Plasmodium falciparum

In about 75 years of drug treatment, between 10^21 and 10^22 malaria parasites tried every single-letter mutation billions of times. The documented result is one new transport activity, one deleted gene and a set of modified enzymes, most with a fitness cost. Chloroquine resistance cost about 10^20 parasites because its first steps do not help alone.

By AI (Claude Fable 5.1, thinking level unavailable) Draft:  September 2026

"Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years.  This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 1020 parasite multiplications." — Nicholas White, Journal of Clinical Investigation, 20041

"The development of drug resistance in malaria, like the development of the sickle cell gene and thalassemia in humans, is a crystal clear example of Darwinian evolution in action." — Michael Behe, The Edge of Evolution, 20072

Summary

Plasmodium falciparum is the single-celled parasite that causes the deadliest human malaria.  Since about 1950 it has been attacked with one drug after another, and its answers have been sequenced.  This article counts how many parasites lived in those years, how many mutations they tried, and what the search bought.  Each change is scored as a gain, a loss, a modification or a transfer of function, using the definitions in Measuring Biological Information.  The human side of the same arms race is covered in Malaria Resistance Alleles.

The main findings:

  1. The search was very large. About 1017 parasites are alive at any moment and fewer than 1020 are born each year.1 Over the 75 years of the drug era that is between 1021 and 1022 parasites and about 1019 new single-letter mutations.3 Every possible single-letter change to the genome arises more than a billion times a year.4
  2. Chloroquine resistance was expensive. It arose at least four times and fewer than ten.5 Nicholas White put the price at about one success per 1020 parasites. That figure is a count of origins divided into a count of parasites. It is a rate of successful emergence and is not a mutation rate.
  3. Michael Behe was right about the price and about the reason for it. He argued in 2007 that chloroquine resistance is rare because more than one change is needed before any of them helps. Two later experiments bear that out. No single mutation lets the transporter carry chloroquine.6 In living parasites the key mutation by itself gives no resistance and slows growth, and the smallest resistant allele has four mutations.7 7
  4. Behe was wrong on two details. He named position 220 as the second required site, and it is not. He supposed that going past the first step of pyrimethamine resistance takes two mutations at once, one in the enzyme and one elsewhere to make up for the damage. The second and third steps turned out to need no such help.8
  5. His critics were right that the mutations need not strike in the same instant. They were wrong that the intermediate steps are neutral. One of them, Nathan Lents, withdrew his account of Behe's claim.9
  6. Pyrimethamine shows the opposite case. Its first step is one mutation that helps at once, and resistance appeared inside single patients after one dose.10 Four steps were climbed because each one paid.
  7. The parasite did many other things in the same years. Eight changes are scored below. One is a gain, the new ability to carry chloroquine. One is a loss. Six are modifications, and most of those carry a measured cost. No new gene and no new protein is among them.
  8. The ledger is a lower bound. At least two adaptive changes cannot be priced, and only changes that someone went looking for are on the list. That weakens the design and young-earth argument and is stated plainly in Part 5.
  9. The extrapolation to mammals is suggestive and is not a proof. About 1019 to 1020 mammals have lived on the standard timeline.11 The parasite's record shows that changes needing two or more unhelpful steps are rare even at that scale. It does not show how many useful changes of that kind a mammal genome offers.

Part 1: The ledger

An organism's ledger has three entries:  how many individuals lived, how often each one mutated, and what the mutations produced.  This part fills in the first two.

How many parasites

A person sick with falciparum malaria carries an enormous number of parasites.  Arjen Dondorp and colleagues measured a parasite protein in the blood of 337 adults in hospital on the Thai-Burmese border and converted it to whole-body counts.  The typical patient carried 7 × 1011 parasites and the typical severe case 1.7 × 1012.12  White's round figure is 1012 for an adult with 2% of red cells infected.1

White also estimated the world total.  People who are ill hold between 5 × 1016 and 5 × 1017 parasites at any time, and carriers without symptoms hold fewer than 3 × 1016.  He rounds the standing total to "about 1017" parasites and the yearly total to "less than 1020" parasites.1  The two figures agree with each other.  The parasite's blood cycle takes 48 hours, so a standing population of 1017 to 5 × 1017 turns over about 183 times a year, which gives 2 × 1019 to 9 × 1019 parasites a year.3  Case counts give the same order.  The World Health Organization estimated 282 million malaria cases in 2024, 95% of them in its African Region, where falciparum is the dominant species.13

Chloroquine came into large-scale use in the early 1950s.14  From then to 2025 is about 75 years and about 13,700 blood-stage generations.  The running total is between 1.5 × 1021 and 7.5 × 1021 parasites.3  Behe's figure for the first fifty years, 5 × 1021, sits inside that range.2

How many mutations

The mutation rate has been measured directly three times.  Each study grew parasites in culture, cloned them at intervals and sequenced whole genomes.

Study Base substitutions per base pair per 48-hour generation
Bopp and colleagues, 201315 1.0 to 9.7 × 10−9
Claessens and colleagues, 201416 3.6 to 4.1 × 10−10 in three strains
Hamilton and colleagues, 201717 2.45 × 10−10 pooled over five isolates

The two later studies sequenced many more clones and agree with each other.  This article uses Hamilton's pooled figure.  Changes from G or C to A or T are the most common kind.17  The genome is 23.3 million base pairs and holds about 5,300 genes.17 18  Multiplying the two gives 0.0057 new base substitutions per parasite, or one parasite in 175.  Small insertions and deletions are about ten times as common, one parasite in 20, and fall mostly in repetitive sequence.17

Entry Value
Parasites alive at one time about 1017
Parasites born per year 2 × 1019 to 1020
Years since large-scale drug use began about 75
Blood-stage generations in that time about 13,700
Parasites born in the drug era 1.5 × 1021 to 7.5 × 1021
Genome size 2.33 × 107 base pairs
Base substitutions per parasite born 0.0057
Base substitutions per year 1 × 1017 to 6 × 1017
Base substitutions in the drug era 9 × 1018 to 4 × 1019

The arithmetic for every row is in the note.3  For comparison, the article on HIV counts about 6 × 1022 virus particles and 1022 mutations in about 100 years.

