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SC01 · SCIENCE THROUGH EVIDENCE

General Biology I: cellular mechanisms and quantitative evidence

Fifty-six original lessons implement all six cellular and molecular biology modules plus two course-wide synthesis destinations. Retained investigation and mixed-assessment work supports an explicit project defense; authored coverage is not certified practical participation or independent mastery.

This is the course outline. Open a unit to choose a lesson; every lesson opens on its own page. Explanations and experiments live inside those lesson pages.

Preparation and course boundaries

Preparation: High-school biology and chemistry, ratios, graph slopes and basic algebra. Logarithms are introduced through a supplied buffer equation; no programming, calculus or physical chemical handling is required.

Course outcome: Defend a cellular mechanism across scientific evidence, chemistry, compartments, metabolism, signaling, inheritance and gene expression; discriminate measurement and sampling alternatives using quantitative inventories and falsifying predictions.

All lessons are directly accessible. Reused foundation explanations are identified where relevant; completing a different course does not award this course's evidence. The 56 registered lessons keep separate predictions, captures, practice responses and reflections.

Module1 — Scientific evidence and biological chemistry7 lessons

Construct controlled causal contrasts, distinguish primary connectivity from conformation, audit biological material and buffer inventories, and test calibration predictions against independent standards.

Separate a biological mechanism from its readout

Compare inhibition40% with artifact0 and20 units. Then change inhibition to0 while retaining the artifact. Record all four readings, not just the result that agrees with your prediction. Explain why a cell-free standard and a bypass answer different questions.

Identify experimental units and use paired contrasts

Set treatment effect0 and batch shift4. Compare the paired estimate with the confounded estimate. Then change the treatment effect while holding batch offset fixed. State the number of biological units and name a violation that pairing cannot remove.

Connect functional groups to a biological atom ledger

Compare two four-residue chains with one eight-residue chain. Reconstruct input and output hydrogen and oxygen counts. Explain why identical total glucose input does not imply identical numbers of ends or released water molecules.

Distinguish pH from a buffer’s finite reserve

Compare pH7 at total4 and8mmol/L, keeping the challenge fixed. Then use pH6 with the smaller total and identify the model boundary. Record invalid approximations as invalid, not as missing evidence to hide.

Fit a molecular assay and challenge its prediction range

Compare q=0 and0.05 at the same intercept. Record fitted coefficients and both withheld residuals. Then change only the intercept and predict which quantities should remain unchanged. Explain why withholding standards makes a stronger range check than examining fitted points alone.

Bound an inferred quantity without hiding model error

Keep signal0.6AU and compare artifact0,0.1 and0.15AU. Identify which displayed bounds remain unchanged and why. Then change the signal while retaining the same artifact; explain the difference between absolute artifact and relative concentration error.

Module2 — Cells, microscopy and membranes9 lessons

Calibrate image evidence, distinguish cellular architecture and compartment roles, conserve finite inventories and audit membrane transport mechanisms against pressure, energy and measurement alternatives.

Calibrate cell dimensions from a shared image scale

Compare(100,60) with(200,100) within the controls and compute each ratio explicitly. Then choose a supported pair of uniformly scaled recipes such as(40,20) and(80,40). Retain the schematic provenance and a source of real-image uncertainty that is absent here.

Connect cellular geometry to exchange constraints

Compare radius4/folding1, radius8/folding1 and radius8/folding2. Retain separate area, volume and ratio values. Name one biological transport variable that the geometric comparison leaves uncontrolled.

Test a finite-capacity carrier without equating saturation with active transport

Compare competitor0 and2 across substrate1,4 and10. Locate half-maximal uptake and distinguish a changingKm from a changingVmax. Propose an assay control that could separate transport saturation from detector saturation. As a separate composition prediction, compare otherwise matched saturated-tail and cis-unsaturated-tail membranes during cooling: which should retain more fluidity? Would that alone establish a faster carrier rate?

Audit an uphill transport cycle before claiming a mechanism

Compare ratio11 and21 at drive20 and30kJ/mol cycles. Locate a case where the specified drive is insufficient. Explain why adding an ionic charge would require an additional electrical contribution rather than reuse of the same neutral ledger.

Module 3 — Enzymes, respiration and photosynthesis11 lessons

Discriminate enzyme-rate mechanisms, audit free-energy coupling and reconstruct carbon, electron, proton and ATP inventories across respiratory and photosynthetic pathways.

Choose an enzyme-rate window before comparing treatments

Compare enzyme factors 1 and 2 using windows 0.1 and 2 min. Calculate the initial slope and endpoint average separately. Record substrate depletion and explain why an apparent failure of proportionality need not prove enzyme inhibition.

Discriminate inhibition from loss of catalytic capacity

Compare inhibitor 0 and 2 at substrate 1, 4 and 10. Before reading the curves, predict whether increasing substrate can recover the reference capacity in each model. Identify one nonkinetic control that would challenge the interpretation.

Separate catalytic temperature effects from enzyme history

Hold 45°C and compare exposure 0, 4 and 10 min. Then compare a cooler condition at the same exposure duration. Keep catalytic factor and active fraction in separate columns instead of treating observed rate as a single-mechanism measurement.

