:1021-58, 2013. (1870 citations) 10.1093/aob/mct067

Wasternack2013JasmonatesBP
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M. Coppola, P. Cascone, Valentina Madonna, I. Di Lelio, F. Esposito, C. Avitabile, A. Romanelli, E. Guerrieri, Alessia Vitiello, F. Pennacchio, R. Rao, and G. Corrado. Plant-to-plant communication triggered by systemin primes anti-herbivore resistance in tomato. Scientific Reports, 2017. (33 citations) 10.1038/s41598-017-15481-8

Coppola2017PlanttoplantCT
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How did color vision evolve?
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Marshall2016HumanCV
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Lee2008TheEO
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The evolution of human color vision is characterized by varying levels of sophistication, density, and spatial distribution of cone classes, and the number and absorption maxima of cone pigments in different species. Most mammals have three pigments, while chickens have six. Humans and their closest primate relatives represent an intermediate level of complexity with four visual pigments: a single member of the ~500 nm family of cone pigments, two highly homologous members of the ~500 nm family, and rhodopsin. The red/green visual pigment gene duplication in the Old World primate lineage occurred about 30-40 million years ago, shortly after the geologic split between Africa and South America.
Nathans1999TheEA
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Yokoyama2008EvolutionOD
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The evolution of human color vision is closely tied to theories about the nature of light, starting from the 17th to 19th centuries. Initially, there was no clear distinction between the properties of light, the eye and retina, and color percepts. Theories about vision before Newton often viewed colors as intermediate stages between black and white. Newton was the first to describe colors in a modern way, using prisms to disperse light and provide a spectrum of colors. He demonstrated that each color band could not be further divided and that different colors had different refrangibility. The recombination of the spectrum resulted in white.
Lee2008TheEO
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The Springer Series in Vision Research includes a volume on Human Colour Vision, edited by Jan Kremers, Rigmor C. Baraas, and N. Justin Marshall. This book provides a comprehensive update on vision research, detailing the entire visual system from molecular processes to behavior. It covers recent developments in the field, new methods, and emerging hypotheses. The book emphasizes the importance of color in human life, used for object detection and discrimination of features, and influencing daily judgments. It is aimed at individuals interested in the biology of color vision, medical aspects of its failure, and other areas of color science.
Marshall2016HumanCV
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Question: Provide an overview of the evolution of human color vision.
answer:
The evolution of human color vision is marked by varying levels of sophistication, density, and spatial distribution of cone classes, and the number and absorption maxima of cone pigments in different species. Humans and their closest primate relatives possess an intermediate level of complexity with four visual pigments: a single member of the ~500 nm family of cone pigments, two highly homologous members of the ~500 nm family, and rhodopsin. The red/green visual pigment gene duplication in the Old World primate lineage happened about 30-40 million years ago (Nathans1999TheEA pages 1-1). The evolution of human color vision is also closely tied to theories about the nature of light, beginning from the 17th to 19th centuries. Newton was the first to describe colors in a modern way by using prisms to disperse light and provide a spectrum of colors (Lee2008TheEO pages 1-2). Color is significant in human life as it is used for object detection and discrimination of features, and influences daily judgments (Marshall2016HumanCV pages 1-4).
References:

J. Nathans. The evolution and physiology of human color vision insights from molecular genetic studies of visual pigments. Neuron, 24:299-312, 1999. (317 citations) 10.1016/S0896-6273(00)80845-4

Nathans1999TheEA
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Barry B. Lee. The evolution of concepts of color vision. Neurociencias, 4 4:209-224, 2008. (13 citations)

Lee2008TheEO
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J. Marshall, S. Collin, J. Kremers, R. Baraas, and N. Marshall. Human color vision. In Springer Series in Vision Research. 2016. (106 citations) 10.1007/978-3-319-44978-4