How thoroughly the genome was searched

There are about 70 million possible single-letter changes to the genome.  At these rates each one arises between 1.6 billion and 8 billion times a year, and about 80 times per generation inside one heavily infected patient.4  An infection starts with 100,000 to 300,000 parasites leaving the liver and can grow to 1012.1  Any change that needs only one specific mutation is therefore on offer in nearly every patient.

Changes that need more than one specific mutation are much rarer.  A specific pair arising in the same generation of the same parasite happens once in about 1.5 × 1020 parasites, which is about once a year worldwide.  A specific pair built in two steps inside one patient, with a first step that neither helps nor harms, arises about once in 1018 to 1019 parasites.  Three specific mutations in one lineage inside one patient would take about 1028 parasites, which is more than have lived.4

These supply figures are this article's arithmetic and are not measurements.  They say how often a mutation arises.  They do not say how often it survives, reaches a mosquito and spreads.  White makes the same distinction.  He treats the emergence of resistance as two events, the mutation and then the selection and spread that follow it.1

Part 2: Chloroquine

What changed in the parasite

The parasite digests hemoglobin inside a compartment called the digestive vacuole.  Chloroquine builds up in that compartment and interferes with the disposal of the toxic heme left over.19  Resistant parasites hold less of the drug there.  The cause is a set of mutations in one gene, pfcrt, whose protein sits in the vacuole membrane.  In 2002 Amar Sidhu, Dominik Verdier-Pinard and David Fidock swapped resistant versions of the gene into sensitive parasites and the parasites became resistant.19

The normal protein exports small peptides from the vacuole and does not carry chloroquine.20  The mutant protein does carry it.6  Every resistant form has lysine replaced at position 76, usually by threonine, a change written K76T.  The resistant forms carry between four and ten changes in all.6

Score:  gain, observed in its effect and inferred in its origin.  The protein does something it could not do before, so by the series definitions this is a gain of an activity.  It comes with a cost.  When Malawi stopped using chloroquine in 1993, the resistant type fell from 85% of infections in 1992 to 13% in 2000, and in 2001 it was not found in any of the infections tested.21  The resistant parasite is the weaker one whenever the drug is absent.

The review of Behe's book published by Creation Ministries International scores the change differently.  Don Batten wrote that resistance "is due to a fault in a transport protein that moves the poison into the organism’s vacuole."22  The later measurements do not support that.  The drug enters the vacuole without the protein, and the mutant protein lets it out.  Nothing was broken.  A transporter acquired a new cargo.

How many times it arose

Resistance was reported from Colombia and from the border of Cambodia and Thailand in the late 1950s and confirmed in both by 1960.14  In 2002 John Wootton and colleagues typed 342 markers across the genomes of parasites from around the world.  The markers beside pfcrt fell into a few shared patterns, which showed "at least four CQR founder events."5  Later lists name five regions of independent origin:  Colombia, Peru, Papua New Guinea, the Philippines and Southeast Asia.6  The Asian form then spread through Africa.5

Nobody watched any of these origins.  They are inferred from the genomes of parasites sampled afterwards.  What was watched is the clinical failure of the drug and its spread.

What White's number is

White's sentence is quoted at the head of this article.  He gives no working.  His own figures reproduce it:  fewer than 1020 parasites a year for fifty years is fewer than 5 × 1021 parasites, and fewer than ten origins among them is about one per 5 × 1020.1

Three things follow from how the number is built.  It is an estimate and nobody measured it.  It counts successes, meaning lineages that arose, survived, reached a mosquito and spread far enough to be found.  And it says nothing by itself about how many mutations are involved.  White's next sentences make the second point.  He gives the single mutations that defeat atovaquone and pyrimethamine a probability "of approximately 1 in 1012 parasite multiplications" and then notes that laboratories record much higher mutation rates than that.1  The arithmetic of Part 1 agrees.  A specific single mutation arises once in about 1010 parasites, so White's field figure is about a hundred times rarer than the raw supply.

How Behe used it

Behe's book states White's estimate accurately and attributes it to him:

"Nicholas White of Mahidol University in Thailand points out that if you multiply the number of parasites in a person who is very ill with malaria times the number of people who get malaria per year times the number of years since the introduction of chloroquine, then you can estimate that the odds of a parasite developing resistance to chloroquine is roughly one in a hundred billion billion.  In shorthand scientific notation, that’s one in 1020."2

His argument is a comparison.  Resistance to atovaquone needs one mutation and costs about 1012 parasites.  Chloroquine costs 1020.  He infers the reason:

"Let’s compare the two numbers for the odds of achieving resistance to atovaquone, where just one mutation is needed, versus chloroquine, where (presumably—since if a single mutation could help, chloroquine resistance would originate much more frequently) two are needed."2

He named changes of that difficulty “chloroquine-complexity clusters,” or CCCs.2  He then supposed a change needing twice as many mutations before any benefit, called it a double CCC, priced it at 1040 cells, and proposed that as a tentative limit for all of life.2

Two points about his wording matter for what followed.  Behe never said chloroquine resistance could not evolve.  He called it "a crystal clear example of Darwinian evolution in action."  And he did use the word his critics objected to.  He wrote that "several amino acid mutations appear simultaneously to confer a beneficial effect, such as in chloroquine resistance with mutant PfCRT."2  Elsewhere he put it more carefully, as a change "where two particular amino acids had to appear before there was a net beneficial effect" and not as one where they must appear together.2

The book's parasite counts are not consistent.  Page 59 gives a trillion parasites in each of a billion patients a year, which is 1021 a year.  Page 138 gives 1020 a year.2  White's figure is the lower one.