Separate glycolytic investment, payoff and net cellular demand

Compare glucose amounts 1 and 3 with demand 4. Keep investment, gross formation, net pathway yield and remaining demand balance separate. Explain why oxygen absence does not directly cancel glycolysis but can affect the wider carrier-regeneration context.

Connect an electron-donor inventory to oxygen reduction

Compare donor 4, 8 and 10 with oxygen 3. Then hold donor 8 and change oxygen from 0 to 4. Record both unused inventories and explain why an oxygen-limited endpoint does not determine the respiratory rate before that endpoint.

Combine voltage and pH contributions to chemiosmotic coupling

Compare ΔpH 0 and 1 at voltages 50 and 150 mV. Keep electrical and chemical contributions separate, then compare the four-proton budget with the stated ATP demand. Explain why the result is neither a rate prediction nor a universal proton/ATP ratio.

Separate photon, electron and ATP budgets in photosynthesis

Compare cyclic fractions 0 and 50% at 24 µmol photons. Keep linear/cyclic photon allocations, NADPH, O2 and the separately stipulated ATP contributions in a ledger. Explain which predictions follow stoichiometry and which depend on the chosen ATP coefficients.

Module 4 — Signaling and cell division8 lessons

Discriminate binding, relay and response mechanisms; interpret feedback and checkpoint evidence; and audit DNA, chromosome and population-age boundaries.

Separate receptor binding from a cellular response

Compare receptor amounts 20 and 80 at ligand 2, then compare ligand 2 and 6 at fixed amount. Retain fraction and amount separately. Propose a downstream readout and a control that could reveal equal binding but different signal interpretation.

Follow a molecular switch after its input ends

Compare hydrolysis rates 0.5 and 2 at one activation rate. Separate pulse-end fraction from the post-pulse decay. Use the sustained-input dashed curve only as a modeled counterfactual, not as a performed control experiment.

Use a bypass to test pathway order without overclaiming

Compare receptor activity 25 with bypass absent and present; then change receptor activity to zero while retaining bypass. Record all three readouts. Design a reporter-only control that could challenge a false rescue caused by the assay.

Question the age distribution behind a stage-duration estimate

Compare stage fractions 10% and 30% at cycle duration 20 h. Calculate both estimates and state their assumptions. Design a longitudinal or independent-preparation observation that could challenge the assumed age structure; do not propose culturing or treating cells.

Separate daughter-genome allocation from cell separation

Compare all three outcomes at 2n=6, then change the diploid complement to eight. Retain cell count, nuclear count and each nuclear chromosome count. Explain which spatial measurement distinguishes failed cytokinesis from an altered single-nucleus complement.

Module 5 — Mendelian and chromosomal inheritance9 lessons

Derive genotype and phenotype probabilities from chromosome mechanisms, test segregation and linkage evidence, and distinguish penetrance, epistasis, environment and chromosome-count changes.

Connect meiotic mechanisms to chromosome combinations

At n=3 compare all completed stages, then vary n. Keep chromosomes, DNA molecules, C amount and possible assortment combinations separate. Draw homolog separation before sister separation and explain why the combination count is not the product count of one meiosis.

Distinguish an expected count from an outcome probability

Compare cohort counts four and eight at p=0.25, retaining expectation, exactly-one and at-least-one probabilities. Then change p while holding cohort size. Explain an observation that would challenge the independence assumption rather than only the probability value.

Recover interval recombination without losing double crossovers

Compare double-class totals zero and 20 while keeping both single-class totals fixed. Write all eight marker classes, check the total and recompute interval and outer fractions. Explain why this is a count-comparison model rather than a mechanistic claim that changing only double exchanges leaves every real process unchanged.

Explain a phenotype ratio with a biochemical interaction

Compare A-function probabilities 0.5 and 0.75 at B probability 0.75. Then change B alone. Check that categories remain exhaustive and identify an intermediate readout that would discriminate the pathway from an unrelated scoring artifact.

Module 6 — Molecular genetics, regulation and evidence10 lessons

Trace DNA/RNA direction and molecular inventories, discriminate expression mechanisms and interpret virtual sequence/amplification/fragment evidence without overclaiming identity or function.

Discriminate DNA replication hypotheses using successive evidence

Compare both hypotheses after one, two and three rounds. Retain duplex fractions and heavy-strand fraction separately. Explain which observation distinguishes semiconservative from conservative and which additional generation challenges a dispersive alternative.

Relate replication direction to parallel-fork completion time

Compare one and three origins for 300 kb, then increase region length at fixed origin count. Draw both template orientations at one fork and label every new strand 5′→3′. State how a late-firing central origin would invalidate the equal-start prediction.

Track template direction and processed transcript length

Compare exon retention and skipping with the same tail, then vary tail without changing exon choice. Keep primary RNA, mature RNA, coding length and residue count separate. Independently derive the short template example with both end labels.

Evaluate a sequence change in its reading-frame context

Compare reference, synonymous, missense, early-stop and insertion packets at offset zero. Predict triplet groups before opening the ledger. Then use offset one as an intentionally wrong-frame contrast and explain why sequence identity without orientation/frame is insufficient.