Marshall2016HumanCV
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What color were dinosaurs?
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Brown2017AnEP
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Turner2016ASL
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The text discusses the color of dinosaur eggs, specifically those of oviraptorids, which were found to be blue-green. This coloration is associated with modern bird behaviors such as paternal care, communal nesting, and postmating sexual signaling. The color is also thought to have evolved for intraspecific signaling. The text suggests that these behaviors and the associated egg coloration may have originated with dinosaurs. The text also mentions that the color of the eggs may have been influenced by the environment, with blue-green eggs being laid in areas where they would contrast with the nesting background.
Wiemann2017DinosaurOO
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The text discusses a study on the Psittacosaurus dinosaur's color pattern, which was used to deduce its environment. The study, led by Innes Cuthill at the University of Bristol, focused on countershading, a common camouflage technique involving darker coloration on the back and lighter on the underside. The team found that the intensity of these shades and the transition from dark to pale varied among species, correlating with the lighting conditions of their habitats. This suggests that dinosaur coloration was likely influenced by their environment and not limited to just grey and green.
Vinther2017TheTC
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Li2010PlumageCP
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The text discusses a study investigating the presence of iridescent plumage in dinosaurs, specifically the Microraptor. The study found that the Microraptor, part of the Paraves clade, had melanosome characteristics and plumage similar to iridescent avian feathers. The researchers also examined melanosome morphology in a diverse set of iridescent feathers from extant birds, finding that melanosomes from iridescent feathers were significantly longer and narrower than those from black feathers. This suggests that some dinosaurs, like the Microraptor, may have had iridescent plumage, indicating that they were not just grey and green.
Li2012ReconstructionOM
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Question: Were dinosaurs really just grey and green? What do recent scientific studies suggest about their true colors?
answer:
Recent scientific studies suggest that dinosaurs exhibited a wider range of colors than just grey and green. A study led by Innes Cuthill at the University of Bristol on the Psittacosaurus dinosaur's color pattern found variations in countershading, suggesting that dinosaur coloration was influenced by their environment (Vinther2017TheTC). Another study on the Microraptor, a member of the Paraves clade, found evidence of iridescent plumage, indicating the presence of colors beyond grey and green (Li2012ReconstructionOM). Additionally, research on oviraptorid dinosaur eggs revealed a blue-green coloration, suggesting that this color may have been used for intraspecific signaling and could have been influenced by the nesting environment (Wiemann2017DinosaurOO). These studies collectively suggest a more diverse color palette in dinosaurs than previously assumed.
References:

J. Vinther. The true colors of dinosaurs. Scientific American, 316 3:50-57, 2017. (2 citations) 10.1038/scientificamerican0317-50

Vinther2017TheTC
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Quanguo Li, K. Gao, Qingjin Meng, J. Clarke, M. Shawkey, L. D’Alba, R. Pei, Michael Ellison, M. Norell, and J. Vinther. Reconstruction of microraptor and the evolution of iridescent plumage. Science, 335:1215 - 1219, 2012. (175 citations) 10.1126/science.1213780

Li2012ReconstructionOM
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J. Wiemann, J. Wiemann, Tzu-Ruei Yang, Philipp N. N Sander, Philipp N. N Sander, Marion Schneider, M. Engeser, S. Kath‐Schorr, Christa E. Müller, and P. M. Sander. Dinosaur origin of egg color: oviraptors laid blue-green eggs. PeerJ, 2017. (37 citations) 10.7717/peerj.3706