What the experiments found

Summers and colleagues, 2014.  Robert Summers, Rowena Martin and their group put more than 100 versions of the protein on the surface of frog eggs and measured how much radioactive chloroquine each one carried.6  K76T alone carried none.  The change N75E alone carried none.  The two together carried about 19% as much as the full resistant protein.6  A second route, K76T with N326D, also worked.  Four mutations gave full activity.  The order mattered, because many orders pass through a drop in transport.  The authors summed it up:

"A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity."6

The study measured transport in frog eggs.  It did not measure whether a parasite with one or two of the mutations grows better or worse.  When two three-mutation versions were put into living parasites, they lowered the drug level inside but did not raise the dose needed to kill.6

Gabryszewski and colleagues, 2016.  Stanislaw Gabryszewski, David Fidock and colleagues did the experiment in parasites.  They took the smallest known resistant form, the Ecuadorian one with four mutations, and wrote every combination of those four into the gene of living parasites, sixteen lines in all.  They measured drug resistance and, by growing each line in competition with the unmutated one, the growth rate.7  Their findings:

  • K76T alone gave no resistance and slowed growth. "PfCRT K76T was insufficient for CQR and had a deleterious impact on parasite growth that was exacerbated by CQ."7
  • The growth effects of the intermediate forms ranged from 26% slower to 11% faster per generation, and most were neutral or slower.7
  • Four mutations is, in their words, "the smallest number required for resistance" to chloroquine.7
  • Paths that add one mutation at a time run through valleys of lower fitness. The best such path had a probability near 5 × 10−7 in their simulation, against 3 × 10−4 for the matching four-step path in the pyrimethamine gene.7

Their conclusion:

"Based on our combined IC50 and growth data, the most likely scenario would be the near-simultaneous emergence of three to four mutations."7

The authors are mainstream malaria geneticists and do not mention Behe.  The result has limits.  It is one resistant form, in one parasite strain, in culture.

The exchange, and who was right

Summers 2014 set off an argument that ran from July 2014 to February 2019.  Each party is quoted here from its own page.

Who Claim, in their words Assessment
Behe, 14 July 2014 "the need for an organism to acquire multiple mutations in some situations before a relevant selectable function appears is now an established experimental fact."23 Correct for transport. In the same post he concedes that position 220 was the wrong second site.23
Casey Luskin, 16 July 2014 "It can no longer be denied that the critics were dead wrong: chloroquine resistance does not arise at all until two mutations or more are present."24 Right about the two mutations. He also calls 1020 "an empirically observed data point" and that overstates an estimate.
PZ Myers, 17 July 2014 "That the malaria parasite needs two mutations was never a point of contention, nor was it particularly worrisome. What was wrong with Behe’s work is that he naively claimed that the two mutations had to occur simultanously in the same individual organism"25 Fair that strict simultaneity is not required. Behe's book does use the word.
Behe, 21 July 2014 It is "utterly parsimonious and consistent with all the data" to think "that a first, required mutation to PfCRT is strongly deleterious while the second may partially rescue the normal, required function of the protein" and the word simultaneous is "entirely reasonable shorthand" for that.26 An inference in 2014. Gabryszewski 2016 later measured K76T alone as harmful to growth.
Kenneth Miller, 2014 "But Behe was dead wrong about it being “strongly deleterious.” In fact, it seems to have no effect on transport activity at all. A neutral mutation like this can easily propagate through a population"27 Wrong. No effect on transport in a frog egg is not the same as no effect on a parasite's growth, and the parasite measurement went against him.
Miller, 2014 "the problem with the logic of The Edge isn’t the specific figure of one chance in 1020, but the way in such probabilities are multiplied."27 Partly right. See below.
Larry Moran, August 2014 "There's no need to invoke simultaneous mutations and no need to assume that one of the mutations is deleterious."28 The only critic who calculated. His result, the right pair once per million patients, agrees that the event is very rare.
Lents, Swamidass and Lenski, 2019 "His calculations have already been refuted" and "it has long been known that neutral and even deleterious mutations can provide stepping stones to future adaptations."29 The estimate was never refuted. Myers and Miller both granted it.
Luskin, 19 February 2019 "Behe never says that chloroquine resistance is too complex to evolve."30 Correct. Lents's article now reads: "An earlier version of this article misrepresented Behe’s claims about the evolution of chloroquine resistance in malaria. The author regrets the error."9

Four conclusions can be drawn.

The number was never in dispute.  Miller wrote that "none of the criticisms took issue with that number at all."31  Moran's own calculation gave one right pair per million patients, which is about one per 1018 parasites, before any losses in transmission.28

Behe's central inference held.  More than one change is needed before the parasite gains anything, and the first change by itself does harm.  That is what he argued in 2007 from the rarity alone.