Combine positive and negative regulation in an operon model

Record all four input combinations and identify which comparison isolates repression versus positive activation. Propose an independent reporter calibration that could distinguish a biological regulatory effect from a changing detector response.

Challenge ideal doubling in a conceptual amplification record

Compare efficiencies 1 and 0.8 at ten and twenty cycles. Retain the ratio to ideal doubling and identify where the formula’s fixed-efficiency assumption would need empirical validation. State separate roles for negative and positive controls.

Course-wide synthesis and project defense2 lessons

Defend a six-module cellular mechanism using causal, material, probabilistic and observation boundaries; preserve first evidence and distinguish authored learning from independent practical/mastery validation.

Defend a molecular mechanism across biological and measurement layers

Compare activity100/artifact0, activity60/artifact0.10 and activity60/artifact0. Keep biological rate, sample signal, standard shift and both inverse estimates separate. Before opening the ledger, predict which contrasts distinguish activity from artifact. Then state one artifact that the matched-standard correction would not remove.

Audit an inheritance claim when surviving offspring are a selected sample

Compare survival factors1 and0.5 at r=0.2, retaining all four initial and surviving categories. Then vary r with survival fixed. Derive the selected denominator before reading the output. Propose an independent observation that could distinguish altered recombination from genotype-specific survival or scoring.

Investigation portfolio

Keep predictions before comparison, complete raw records and units, explain competing models and test a changed case. Supplied and simulated data are labeled in each lesson. A saved notebook is not proof of experimental technique or correct reasoning.

Pathway and measurement discrimination

Evidence to retain: Retain competing predictions, matched contrasts, standard/bypass roles and three paired preparation differences; expose a batch-confounded alternative.

Boundary: Fictional mechanisms and exact synthetic responses. Pairing is not a universal cure for interference or treatment interactions; physical preparation and independent biological data require separate evidence.

Calibrated imaging and cell architecture audit

Evidence to retain: Preserve reference/object pixel ratios, test uniform resizing, distinguish resolving criteria from enlargement, and calculate area/volume under changed size and folding.

Boundary: Original schematics, not measured microscopy. Real-image calibration, segmentation and specimen preparation remain separate supervised practical evidence.

Finite transport and energetic constraints

Evidence to retain: Reconstruct solute conservation over time, combine pressure and osmotic terms, contrast carrier and linear rates, and audit an uphill neutral-solute cycle.

Boundary: Well-mixed idealized compartments and supplied kinetic/energetic laws; no physical membrane, pressure or chemical manipulation.

Enzyme mechanism discrimination

Evidence to retain: Select and justify an initial-rate window; compare substrate-response hypotheses and exposure histories; distinguish activation-barrier changes from coupled state-dependent free energy.

Boundary: Original assigned models, not assays of a named enzyme. No enzyme handling, heating or chemical intervention is requested.

Respiratory and cofactor inventory audit

Evidence to retain: Separate ATP investment/payoff/demand; preserve diverted pyruvate; compare electron-donor/acceptor limits and proton-driving terms; reconstruct fermentation carbon and NAD+ regeneration.

Boundary: Idealized endpoint/stoichiometric ledgers do not establish actual fluxes, ATP yield, physical respiratory measurements or a unique mechanism.

Binding, pulse termination and conditional rescue

Evidence to retain: Retain occupancy versus amount, pulse-end and decay values, upstream/downstream rescue readings and transient-versus-steady feedback comparisons; propose controls that separate biological mechanisms from detector effects.

Boundary: Original supplied models with explicit kinetic assumptions, not measurements of a named receptor or a physical cell intervention.

Division counts and population inference

Evidence to retain: Draw cell/nuclear counting boundaries, compare age-distribution estimates, distinguish checkpoint passage from repair and use spatial nuclear evidence to interpret total DNA.

Boundary: No cell culture, chemical treatment or specimen experiment. Biological replication and actual supervised practical skill remain external requirements.

Conditional probability and segregation evidence

Evidence to retain: Trace completed meiotic stages, normalize genotype probabilities after selection, compare binomial event definitions and test a predeclared ratio under a fixed rule.

Boundary: Fictional marker probabilities and supplied counts; no breeding, family diagnosis or performed biological experiment.

Linkage, interaction and chromosome mechanism

Evidence to retain: Classify eight marker strings, count double recombinants, state sex-conditional denominators, audit a two-gene pathway and crossing reaction norms, and trace formal nondisjunction products.

Boundary: Virtual evidence without viability or clinical claims. Physical chromosome analysis, independent biological replication and practical skills require supervised institutional review.

Replication, orientation and coding inventory

Evidence to retain: Compare label-class predictions across rounds; calculate fork completion under geometry assumptions; derive a transcript with end labels; separate exon/tail/coding lengths; regroup fictional codons and stop at the first in-frame stop.

Boundary: Virtual original packets, not isotope handling, culture, engineered genes or measured molecular evidence.

Expression-mechanism discrimination

Evidence to retain: Compare equal RNA pools with unequal turnover, all four operon conditions and local-versus-shared reporter effects, retaining controls and alternative mechanisms.