Wiemann2017DinosaurOO
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Climate affects on weather?
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The review by Franco et al. (2020) discusses the impact of climate change on atmospheric and oceanic circulation in the southwestern South Atlantic. The study observes that atmospheric circulation anomalies align with anthropogenic climate change. The Brazil Current has reportedly intensified and shifted southwards due to changes in near-surface wind patterns, causing significant ocean warming along its path. These changes have led to a poleward shift of important pelagic species and a transition from cold-water to warm-water species in Uruguay's industrial fisheries. The study also notes the adverse effects of climate change on small-scale fisheries, including mass mortalities and harmful algal blooms.
Franco2020ClimateCI
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Voosen2020ClimateCS
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Soldatenko2022OnTE
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The article discusses how ocean currents, specifically the Agulhas Current, are responding to climate change in unexpected ways. Contrary to predictions that the poleward flow of tropical waters would intensify with global warming and stronger winds, observations over a 22-year period showed that the current did not grow stronger. Instead, it widened, possibly due to increased wind energy producing turbulent eddies. The Agulhas Current, which flows southward along the western boundary of the Indian Ocean, has a warming effect on the Atlantic Ocean. With climate change, westerly winds are expected to intensify and recede south, potentially increasing Agulhas leakage.
Miller2017OceanCR
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Climate change impacts global ocean circulation, sea-level rise, and greenhouse gas concentrations. Warming affects the water's ability to absorb carbon dioxide, altering the amount of this gas removed from the atmosphere. It also intensifies upwelling at major sites, increasing phytoplankton production and greenhouse gas release. Freshening waters, due to enhanced hydrological cycle and ice melt, alter seawater density and affect global circulation. Warmer water creates a stratified layer, isolating nutrient-rich deeper waters and expanding nutrient-deficient areas. This impacts carbon and nitrogen cycles and marine ecosystems, potentially leaving more carbon dioxide in the air and contributing to global heating.
Lewis-Brown2008TheIO
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Stetson2006TheIO
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Question: How is climate change affecting ocean currents and global weather patterns?
answer:
Climate change impacts global ocean circulation and weather patterns in several ways. Warming affects the water's ability to absorb carbon dioxide, altering the amount of gas removed from the atmosphere and intensifying upwelling at major sites, which increases phytoplankton production and greenhouse gas release (Lewis-Brown2008TheIO pages 117-118). Freshening waters due to an enhanced hydrological cycle and ice melt alter seawater density, affecting global circulation (Lewis-Brown2008TheIO pages 117-118). Ocean currents, such as the Brazil Current and Agulhas Current, have reportedly intensified and shifted due to changes in near-surface wind patterns, causing significant ocean warming along their paths (Franco2020ClimateCI pages 1-2; Miller2017OceanCR pages 1-2). These changes have led to shifts in marine species distributions and transitions from cold-water to warm-water species in certain fisheries (Franco2020ClimateCI pages 1-2). However, contrary to predictions, some currents like the Agulhas Current did not grow stronger with global warming but instead widened due to increased wind energy producing turbulent eddies (Miller2017OceanCR pages 1-2).
References:

E. Lewis-Brown, P. C. Reid, A. Andersson, R. Arthurton, N. Bates, M. Barangé, U. Bathmann, G. Beaugrand, W. Berger, N. Bindoff, H. Cattle, P. Chisholm, J. Church, D. de Gusmão, H. Drange, S. Dye, M. Edwards, A. Fischer, J. Flueckiger, T. Furevik, J. Gascard, R. Hopcroft, D. Iglesias-Rodriguez, C. Le Quere, M. Le Tissier, S. Kasten, M. Kendall, R. Knutti, F. Mackenzie, G. Malin, D. Martinson, W. Maslowski, R. Matear, C. Mauritzen, M. Meredith, C. Paull, R. Pingree, J. Raven, S. Rintoul, I. Salter, G. Schmidt, K. Shimada, M. Sparrow, D. Stevens, P. Tréguer, A. Tudhope, C. Turley, M. Visbeck, M. Vogt, C. Wallace, Zhaomin Wang, R. Washington, and R. Wood. The impacts of the oceans on climate change. In Electronics System-integration Technology Conference, 29-32. 2008. (60 citations) 10.1109/estc.2008.4684318

Lewis-Brown2008TheIO
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B. Franco, O. Defeo, A. Piola, M. Barreiro, Hu Yang, L. Ortega, I. Gianelli, J. P. Castello, C. Vera, C. Buratti, M. Pájaro, L. Pezzi, and O. O. Möller. Climate change impacts on the atmospheric circulation, ocean, and fisheries in the southwest south atlantic ocean: a review. Climatic Change, pages 1-19, 2020. (47 citations) 10.1007/s10584-020-02783-6

Franco2020ClimateCI
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Johanna L. Miller. Ocean currents respond to climate change in unexpected ways. Physics Today, 70:17-18, 2017. (3 citations) 10.1063/PT.3.3415