Strict simultaneity is not needed for the first pair.  On the arithmetic of Part 1, a pair of mutations struck in the same generation costs about 1.5 × 1020 parasites, and a pair built in two steps inside one patient costs 1018 to 1019.  The critics were right about that.  It does not rescue a step-by-step account, because the smallest resistant form needs four mutations and no form with one, two or three has been found established in the field.7

Miller's objection to the double CCC is sound as far as it goes.  Costs multiply only when nothing on the way is useful.  If the first CCC helps the organism, it spreads, and the second CCC then costs another 1020, which makes 2 × 1020 and not 1040.  Behe's text does state the condition:  his double CCC is a change that needs all its mutations before any benefit.  The open question is how often living things require such changes, and the malaria record cannot answer it.

Part 3: Pyrimethamine, and why it was fast

What was watched

Pyrimethamine blocks an enzyme called DHFR, which the parasite needs to make the building blocks of DNA.  In 1959 Robert Burgess and Martin Young reported what happened when volunteers infected with falciparum malaria were given one small dose.  "Of seven cases observed after 25-mg treatment, five relapsed."  The relapsed infections no longer responded to the drug at any dose, and the resistance passed through mosquitoes to another patient.10  Resistance had arisen inside single patients after one dose.  White's review says of the pyrimethamine combination known as SP that resistance to it "has developed much more rapidly" than resistance to chloroquine.1

The four steps

The mutations were identified decades later.  They are four changes in DHFR, written S108N, N51I, C59R and I164L.  In 2009 Elena Lozovsky, Daniel Hartl and colleagues built all sixteen combinations of the four and measured each one.  The enzymes were tested in bacteria and not in parasites.8

  • Two of the four single mutants resist the drug without any help. The other two are no better than the original.8
  • A simulated population climbing one mutation at a time took three paths in 87.5% of runs. All three start with S108N.8
  • The forms common in the field are the intermediate stages of those three paths.
  • The climb has a price. The four-mutation enzyme excludes the drug about 500 times better and works about 6 times worse. The fourth mutation slows growth without the drug by 30% to 40%.8

Behe supposed otherwise in 2007.  His reasoning was that the later mutations "seem to interfere with the normal work of the protein" and that each would need a second mutation in some other gene to make up for it.  He concluded:  "In other words, to move to the next level of resistance after the first mutation, two further, simultaneous mutations seem to be necessary."  He added:  "That double mutant is, it seems, roughly as rare as a CCC."2  The measurements do not support that for the second and third steps.  Each raises resistance, and the forms carrying them "are not manifestly impaired" in growth.8  For the fourth step Behe's idea has support.  That step does slow growth, and Part 5 describes a change in another gene that appears to make up for it.

Score:  modification, shifted, with activity down.  The enzyme does the same job.  It binds the drug less and its own substrate less well.  The first step was observed in patients.  The order of the later steps is inferred from laboratory measurements and from which forms are common.

The contrast, in numbers

Pyrimethamine Chloroquine
Mutations needed before any benefit 1 more than 1 in transport, 4 for resistance in parasites
How often the first useful form arises once in about 1010 parasites once in 1018 to 1019 for a pair
White's estimate of successful emergence 1 in 1012 1 in 1020
Time to resistance one dose, in single patients about a decade of wide use
Independent origins five of seven treated volunteers; one origin for the highly resistant form in Southeast Asia at least four and fewer than ten worldwide

The supply figures in the second row are from Part 1.4  White's two estimates differ by a factor of 108.  The supply of a single mutation and of a two-step pair differ by about the same factor.  So the difference in price between the two drugs is roughly what the need for a second unhelpful step predicts.  This is a consistency check on Behe's reading and is not a proof of it, because the supply figures rest on assumed numbers of generations.

What the contrast shows

It supports the ordinary account of evolution where each step pays.  Four mutations accumulated in one enzyme in a few decades, each one selected.  Anyone who claims that natural selection cannot assemble a change of several mutations is answered by this case.

It supports Behe's point where the steps do not pay.  The same parasite, in the same numbers, with the same mutation rate, needed a hundred million times as many individuals when the first step gave nothing.

Even the step-by-step path was climbed rarely.  The first step arises in every heavily infected patient.  The highly resistant forms did not.  Shalini Nair and colleagues reported "a single origin of resistant dhfr alleles sampled over a large region of SE Asia."32  The highly resistant form in Africa arrived from Asia.33  White concluded that "even for SP, multiple de novo emergence of resistance has not been a frequent event."1

Part 4: The rest of the ledger

An organism is benchmarked by everything it did, and chloroquine is only one entry.  This part lists every other adaptive change found in the sources read for this article.

Sulfadoxine

Sulfadoxine blocks DHPS, another enzyme on the same chemical pathway as DHFR.  Resistance comes from amino-acid changes in that enzyme, chiefly A437G and K540E.34  Richard Pearce and colleagues typed the markers beside the gene in parasites from across Africa and found that resistant forms fell into "five major lineages each of which had a unique geographical distribution."34  Score:  modification, shifted.  The origins are inferred from the markers.

Atovaquone

Atovaquone blocks cytochrome b, part of the parasite's energy supply.  When it was given alone to patients in Thailand, about a third were not cured, and the parasites that came back were far less sensitive to it.35  One amino-acid change, Y268S, was found in a returning infection and raised the dose needed by more than nine thousand times.36  The changed enzyme runs at about 60% of normal speed.37  Score:  modification, down.  This one was watched, in patients and in culture.

Mefloquine

Mefloquine came into use on the borders of Thailand in 1984, "but substantial resistance developed within 6 years."  The main cause is extra copies of a pump gene, pfmdr1, that the parasite already had.38  Score:  modification, up.  More copies of an existing gene make more of an existing pump.  No new sequence was written.