Boundary: No cellular intervention or gene editing. Written design and model traces do not fulfill actual laboratory participation.

Sequence and biotechnology evidence audit

Evidence to retain: Compare read hypotheses and omitted alternatives, challenge fixed amplification efficiency, and conserve fragment lengths while separating topology, fragment number and band count.

Boundary: No diagnostic interpretation, biological sample collection, primers, operating recipes or physical amplification/gel work. Privacy, provenance and independent confirmation remain necessary in real applications.

Integrated mechanism, assay and ascertainment challenge

Evidence to retain: Retain activity-versus-artifact contrasts and matched standards, reconstruct initial versus surviving marker categories and identify genuinely independent evidence that separates biological mechanisms from observation/selection alternatives.

Boundary: Original calculated packets only; no culture, breeding, genetic manipulation, actual specimen observation, clinical result or certified practical participation.

Mixed assessment and cumulative project

Open the retained response and project workspaces. Practice, saved work and independently reviewed proficiency remain separate.

Mixed assessment and retained reasoning

These 34 course-specific public tasks are practice, not a secure examination. Each retains up to three immutable written responses, known feedback exposure before each response, and human rubric critiques. Drafts remain editable. No text-length check or self-reported review certifies correctness, independence, laboratory skill or mastery.

1. A rescued response with a shifted standard

Original fictional readings are untreated120, treated80, downstream bypass120 and fixed product standard120 although its reference value is100. Under a shared additive artifact, compute the matched treatment contrast. Explain what the standard diagnoses, what rescue supports only conditionally, and one observation that could challenge the shared-artifact assumption.

Course-specific review criteria

  • Compute a signed matched contrast without confusing offset with treatment effect.
  • Distinguish biological and cell-free control roles.
  • State a discriminating prediction and a limit of rescue specificity.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

2. Same building blocks, different inventories

Compare three separate five-residue glucose chains with one fifteen-residue acyclic chain. Count formal condensation waters and explain why formula/count evidence does not determine linkage specificity. Separately, distinguish four peptide hydrolyses in a twelve-residue no-crosslink chain from unfolding without hydrolysis.

Course-specific review criteria

  • Count n−1 links per separate acyclic chain.
  • Preserve material while separating structure from composition.
  • Distinguish primary-chain cleavage from conformation and function.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

3. Two identical pH readings, unequal reserves

Two ideal1L buffers have pKa7 and pH7 but total conjugate-pair amounts4 and8mmol. A1mmol acid challenge is modeled. Compute both final ratios and pH values, and state why the same approximation must be rejected if base is exhausted.

Course-specific review criteria

  • Recover component amounts from ratio and total.
  • Apply material balance before the logarithm.
  • State the approximation boundary without inventing an invalid pH.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

4. A precise-looking inference with missing bias

A model y=0.1+0.5c gives reported signal0.6AU. Signal, intercept and slope bounds are±0.02AU,±0.01AU and±0.025AU/(mmol/L). Compute nominal concentration and worst-case interval. Then consider an omitted+0.15AU sample-only artifact; compare its corrected reference with that interval and propose a discriminating validation check.

Course-specific review criteria

  • Invert the line with consistent units.
  • Use monotonic worst-case endpoints, not an invented confidence probability.
  • Separate included error from model bias and propose evidence that tests the omitted mechanism.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

5. An enlarged image and an exchange claim

An original schematic has a5µm bar spanning80pixels and a cell axis120pixels. Find cell length before and after uniform2× enlargement. Separately, two ideal spherical cells have radii2 and6µm at equal folding. Compare area/volume and explain why neither enlargement nor area/volume alone proves a biological transport advantage.

Course-specific review criteria

  • Use a shared calibrated pixel ratio.
  • Distinguish digital size from resolving ability.
  • Calculate geometric ratio while naming omitted transport variables.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

6. Different conserved quantities, different transport questions

A closed1L compartment begins at3mmol/L and a4L compartment at8mmol/L for a neutral permeating solute. Find their common equilibrium concentration. Separately, a plant-cell initial state has inside0.2mol/L, outside0.1mol/L, inside pressure0.3MPa and outside pressure0 at298K. UseR0.008314MPaL/(molK) to determine initial water direction; explain why this does not give final cell volume.

Course-specific review criteria

  • Conserve amount rather than simply average concentrations.
  • Include pressure and solute contributions with consistent units.
  • Separate a solute-equilibrium endpoint from an initial water-potential comparison.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

7. A plateau and a feasible energy ledger

A carrier model hasVmax120nmol/min and apparentKm3mmol/L. Calculate initial rate atS3mmol/L. Separately, two neutral solutes move uphill against a10-fold ratio per cycle at298K with20kJ/mol cycles of drive. UseR0.008314kJ/(molK) to estimate combinedΔG. Explain why neither a plateau nor a favorable ledger proves ATP-driven transport by a named protein.