Miller2017OceanCR
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Why are insects declining?
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Muñoz2015EffectsOR
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Surveys conducted in German nature reserves indicate a significant decrease in insect biomass. The Krefeld Entomological Society observed that the total mass of their insect catch had dropped by nearly 80% since 1989. This decline was consistent across more than a dozen other sites. Some attribute the decrease in insects on windshields to more aerodynamic cars, but others, like Scott Black of the Xerces Society for Invertebrate Conservation, suggest that the decline is due to a decrease in insect populations.
Vogel2017WhereHA
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The text suggests that insect mortality is positively correlated with traffic volume. However, higher mortality rates were found at intermediate traffic volumes compared to high and low traffic rates. This is due to the 'catapult' effect, where cars traveling at speeds over 55 mph generate wind gusts that prevent insects from colliding with the vehicle. Insect mortality also peaks during periods of increased traffic, such as weekends and holidays. The effect of traffic volume on insects can be difficult to quantify due to problems identifying individual species. Road size and surface conditions also influence insect mortality, with pavement attracting many insect species.
Muñoz2015EffectsOR
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The text refersThe text discusses to a publication the "wind by Emily Kshield phenomenon,". Meine a term coinedke titled " by entomThe insect crisisologist Anders P: the fallape Møller, referring of the tiny empires that to the noticeable run the world decline in insects" in the splattered on American Entom car windshologist, ields over time2022.. Mø The document discussesller conducted a a decline in study from insect populations,1997 to which could potentially present, driving explain the observation through undevelop of fewer bugsed areas in on a windshield Denmark and collecting in the Bay insects on wind Area compared toshields. previous decades. His findings documented However, the significant insect declines text does not not associated with provide specific details local urban or or numbers to agricultural development. support this. 7 This phenomenon is also discussed in Oliver Milman's book "The Insect Crisis," which provides comprehensive evidence of widespread insect decline.
Meineke2022TheIC
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Vogel2017WhereHA
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Question: Why are there fewer bugs on my windshield when I drive through the bay area than previous decades?
answer:
The decrease in insects on windshields, also known as the "windshield phenomenon," is attributed to a significant decline in insect populations observed in various studies, rather than changes in car aerodynamics or driving conditions (Vogel2017WhereHA pages 1-2, Meineke2022TheIC pages 1-1). The Krefeld Entomological Society found that insect biomass dropped by nearly 80% since 1989, a trend consistent across multiple sites (Vogel2017WhereHA pages 1-2). This decrease is not associated with local urban or agricultural development (Meineke2022TheIC pages 1-1). Traffic volume can influence insect mortality, but the 'catapult' effect, where cars traveling at speeds over 55 mph generate wind gusts that prevent insects from colliding with the vehicle, can reduce insect collisions at high traffic volumes (Muñoz2015EffectsOR pages 13-14). However, this effect does not account for the observed magnitude of insect decline.
References:

G. Vogel. Where have all the insects gone? Science, 356 6338:576-579, 2017. (142 citations) 10.1126/science.356.6338.576

Vogel2017WhereHA
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P. Muñoz, F. Torres, and A. Megías. Effects of roads on insects: a review. Biodiversity and Conservation, 24:659-682, 2015. (104 citations) 10.1007/s10531-014-0831-2

Muñoz2015EffectsOR
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Emily K. Meineke. The insect crisis: the fall of the tiny empires that run the world. American Entomologist, 2022. (2 citations) 10.1093/ae/tmac044

Meineke2022TheIC
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Do black holes affect galaxies?
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The study by Choi et al. (2018) used cosmological hydrodynamical simulations to investigate the impact of feedback from accreting black holes on the evolution of massive galaxies. The research found that Active Galactic Nucleus (AGN) feedback, arising from winds and X-ray radiation, can alter the stellar density distribution, reduce core density within the central 1 kpc by 0.3 dex from z = 1, and enhance the size growth of massive galaxies. AGN feedback plays a crucial role in transforming galaxies from blue compact galaxies into red extended galaxies by quenching star formation and preventing new accretion of cold gas. This leads to gas-poor or mixed subsequent mergers, building up an extended stellar envelope.
Choi2018TheRO
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Black holes impact the structure and evolution of galaxies through radiation pressure, absorption by resonance lines, and jets, which can produce energy-driven and momentum-driven winds. Radiation pressure is significant near black holes, determining the Eddington limit, and can be almost 100% efficient in transferring momentum from photons to gas. This process, however, is limited by the low momentum of photons and the requirement of dust covering a large solid angle. Jets can deposit most of their energy outside their host galaxies. Observations suggest that quasars can accelerate winds with speeds of thousands to tens of thousands of kilometres per second, potentially playing a role in the 'quenching' of post-starburst galaxies.
Cattaneo2009TheRO
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Khan2012MERGERSOU
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All massive galaxies host central black holes with masses ranging from millions to billions of solar masses. The growth of these black holes releases vast amounts of energy, powering quasars and other active galactic nuclei. A fraction of this energy, if absorbed by the host galaxy, could halt star formation by heating and ejecting ambient gas. This process is considered a potential cause for the decline of star formation in large elliptical galaxies, which typically have little cold gas and few young stars. Galaxies are categorized into two types: ellipticals and spirals. Each type's central bulge contains a black hole, whose mass is proportional to the bulge's stellar mass.
Cattaneo2009TheRO
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Khan2012MERGERSOU
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Barausse2012TheEO
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Question: How do black holes influence the structure and evolution of galaxies?
answer:
Black holes, particularly those at the centers of galaxies, significantly influence the structure and evolution of galaxies. They release vast amounts of energy, powering quasars and other active galactic nuclei (AGN), which can alter the stellar density distribution and enhance the size growth of massive galaxies (Choi2018TheRO pages 1-1). The energy output from black holes can halt star formation by heating and ejecting ambient gas, a process considered a potential cause for the decline of star formation in large elliptical galaxies (Cattaneo2009TheRO pages 1-2). Additionally, black holes impact galaxies through radiation pressure, absorption by resonance lines, and jets. These jets can produce energy-driven and momentum-driven winds, potentially playing a role in the 'quenching' of post-starburst galaxies (Cattaneo2009TheRO pages 4-5). AGN feedback from black holes can transform galaxies from blue compact galaxies into red extended galaxies by quenching star formation and preventing new accretion of cold gas (Choi2018TheRO pages 1-1).
References:

A. Cattaneo, S. Faber, J. Binney, A. Dekel, J. Kormendy, R. Mushotzky, A. Babul, P. Best, M. Brüggen, A. Fabian, C. Frenk, Arman Khalatyan, H. Netzer, A. Mahdavi, J. Silk, M. Steinmetz, and L. Wisotzki. The role of black holes in galaxy formation and evolution. Nature, 460:213-219, 2009. (261 citations) 10.1038/nature08135

Cattaneo2009TheRO
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E. Choi, R. Somerville, J. Ostriker, T. Naab, and M. Hirschmann. The role of black hole feedback on size and structural evolution in massive galaxies. The Astrophysical Journal, 2018. (48 citations) 10.3847/1538-4357/aae076

Choi2018TheRO
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PaperQA is more than just a search tool; it is an adaptive system that uses tools based on the question and intermediate research. These tools include:

  • SEARCH: finding relevant papers from online databases, such as Arxiv and Pubmed;
  • GATHER_EVIDENCE: parsing and summarizing text from these papers;
  • ANSWER_QUESTION: ranking the relevance of the gathered context and synthesizing information into a final answer.

This process is non-linear. For example, if PaperQA sees a paper that uses a different word to refer to a concept, it can go back and search again with the new nomenclature. Compared to a standard RAG, PaperQA makes four key changes (each improved performance, measured via ablation testing):

  1. PaperQA breaks down the Retrieve and Generate (RAG) process into tools for an AI agent, enabling it to perform multiple searches with various keywords whenever the information at hand isn't enough.
  2. PaperQA employs a Map-Reduce inspired approach to summarization, where the AI first collects (maps) evidence from a range of sources and then condenses (reduces) this information to provide an answer. This increases the amount of sources that can be considered, enabling the LLM to provide preliminary insights before composing the final answer.
  3. PaperQA uses a hybrid search approach to work on all accessible papers, which number in the 100s of million. Namely, PaperQA uses LLM-assisted keyword search at the corpus level and semantic search at the granular level of pages of text.
  4. PaperQA implements prior-knowledge prompting strategies to access and utilize the underlying knowledge embedded within language models, when needed finding evidence in the scientific literature, and uses the resulting answer as a type of posterior knowledge.

Importantly, PaperQA builds upon the unique structure of scientific literature – its citation graph and categorization into journals and fields. This is only possible due to the excellent contributions of the Semantic Scholar team at Allen Institute for AI, whose API for exploring the citation graph of science is a key feature of PaperQA. We plan to make the full WikiCrow and PaperQA code available on GitHub soon. Until then, the essential aspects of the PaperQA algorithm are available (although you will need access to your own repository of full text scientific articles), as well as the prompts used for WikiCrow.