Artemisinin

In 2004 White wrote that resistance to artemisinin "has not yet been identified and cannot be induced yet in the laboratory, which suggests that it may be a very rare event."1  It turned out to be common.  Frédéric Ariey and colleagues grew a sensitive parasite under rising doses for five years and found a single amino-acid change in a protein called kelch13 after 30 cycles of drug.  In Cambodia they found 17 different mutant forms of the same protein, each with one change.39  The same mutations arose independently in different parts of Southeast Asia.40  They then arose in Africa, in Rwanda and separately in Uganda.41 42

The resistance is partial.  The drug clears the parasites more slowly.  The mechanism is a reduction:  artemisinin is activated by digested hemoglobin, and a parasite with the mutant protein takes in less hemoglobin.  Jakob Birnbaum and colleagues found that "reduced activity of Kelch13 and its interactors diminishes hemoglobin endocytosis and thereby ART activation, resulting in parasite resistance."43  Score:  modification, down.  The first appearance was watched in the laboratory.  The field origins are inferred.

Hiding from the diagnostic test

The common rapid test for malaria detects a parasite protein called HRP2.  Parasites that have lost the gene are not detected, so the patient is not treated and the parasite is passed on.  In Ethiopia the tests would miss 9.7% of cases for this reason, and the authors propose "strong positive selection for pfhrp2 deletion owing to RDT-based test-and-treatment."44  By 2024 such parasites had been reported in 42 countries.13  Score:  loss.

Antigenic variation

The parasite puts a protein called PfEMP1 on the surface of the red cell it occupies.  The immune system learns to recognise it.  The genome holds 59 genes for different versions of the protein, the var genes.18  Two different things happen with them, and they should not be confused.

Switching.  Each parasite shows one version at a time and its descendants sometimes switch to another.  David Roberts and colleagues measured this in culture, with no immune system present, "at the rate of 2% per generation."45  Nothing mutates.  The genes are already in the genome and the parasite changes which one it reads.  This is a standing mechanism that runs in every infection.  It is not scored, because no sequence changes.

Recombination.  The var genes also swap segments with each other during ordinary cell division, which makes new genes.  Antoine Claessens and colleagues sequenced cloned parasites and watched it happen.  In one strain, "for every 48-hour intraerythrocytic generation approximately 0.2% of parasites will have undergone a var exon 1 recombination event producing a new chimeric var gene."  The joins kept the reading frame and the layout of the protein's parts.16  In a patient with 1012 parasites that is about two billion new var genes every two days.

This is the largest source of new sequence in the parasite, and it was watched.  Three cautions apply.  The new genes are assembled from pieces of existing var genes by a process that preserves their structure.  The cultures had no immune system, so no new version was shown to help the parasite.  And the origin of the var system itself was not watched.  It is inferred from comparing species.  This article reports the recombination as observed and leaves it unscored, because the series scores only changes shown to help.

Invasion ligands

The parasite enters red cells by binding proteins on their surface, and it has several ways in.  Janine Stubbs and colleagues showed that a parasite can change from one route to another by turning on a gene it already carries, PfRh4, and that the change "is reversible and depends on parasite ligand use."46  This too is a change in which genes are read.  It was watched in culture and is not scored.

The ledger in one table

Change Pressure What changed Score Price in parasites
PfCRT Chloroquine 4 to 10 amino acids; the transporter carries the drug Gain, with a growth cost about 1020 per origin
DHFR Pyrimethamine 1 to 4 amino acids Modification, shifted about 1012 for the first step
DHPS Sulfadoxine 1 or 2 amino acids in the African forms Modification, shifted not estimated
Cytochrome b Atovaquone 1 amino acid Modification, down about 1012
pfmdr1 Mefloquine Extra copies Modification, up not estimated
Kelch13 Artemisinin 1 amino acid, many alternatives Modification, down not estimated
gch1 Cost of antifolate resistance Extra copies Modification, up cannot be estimated
pfhrp2 Diagnostic test Gene deleted Loss not estimated
Chromosome 13 region Linked to pyrimethamine Unknown Cannot be scored cannot be estimated

The prices in the first, second and fourth rows are White's estimates.1 1  The last three rows of the table are taken up in Part 5.

Eight changes can be scored.  One is a gain.  One is a loss.  Six are modifications, and two of those are extra copies of a gene.  Where the working of the changed protein has been measured, it is lower:  DHFR, cytochrome b, kelch13, and PfCRT in its growth cost.  None of the eight is a new gene, a new protein, or a new binding between two proteins.  Behe made the last point in 2007:  "Nor has malaria developed new cellular protein-protein interactions."2  Nothing found for this article contradicts him.

Part 5: What cannot be priced, and what the ledger adds up to

Gains that cannot be priced

Extra copies of gch1.  The gene makes the first enzyme of the pathway that pyrimethamine and sulfadoxine attack.  Shalini Nair and colleagues found extra copies in 72% of parasites in Thailand, where those drugs were used heavily, and in 2% in neighbouring Laos, where they were not.  The extra copies came in five sizes and arose at least three separate times.  Parasites with the most resistant form of DHFR carried the most copies, which suggests that the copies make up for the damage done to that enzyme.47  Nobody knows when or where each origin happened, so nobody can say how many parasites were searched to find it.

The sweep on chromosome 13.  Sarah Volkman and colleagues found a stretch of 160,000 base pairs with almost no variation in pyrimethamine-resistant parasites.48  That pattern means something in the stretch spread fast and recently.  Lozovsky and colleagues suggested what it might be:

"It is an interesting, testable hypothesis that this region of chromosome 13 may include 1 or more mutations that also alleviate the deleterious fitness effects of DHFR resistance alleles."8

The gene has not been named and the mutation is unknown.  It cannot be scored and it cannot be priced.