Course-specific review criteria

  • Use the half-maximal condition correctly.
  • Apply the dimensionless ratio and correct per-cycle stoichiometry.
  • Distinguish finite capacity, energetic feasibility and demonstrated coupling mechanism.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

8. Enrichment is not localization proof; stability is not equilibrium

A protein-normalized fraction contains25% cytosolic material. Target response is20units in cytosol and100 in pure organelle material. Calculate mixture response and fold enrichment over cytosol. Separately, a maintained compartment has pump3 and effective leak coefficient1.5, with cytosolicpH7. Find compartmentpH and hydrogen-ion ratio, and bound the biological interpretation of both calculations.

Course-specific review criteria

  • Apply a linear mixture without claiming total recovery.
  • Distinguish steady flux balance from thermodynamic equilibrium.
  • Give an independent control for localization or gradient mechanism.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

9. A lower endpoint need not identify inhibition

A supplied enzyme record obeys P(t)=8(1−exp(−0.5t)) µmol with time in minutes. Find the initial slope and the average rate over 1 min. Separately, a temperature-history model has undamaged rate factor 3 and active fraction exp(−0.2t); find rate factor after 5 min. Explain two different reasons a lower observed rate need not uniquely identify competitive inhibition.

Course-specific review criteria

  • Distinguish a derivative-at-start interpretation from an endpoint average.
  • Separate active fraction from undamaged catalytic tendency.
  • Propose controls that distinguish depletion/history from an inhibitor hypothesis.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

10. Two favorable-energy claims with different boundaries

A reaction has ΔG°=+10 kJ/mol, Q=10 and T=298 K. Couple it to −20 kJ/mol using R=0.008314 kJ/(mol K). Find net ΔG. Separately, a favorable 100 mV proton voltage with no pH difference supplies energy using F=96.485 kJ/(mol V); would three protons meet a 40 kJ/mol ATP demand? State why either ledger alone is insufficient to establish a measured biological rate.

Course-specific review criteria

  • Use actual rather than standard free energy and a dimensionless Q.
  • Convert mV to V and retain the stipulated proton count.
  • Distinguish energetic feasibility from actual coupling and kinetics.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

11. Keep entry, cycle and terminal acceptance separate

Three µmol pyruvate undergo entry oxidation and three complete cycle turns, excluding prior glycolysis. Calculate their combined CO2, NADH, FADH2 and GTP-equivalent outputs. Then a separate ideal terminal ledger contains 5 µmol NADH and 4 µmol O2: calculate O2 consumed and electron transfer. Explain why neither ledger identifies the immediate origin of an isotopically labeled CO2 carbon or a universal ATP yield.

Course-specific review criteria

  • Separate pyruvate-entry and cycle contributions.
  • Use two electrons per NADH and four per O2.
  • Distinguish net stoichiometry from positional tracing and coupled ATP yield.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

12. Cofactor recycling and a demand deficit

Four µmol glucose are processed by standard glycolysis and entirely through the lactate branch. Calculate gross ATP, investment, net ATP, lactate, NADH regenerated to NAD+ and fermentation CO2. If other ATP demand is 10 µmol, describe the supply-demand balance without claiming a negative molecular pool.

Course-specific review criteria

  • Keep gross, net and demand-adjusted ATP distinct.
  • Balance carbon and cofactor regeneration in the specified branch.
  • Distinguish fermentation from anaerobic respiration and a deficit from a physical negative inventory.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

13. More ATP but less net carbon export

Use the supplied light budget: 24 µmol productive photons, linear flow 4 photons/NADPH and 8 photons/O2, ATP coefficients 3/8 per linear photon and 1/2 per cyclic photon. Compare all-linear with 50% cyclic allocation. For each case, calculate the maximum ideal Calvin net triose export using 9 ATP and 6 NADPH per triose, with adequate CO2. Identify which conclusions depend on the stipulated ATP coefficients.

Course-specific review criteria

  • Separate photon allocations and branch-specific products.
  • Use the smaller ATP/9 or NADPH/6 budget.
  • Distinguish oxygen origin and ideal productive-photon counts from universal biological efficiency.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

14. Equal affinity, different output

Two cell types have Kd=4 nmol/L and free ligand 4 nmol/L in excess. Receptor amounts are 40 and 120 units. Calculate occupancy and bound amounts. The first cell gives a stronger reporter response despite fewer bound units. Does that contradict the binding model? Propose one downstream and one assay explanation.

Course-specific review criteria

  • Separate fraction from amount.
  • Do not equate occupancy with all downstream outputs.
  • Propose discriminating controls.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

15. A decaying signal need not be perfect adaptation

A switch is 0.6 active when receptor activation ends; hydrolysis rate is 1 min⁻¹. Find its fraction one minute later. Separately, a sustained-input feedback model obeys 2x²+x−3=0 at steady state. Find the nonnegative response and explain why neither a pulse decay nor a decline to that plateau proves perfect adaptation under sustained input.

Course-specific review criteria

  • Use exponential decay only after activation ends.
  • Solve the nonnegative steady root.
  • Distinguish changed input from adaptation.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

16. One DNA total, different nuclear organization

An organism has 2n=8. Give G2 chromosome and complete nuclear DNA-molecule counts. After one normal nuclear division with failed cytokinesis, give cells, nuclei and chromosomes per nucleus. Contrast one sister-pair segregation error followed by successful cytokinesis. Which observation distinguishes these outcomes beyond aggregate DNA?