Benchmarking PaperQA

In our evaluations, PaperQA outperforms GPT-4, Perplexity, and other LLMs, as well as commercial RAG systems on several benchmarks. We show excellent performance on two scientific question-answering benchmarks - MedQA-USMLE and PubMedQA Blind, the latter of which is a modified version of PubMedQA, where original contexts are removed to challenge the system to find the papers to retrieve the context. Additionally, PaperQA outperforms a range of systems on LitQA, a new benchmark that we developed to validate our performance. LitQA consists of multiple-choice questions that are difficult or impossible to answer accurately without retrieval of one or more specific papers, all of which  were published after the training cutoff dates of GPT-4 and Claude 2 in 2022. Today, LitQA is small, with only 50 questions, as it is extraordinarily time-consuming to generate and validate these types of questions, but we plan to scale it up in the future. Also note that we performed this testing in October 2023 (outside of Gemini Pro in December 2023) and did not try to optimize any of the commercial systems here, so it’s possible they could be engineered for higher performance, or would have higher performance if tested today.

WikiCrow Mechanics

We carefully prompt the PaperQA agent to collect information on specific genes from scientific papers for each essential Wikipedia article section: Structure, Function, Interactions and Clinical Significance. To develop these prompts, we started with Wikipedia’s existing molecular biology style guide, then made significant changes over several empirical iterations. This highlights the continued importance of prompt engineering and the need for improved alignment strategies. 

Afterwards, we use another LLM call to edit these four independent sections into a coherent and concise Wikipedia-style article, appending an Overview paragraph to the top, while maintaining all citations. The specific prompts used are available. Additionally, we are in conversations with Wikipedia about hosting these articles, and will continue to make our versions available programmatically; for example you can use this gsutil command to list all genes available for download: gsutil ls gs://fh-public/wikicrow/

Statements from human-written Wikipedia articles usually failed evaluation due to irrelevant, inappropriate, or absent citation support. We believe this stems from the varying quality of authorship, as well as the format of Wikipedia not requiring all statements to be justified with peer reviewed articles. Interestingly, statements from WikiCrow AI generated articles follow an opposite pattern, where the majority of statements fail due to incorrect transmission of information from the cited article. This was typically due to the model’s difficulty discerning highly similar gene names (e.g., GSDMD vs. GSDME), or failure to parse the logic of complex sentences, such as “knockdown of a repressive gene”, which is a clause with multiple negatives.

Evaluation of performance of LLMs powered by RAG is a new area of study, and this evaluation strategy has several limitations and challenges, which we highlight here:

  • We do not evaluate absolute statement accuracy: We only evaluate whether statements are cited and whether they are true as cited; we do not evaluate whether statements are objectively accurate. Statements that are accurate but either not cited or incorrectly cited, which are probably more common in human-written Wikipedia articles, are scored as incorrect on either the “properly cited” criterion or the “true as cited” criterion.  Trivially correct statements are excluded from evaluation
  • Evaluation is challenging to blind: WikiCrow-written articles use significantly more references to bolster individual claims, so it is usually easy to tell which articles were written by humans and which were written by WikiCrow in evaluations.
  • Inconsistent citation strategies: Humans use inconsistent citation strategies which require subjective evaluation. For example, we identified several cases of circular references in human-written Wikipedia articles, and we also identified several cases where human articles would cite large database entries like Entrez, rather than primary literature, which were difficult to evaluate. The need to make subjective decisions about whether to exclude such statements raises bias concerns.
  • Sample exclusion: Articles generated both by WikiCrow and by humans often contain trivial statements of fact, which also need to be excluded from evaluation on a subjective basis.

Despite these challenges, we think that our evaluation system is a reasonably accurate reflection of the “ground truth” quality of human-written and WikiCrow-written articles. If you have suggestions about how to improve evaluation, let us know, or consider applying to join our Assessment Team!

Conclusion

We built WikiCrow and PaperQA as foundational tools both for human researchers and for the AI Scientists we are building at FutureHouse. We plan for PaperQA to be one of many tools available to our AI Scientists, aiding in knowledge synthesis, experimental planning, hypothesis generation, and more. Moreover, PaperQA will be part of a closed-loop system, ensuring continuous and informed progression from theory to experimentation.

In addition, we believe that the WikiCrow approach will eventually enable synthesis and curation of all human scientific knowledge, in collaboration with human editors. Some directions we expect to explore include the use of dedicated models that are fine-tuned on Wikipedia edits, and improved alignment strategies to reduce the amount of prompt engineering that is needed for generation of comprehensive and coherent articles for a given topic. In the long run, we even envision a “Super-pedia,” where articles are generated about any topic in real time, on-demand, with the most up-to-date information. If you’re excited to work on this, get in touch.

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