Everything nobody looked for.  Drug resistance is found because patients stop getting better.  An adaptation to a new mosquito or to a change in human immunity would leave no such signal.  Volkman's survey found "multiple regions with signatures of selective sweeps" and most of them are unexplained.

The ledger is therefore a lower bound on what the parasite produced.  The true count of adaptive changes is higher than eight, by an unknown amount.  That weakens the argument this series makes, and the weakness cannot be removed with the data that exist.

The unit of account

The series measures unique functional sequence:  nucleotides that were originated and not copied, per organism born.  For this parasite the count is small.  Taking the most changed form of each gene, the scored changes add up to 18 amino acids, each needing at least one nucleotide.  Counting the alternative forms found in different places raises that to something under 100.  Extra gene copies and the deleted gene add none.  Divided by the parasites born in the drug era, the rate is between 2 × 10−21 and 7 × 10−20 nucleotides per parasite.49  The same calculation on the figures in the HIV article gives about 8 × 10−20 per virus particle.

Two cautions go with the number.  It is a lower bound, for the reasons just given.  And it counts sequence, which is a different thing from function.  The ability to carry chloroquine is a real new activity and it took a handful of nucleotides.

How many mammals

Behe's own estimate was 5,000 species of a million animals each, one generation a year for 200 million years, which comes to 1018.2  A million per species is too low for bats and rodents.  A census of living wild mammals published in 2023 allows a better figure.  It found that bats make up two-thirds of all individual wild land mammals and less than a tenth of their total weight of 20 million tonnes.50  At ten grams a bat that is at most 3 × 1011 wild land mammals alive today.  At one generation a year for 200 million years the total is 6 × 1019.11

That figure could be wrong by a factor of ten in either direction, because nobody knows how abundant mammals were in the past.  It is of the same order as the number of malaria parasites born in one year, and about one-eightieth of the number born in the drug era.

Counting individuals understates the mammals' search, however.  A newborn human carries about 63 new mutations, and a newborn parasite carries 0.0057.51  If every mammal is given the human rate, all the mammals that ever lived tried each possible single-letter change about 5 × 1011 times.  The malaria parasite tried each of its possible changes between 1 × 1011 and 6 × 1011 times in 75 years.11  By that measure the two searches are about equal.

Objections and responses

Resistance to a named drug is a narrow target picked after the fact.  Evolution has no target.  This succeeds in part.  The ledger here is a record of how the parasite answered a few very strong pressures, and it says little about adaptations nobody was watching for.  It does not rescue the chloroquine case.  A drug that kills nearly every parasite is about the strongest selection there is, and any change that let a parasite survive would have been found by the same clinics.

Many different solutions would have counted.  Behe answered this in 2007:  "So a CCC isn’t just the odds of a particular protein getting the right mutations; it’s the probability of an effective cluster of mutations arising in an entire organism."2  For chloroquine he is right.  The whole genome was free to find any answer, and it found one gene with two routes.6  For artemisinin the parasite found at least 17 answers in one gene.  So the number of solutions differs from problem to problem.  The objection fails for chloroquine and stands against the extrapolation, because nobody knows the number for any problem a mammal faced.

Mammals have sex, two copies of each gene, and far bigger genomes.  This succeeds in part.  Bigger genomes mean more mutations per birth, and Part 5 shows that this brings the mammals' search level with the parasite's.  Two copies of each gene let a harmful first step hide behind a working copy, which should make some two-step changes easier.  Sex is not an advantage the parasite lacks.  It mates in the mosquito, and the chloroquine-resistant form swept through its populations in "approximately 20-80 sexual generations".5  Against these points, mammals live in thousands of separate species of thousands to millions of animals each, so a rare first step in one species cannot meet a rare second step in another.  The net effect has not been calculated for a case like chloroquine and is listed below as an open question.

Animals adapt from variation already in the population and need not wait for new mutations.  This is true of how fast a population adapts.  It fails as an answer about origin.  Standing variation is mutation that happened earlier, and it is already inside the count of mutations tried.  The parasite had standing variation too, in 1017 living individuals.

Neutral and harmful steps can be stepping stones.  This is true in principle and was the main point of Lents, Swamidass and Lenski.  It failed for chloroquine.  The first step is harmful in the parasite, and no form with one, two or three of the mutations has been found established in the field.7  Stepping stones did carry pyrimethamine resistance, where every stone was a gain in resistance.

All of this is just breaking things.  This objection comes from the creationist side and it fails.  Seven of the eight scored changes are losses or modifications.  The eighth is a gain.  A transporter that carries a new molecule has a new activity, whatever it cost.

White's number is only an estimate.  It is.  It could be wrong by a factor of ten.  Both sides of the 2014 exchange accepted it, and the conclusions here need only its order of magnitude.

Issues and unanswered questions

  1. The cost of a two-step change in a mammal has not been computed here. The needed calculation is the waiting time for a specific pair of mutations, the first mildly harmful, in a sexual population of 104 to 106 animals with two copies of each gene. The related literature is reviewed in Haldane's Dilemma.
  2. Nobody has counted the targets. How many different sets of mutations, anywhere in the genome, would have given chloroquine resistance? The observed answer is two routes in one gene. An experiment that mutates the whole gene under drug would settle part of it.
  3. The smallest selectable form of PfCRT in a patient is unknown. Summers found transport with two mutations. Gabryszewski found resistance only with four. What a parasite with two or three gains inside a treated person has not been measured.
  4. Eleven sources were read in abstract only. They are marked in the source list. The count of chloroquine origins and the chromosome 13 sweep both rest on abstracts.
  5. Miller's 2003 field study was not identified. He gives no citation for the statement that K76T was found in 96% of patients who responded to chloroquine.
  6. The parasite population of the 1950s is unknown. The drug-era totals assume it was as large as today's.
  7. Piperaquine, lumefantrine and quinine resistance were not researched and are missing from the table.