Course-specific review criteria

  • Declare one-cell versus one-nucleus boundaries.
  • Preserve total replicated DNA.
  • Use spatial evidence rather than a ploidy label alone.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

17. A changed stage fraction is not a repair measurement

A terminal stage occupies 20% of a fixed-cycle exponentially growing population with T=15 h. Compare the model duration 15log2(1.2) with the uniform-age estimate. Separately, 60 of 200 synthetic cells carry a damage label; an intact checkpoint arrests those cells but bypass lets all proceed. What can each result establish, and why are five image fields from one preparation not five biological replicates?

Course-specific review criteria

  • State the terminal-stage and fixed-cycle assumptions.
  • Keep progression distinct from repair/survival.
  • Identify the biological replication unit.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

18. Ascertainment before a second cross

A fictional Aa×Aa marker has aa penetrance0.8; other genotypes are never positive. Select a negative offspring and cross with known Aa. Compute posterior genotype probabilities, the next offspring aa probability and positive-phenotype probability. For three independent next offspring, find the probability of at least one positive result.

Course-specific review criteria

  • Normalize phenotype-negative genotype weights.
  • Separate transmission, genotype and penetrance.
  • Use the complement rule only with stated independence.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

19. Reconstruct a three-point packet

Known order A–B–C and phase ABC/abc produce1000 synthetic testcross offspring: parental total700, first-interval singles100, second-interval singles160 and doubles40. Split each pair equally and name the eight marker classes. Find interval fractions, summed short-interval map length and observed outer recombinant fraction.

Course-specific review criteria

  • Identify marker strings rather than positional labels alone.
  • Include doubles in both intervals.
  • Separate map estimate from outer recombination.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

20. A statistical departure is not a unique mechanism

A fixed recessive fraction0.25 predicts25 and75 of100 offspring; observed counts are35 and65. Calculate Pearson χ² and compare with the supplied one-df threshold3.841. Separately, a two-step pigment pathway with independent functional probabilities0.5 and0.75 yields which phenotype fractions? Explain why neither a ratio nor its rejection proves a unique enzyme mechanism.

Course-specific review criteria

  • Use expected counts and the predeclared rule.
  • Keep statistical and mechanistic claims distinct.
  • Partition exhaustive pathway categories.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

21. Transmission and chromosome allocation are different ledgers

In the stipulated equal XX/XY model, maternal Xr probability0.25 and paternal Xr give what positive fraction in each class and overall? Separately, normal n=4 with one meiosis-II sister error in one cell gives which four formal product counts, and which counts after union with normal n=4 gametes? State what neither model predicts.

Course-specific review criteria

  • Separate conditional and whole-cohort fractions.
  • Trace the specified division stage.
  • Avoid clinical or viability inference.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

22. A changing mean with unchanged reaction norms

Fictional genotype means are A=10+2E and B=14−E. At E=2 compare a50% A mixture with a75% A mixture. Then hold composition50% A and change E to4. Locate the crossing environment and state what additional data would be needed to estimate heritability.

Course-specific review criteria

  • Keep composition and environment contrasts separate.
  • Solve the crossing condition.
  • Do not infer variance-based properties from mean curves alone.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

23. Old material and completion geometry

After three complete rounds in light precursor, compare semiconservative and conservative heavy/hybrid/light duplex fractions starting from fully heavy DNA. Separately, a400 kb linear region has four simultaneous central origins and fork speed2 kb/min. Estimate completion and identify two omissions.

Course-specific review criteria

  • Separate strand inventory from duplex packaging.
  • Use two forks per central origin.
  • State ideal geometry and timing limits.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

24. Sequence and length use different boundaries

Template DNA is3′–TACCTTAAACGAATT–5′. Derive5′→3′ RNA and translate with the supplied standard assignments AUG Met,GAA Glu,UUU Phe,GCU Ala,UAA stop. Separately a processed exon total420 nt includes45 nt5′UTR,42 nt3′UTR and one stop codon, plus80 nt tail. Find mature length excluding cap nucleotide and residue count.

Course-specific review criteria

  • Preserve antiparallel direction and complement.
  • Stop at the first in-frame stop.
  • Exclude UTRs, tail and stop from amino-acid count.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

25. Equal RNA pools, unequal causal mechanisms

RNA systems have production10 units/min with half-life4 min, or production20 with half-life2 min. Compare steady pools and fluxes. In a separate same-cell reporter model, A enhancer is disrupted while B is intact, basal10 and enhancer gain90×activator with activator0.5. Predict outputs and explain cis versus trans evidence.

Course-specific review criteria

  • Separate pool size from turnover.
  • Use the same shared activator for both reporters.
  • Name assay/copy-number assumptions.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

26. Two comparisons do not eliminate every hypothesis

A fictional operon has leak2, permissive basal8 and activator gain4. Compare inducer present/low preferred carbon with inducer absent/low preferred carbon. Separately four reads contain two alternate bases: compare balanced probability0.5 with reference-error probability0.1 using the likelihood ratio. State what neither output establishes.