Verdict

Counted per site, the malaria parasite searched its genome in 75 years about as thoroughly as all mammals could have searched theirs in 200 million.  What it found is documented better than for almost any other organism.  It found one new activity, one deletion, and six adjustments to proteins it already had, most of them at a cost.  None of those is a new gene.  The new var genes that recombination turns out every generation are assembled from existing ones and have not been shown to help the parasite.

Behe's reading of chloroquine resistance has held up.  The change was rare because several mutations were needed before any helped, and later experiments by mainstream laboratories confirmed both the need and the harm done by the first step.  He was wrong about one of the two positions and wrong about pyrimethamine.  His critics were right that the mutations need not arrive in the same instant and wrong that the path was neutral.

The extrapolation to mammals is weaker than the ledger.  The ledger is a lower bound.  Mammals have larger genomes and two copies of each gene.  The number of useful multi-step changes open to a mammal is unknown.  What the parasite does establish is a measured price:  when the first steps of a change do not pay, about 1020 organisms were needed to find it.  Any account of mammal evolution that calls for many such changes has to show where the organisms came from.

Sources


  1. 1.

    White, Nicholas J.  “Antimalarial drug resistance.”  Journal of Clinical Investigation 113(8):1084–1092.  Apr 2004.  A review by the Mahidol and Oxford malaria clinician.  Free to read at the journal.  Read from the publisher PDF;  page numbers are the printed folios.  The PDF text flattens exponents, which were restored from context.

    1. 1a.

      Page 1085:  “Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14).  This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 1020 parasite multiplications.”  Reference 14 is Su, Kirkman, Fujioka and Wellems 1997, Cell 91:593–603.  The reference number is left out of the pull quote at the head of the article. ↩ ↩

    2. 1b.

      Page 1091:  “This is particularly powerful in malaria, because there are only about 1017 malaria parasites in the entire world.”  “As there is a cumulative total of less than 1020 malaria parasites in existence in one year, such a simultaneously resistant parasite would arise spontaneously roughly once every 10,000 years”.  Page 1087:  “these ill people would contain between 5 × 1016 and 5 × 1017 malaria parasites (8).”  “we have estimated that there must be less than 3 × 1016 malaria parasites in the world's asymptomatic carriers (Figure 5) (8).”  Reference 8 is White and Pongtavornpinyo 2003, Proceedings of the Royal Society B 270:545–554, which was not obtained. ↩ ↩ ↩ ↩

    3. 1c.

      Page 1085:  “To put this in context, an adult with approximately 2% parasitemia has 1012 parasites in his or her body.” ↩

    4. 1d.

      Page 1084:  “In this review, the emergence of resistance to current antimalarial drugs is considered in two parts: first, the initial genetic event that produces the resistant mutant, and second, the subsequent selection process in which the survival advantage in the presence of the antimalarial drug leads to preferential transmission and the spread of resistance (8).” ↩

    5. 1e.

      Page 1087:  “Thus approximately 100,000–300,000 merozoites are liberated into the bloodstream to begin the 48-hour asexual reproduction cycle.”  The tenfold growth per generation is this article's assumption. ↩ ↩

    6. 1f.

      Page 1085:  “The single point mutations in the gene encoding cytochrome b (cytB), which confer atovaquone resistance, or in the gene encoding dihydrofolate reductase (dhfr), which confer pyrimethamine resistance, have a per-parasite probability of arising de novo of approximately 1 in 1012 parasite multiplications (5).”  The sentence after the next says that much higher mutation rates than 1 in 1012 are recorded in the laboratory, citing Rathod, McErlean and Lee 1997.  It is paraphrased here because the published sentence contains a misprint. ↩ ↩

    7. 1g.

      Page 1084:  “P. falciparum is now highly resistant to chloroquine in most malaria-affected areas.  Resistance to SP is also widespread and has developed much more rapidly.”  SP is sulfadoxine with pyrimethamine. ↩

    8. 1h.

      Page 1086:  “By examination of the sequence of the regions flanking the Pfdhfr gene, it has become apparent that, even for SP, multiple de novo emergence of resistance has not been a frequent event, and that, instead, a single parasite (with a mutation in Pfdhfr at positions 51, 59, and 108) has in recent years swept across each of these continents (24–26).” ↩

    9. 1i.

      Page 1091:  “Stable, therapeutically significant resistance to the artemisinin derivatives has not yet been identified and cannot be induced yet in the laboratory, which suggests that it may be a very rare event.” ↩

  2. 2.

    Behe, Michael J.  The Edge of Evolution: The Search for the Limits of Darwinism.  Free Press.  2007.  Behe is a biochemist at Lehigh University and a senior fellow of the Discovery Institute.  The wording was read from the publisher's e-book.  Page numbers were pinned on the archive.org scan of the 2007 hardback, item isbn_9780743296205, read by search-inside because the item cannot be borrowed.  Printed page equals scan leaf minus 14.  That offset was anchored on the scan's own page map at leaf 65, page 51, and leaf 152, page 138, and agrees with the pages Luskin 2019 and Durrett and Schmidt 2009 cite.  The scan's text destroys exponents, so exponents are from the e-book.

    1. 2a.

      Page 51:  “The development of drug resistance in malaria, like the development of the sickle cell gene and thalassemia in humans, is a crystal clear example of Darwinian evolution in action.” ↩

    2. 2b.