Course-specific review criteria

  • Separate repression from positive activation.
  • Cancel the common binomial coefficient correctly.
  • Do not treat relative likelihood as a posterior or function proof.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

27. Quantity and band pattern do not establish identity

Ten initial virtual copies undergo ten cycles at efficiency0.8. Compare with ideal doubling. A separate8000 bp circular molecule has cuts1000 and5000: give fragment and distinct-size-band counts, then contrast linear topology. State controls and claims still unsupported.

Course-specific review criteria

  • Compound the actual multiplier.
  • Conserve fragment inventory and include wraparound.
  • Separate amount/pattern from sequence identity and physical validation.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

28. Material balance and a biased detector

Two chains each contain four glucose units joined by three formal condensation links. Give total chain C/H/O inventory and released waters, then verify initial atoms are recovered when waters are included. Separately calibration signal0.2+0.02×rate gives sample0.9; a matrix-matched rate10 standard reads0.5 rather than expected0.4. Find corrected rate and name an artifact the correction excludes.

Course-specific review criteria

  • Conserve atoms through formal condensation.
  • Distinguish material balance from a biological synthesis protocol.
  • Invert only after estimating the shared additive shift.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

29. A concentration gradient and a localization claim

A1 L compartment initially has2 mmol/L solute and a4 L compartment has7 mmol/L. If only passive exchange occurs with fixed volumes, find total amount and eventual common concentration. Separately a fraction contains80% target organelle and20% cytosol; target concentration is100 units in pure organelle and20 in cytosol. Predict measured concentration and explain why it does not establish exclusive localization.

Course-specific review criteria

  • Use volume-weighted material conservation.
  • Separate concentration from total amount.
  • Retain contamination and independent marker controls.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

30. Flux, carbon and energetic limits

Three moles of glucose complete glycolysis; only half their pyruvate enters the supplied pyruvate-oxidation/citric-cycle ledger. Find net glycolytic ATP and NADH, entry/cycle CO2 and retained pyruvate carbon. Separately an ideal carbon-fixation packet has18 mol ATP and8 mol NADPH with net triose costs9 mol ATP and6 mol NADPH per mol net triose. Find net export and leftovers, naming omitted biological limits.

Course-specific review criteria

  • Separate glycolysis, entry and cycle products.
  • Preserve carbon despite incomplete entry.
  • Use the limiting resource and distinguish a budget from a rate.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

31. Response rescue does not repair every upstream state

A supplied receptor readout30 drives relay30 and reporter2×relay. A bypass clamps relay100 without changing receptor. Predict outputs and explain what rescue does not prove. Separately a2n=8 cell completes replication, mitosis and normal nuclear division but fails cytokinesis. Give G2 DNA molecules and resulting cell/nuclear counts.

Course-specific review criteria

  • Locate the bypass with multiple readouts.
  • Do not infer direct binding or universal recovery.
  • Distinguish DNA, chromosome and cell/nucleus boundaries.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

32. Conditioning and survival change denominators

Under fully penetrant recessive aa-only phenotype in Aa×Aa, select a phenotype-negative offspring and cross with known Aa. Find its Aa probability and next-offspring aa probability. Separately AB/ab testcross has true r0.3 and AB survival0.5; others survive fully. Per1000 initial expected offspring, find survivors and the naive recombinant fraction among them.

Course-specific review criteria

  • Normalize the selected genotype distribution.
  • Separate gamete probability from surviving sample fraction.
  • Do not identify a crossover change from selected counts alone.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

33. A coding packet and a stable RNA pool

Template3′–TACCTTAAACGAATT–5′ gives which5′→3′ RNA? Translate using AUG Met,GAA Glu,UUU Phe,GCU Ala,UAA stop. If the second codon becomes UAA, what can be stated about the supplied peptide and what remains unknown? Separately compare steady RNA pools for production10/half-life4 and production20/half-life2.

Course-specific review criteria

  • Respect direction and first-stop termination.
  • Separate molecular consequence from phenotype.
  • Distinguish pool from turnover flux.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

34. Design an observation that can overturn the claim

A fictional report says: “A linked marker causes enzyme failure because a selected offspring group has lower fluorescence; all repeated readings agree.” Propose a six-layer audit covering inheritance/selection, expression, protein/activity, compartment/metabolic constraints, assay calibration and independent replication. Identify what can be learned virtually and what requires genuine supervised or independent evidence.

Course-specific review criteria

  • Offer discriminating alternatives rather than a list of confirming measurements.
  • Separate technical repetition from biological replication.
  • State practical, privacy and independent-assessment boundaries.

Include calculations with units, source or dataset provenance, assumptions, competing explanations and limitations as relevant. The draft is saved but is not a locked response until submitted.

0/3 responses retained. No recorded feedback exposure for this task version. Earlier versions may already be familiar. Public inspectability still prevents certification of unfamiliarity.

Retain a criterion-by-criterion human review

Reviewer identity and role are declarations, not authenticated credentials. Unsaved review fields below are lost on navigation. Review every criterion with an exact quotation, calculation or evidence citation and a next step.

General Biology I full-course mechanism and evidence defense

Integrate original first predictions, complete virtual ledgers and independent changed-case reasoning across all six modules. This authored workflow does not certify actual practical participation, learner mastery, institutional equivalence or college credit.

  1. Define a six-layer causal claim

    Choose a novel cellular claim and connect chemistry/material, compartments, metabolism, signaling/division, inheritance and molecular expression to its observation process. Identify at least two plausible alternatives.

    Evidence to retain: First causal diagram, prior predictions, biological unit, safe scope and a falsifying observation retained before feedback.

  2. Construct and challenge quantitative evidence

    Use at least one original evidence packet from each module; retain settings, raw quantities, calculations and a conflicting or rejected case. Include material/energy conservation, conditional probability and one measurement or age-distribution assumption.

    Evidence to retain: Six-module notebook references, units, boundaries, uncertainty and reproducible independent calculations rather than copied final values.

  3. Design independent discrimination

    Explain which controls distinguish the favored mechanism from assay, selection, environment and shared-calibration alternatives. State how actual biological replication and apparatus validation would be obtained only under qualified supervision.

    Evidence to retain: Control-specific predictions, sampling/assignment plan, calibration rationale and explicit proposed-versus-performed status.

  4. Complete unfamiliar cumulative transfer

    Respond to a reviewer-supplied changed packet spanning at least two modules, with original prompt and first response retained before feedback. Disclose public solution exposure and explain why the case is genuinely changed.

    Evidence to retain: Versioned task record, prior reasoning, criterion-linked human evaluation and no automatic mastery award from prose submission.

  5. Defend, critique and revise

    Submit a first integrated report, obtain evidence-citing human critique, retain it and produce a justified revision. Separate exact model conclusions from biological claims still awaiting real evidence.

    Evidence to retain: First report, raw evidence references, review, revision and one new falsifiable prediction.

  6. Record practical and release gates honestly

    Prepare a locally reviewed safe practical proposal appropriate to institutional facilities. Record execution, raw observations and supervision only if they genuinely occur; otherwise retain these as pending external requirements.

    Evidence to retain: Actual instrument/specimen work, approved safety review and independent practical assessment must be supplied externally, not fabricated by virtual recipes.

Project review criteria

  • Coverage of all six modules through actual causal and quantitative reasoning
  • Reproducible material, energy, chromosome and probability accounting
  • Controls and evidence that distinguish competing mechanisms
  • Biological replication, calibration, uncertainty and sampling boundaries
  • Genuinely unfamiliar transfer with exposure disclosed
  • Preserved first reasoning, evidence-linked critique and justified revision
  • Real supervised practical evidence and institutional decisions remain separate from authored content and app persistence

Retain raw-data identifiers, provenance, units, prior predictions, methods, calculations, competing explanations and safety boundaries. State explicitly when data are simulated, supplied or genuinely observed. This saved text cannot verify a real experiment; do not invent measurements or completed supervised work. Maximum 12,000 characters; retain larger evidence files separately and cite them.

A nonempty report is only a saved submission. First and revised reports remain separate and cannot be overwritten. A critique of the first report is required before retaining one revision.

Fresh transfer direction

An independent reviewer changes the causal pathway, genotype/phase, compartment boundary, sequence orientation, energy budget or observation bias. The learner must defend a new mechanism and falsifying prediction using multiple representations. Renamed public examples and exposed solutions do not establish unfamiliar performance.

A human must supply the actual new task, evidence and conditions before the learner responds. The transfer-direction text is not itself an unseen assessment. Use the retained assignment form after the first project; exposed public task identifier: expanded-public:college-biology1.

Science backups preserve each course's separate responses, exposure, rubric reviews and project history. Older backups do not reset attempts or erase known exposure. Divergent same-version immutable responses and incompatible same-version project histories are rejected rather than silently replaced; preserve both files for review.

Sources and boundaries
  • All 56 planned authored destinations are implemented. Actual supervised practical work, independent learner performance, browser/mobile validation and institutional credit remain separate external gates.
  • Synthetic model captures do not establish physical laboratory participation, calibrated apparatus use, independent biological replication or practical proficiency.
  • Human reviews record declared judgments; neither submitted prose nor public answer exposure establishes independently verified mastery.
  • No institutional credit, college equivalence or medical/biotechnology procedure is represented.

Original LearnAI explanations and tasks use the references for scientific scope. Any attributed dataset or image has its own declared provenance. Laboratory or field activity requires an appropriate educator-approved protocol; no hazardous real-world operation is required by the guided path.

Save a science backup or import one

Science work is stored locally in this browser, separately from mathematics and AI. It does not sync automatically. Use this science-only backup; this checkout's older all-subject export does not include science.

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Matching imported notebook drafts replace their current drafts. Omitted lessons and known first attempts remain. Export your current work first if you want to retain both drafts.

Complete file sets and course backups

A file set can hold more work than one science file. Keep its manifest and every part together. Each file is limited to 36 MB. This format needs this version of LearnAI or a compatible newer version; older versions can use only the legacy single-file backup above.

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