      Figure 7.4, page 144:  “the value of 5 x 1021 is calculated from 1020 malaria cells each year for the past fifty years, the approximate time since chloroquine was introduced.”  From the figure caption. ↩

    3. 2c.

      Page 57:  “Nicholas White of Mahidol University in Thailand points out that if you multiply the number of parasites in a person who is very ill with malaria times the number of people who get malaria per year times the number of years since the introduction of chloroquine, then you can estimate that the odds of a parasite developing resistance to chloroquine is roughly one in a hundred billion billion.  In shorthand scientific notation, that’s one in 1020.”  Behe's endnote 16 cites White 2004.  White's paper gives the estimate and its inputs and does not spell out the multiplication. ↩

    4. 2d.

      Page 59:  “Let’s compare the two numbers for the odds of achieving resistance to atovaquone, where just one mutation is needed, versus chloroquine, where (presumably—since if a single mutation could help, chloroquine resistance would originate much more frequently) two are needed.” ↩

    5. 2e.

      Page 60:  “Let’s dub mutation clusters of that degree of complexity—1 in 1020—“chloroquine-complexity clusters,” or CCCs.” ↩

    6. 2f.

      Page 63:  “What if a problem arose during the course of life on earth that required a cluster of mutations that was twice as complex as a CCC?  (Let’s call it a double CCC.)  For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed?  In that case the odds would be that for a CCC times itself.  Instead of 1020 cells to solve the evolutionary problem, we would need 1040 cells.”  “Put more pointedly, a double CCC is a reasonable first place to draw a tentative line marking the edge of evolution for all of life on earth.” ↩

    7. 2g.

      Page 101:  “Very, very rarely, several amino acid mutations appear simultaneously to confer a beneficial effect, such as in chloroquine resistance with mutant PfCRT.” ↩

    8. 2h.

      Page 138:  “(This means a chloroquine-type resistance mutation—where two particular amino acids had to appear before there was a net beneficial effect—would occur in each AIDS patient every day.” ↩

    9. 2i.

      Page 59:  “there are an enormous number of parasitic cells (about a trillion) in an infected patient’s body, and about a billion infected people in the world in a year.”  Page 138:  “About a hundred billion billion, 1020, malarial cells are born each year.” ↩

    10. 2j.

      Page 75:  “Some of those extra mutations (but not the first one) seem to interfere with the normal work of the protein.  Perhaps, though, if other mutations in other genes could compensate for these harmful effects, greater resistance could be acquired without causing harm in the process.  In other words, to move to the next level of resistance after the first mutation, two further, simultaneous mutations seem to be necessary.”  Page 76:  “That double mutant is, it seems, roughly as rare as a CCC.”  Behe's source is a 2004 review by Hayton and Su, which was not obtained. ↩

    11. 2k.

      Page 145:  “Nor has malaria developed new cellular protein-protein interactions.” ↩

    12. 2l.

      Page 61:  “There are about five thousand species of modern mammals.  If each species had an average of a million members, and if a new generation appeared each year, and if this went on for two hundred million years, the likelihood of a single CCC appearing in the whole bunch over that entire time would be only about one in a hundred.”  Two endnote markers are left out.  5,000 × 106 × 2 × 108 = 1018. ↩

    13. 2m.

      Page 62:  “So a CCC isn’t just the odds of a particular protein getting the right mutations; it’s the probability of an effective cluster of mutations arising in an entire organism.” ↩

  3. 3.

    Generations per year:  365.25 days ÷ 2 days = 182.6.  Parasites per year:  1017 × 182.6 = 1.8 × 1019 and 5 × 1017 × 182.6 = 9.1 × 1019, from White's standing totals;  White's own yearly figure is less than 1020.1  Drug era:  75 years from the early 1950s to 2025,14 and 75 × 182.6 = 13,700 generations.  Parasites in the drug era:  75 × 2 × 1019 = 1.5 × 1021 and 75 × 1020 = 7.5 × 1021.  Substitutions per parasite:  2.45 × 10−10 × 2.33 × 107 = 0.0057.17 17  Substitutions per year:  2 × 1019 × 0.0057 = 1.1 × 1017 and 1020 × 0.0057 = 5.7 × 1017.  Substitutions in the drug era:  1.5 × 1021 × 0.0057 = 8.6 × 1018 and 7.5 × 1021 × 0.0057 = 4.3 × 1019.  The totals assume the parasite population of the 1950s was as large as today's.  No census exists for the earlier decades. ↩ ↩ ↩ ↩ ↩

  4. 4.

    Possible single-base substitutions:  3 × 2.33 × 107 = 7 × 107.  Rate of one specific substitution:  2.45 × 10−10 ÷ 3 = 8.2 × 10−11 per parasite per generation, or one in 1.2 × 1010.  This treats the three possible substitutions at a site as equally likely.  They are not:  changes from G or C to A or T are the most common.17  Per year:  2 × 1019 × 8.2 × 10−11 = 1.6 × 109 and 1020 × 8.2 × 10−11 = 8.2 × 109.  In a patient with 1012 parasites:  1012 × 8.2 × 10−11 = 82 per generation.  A specific pair in one generation:  (8.2 × 10−11)2 = 6.7 × 10−21, or one in 1.5 × 1020.  A specific pair in two steps in one patient:  White gives 100,000 to 300,000 parasites leaving the liver to begin the 48-hour blood cycle,1 and tenfold growth per generation from there reaches 1012 in about 7 generations.  Assume 8, so that a neutral single mutant reaches a frequency of 8 × 8.2 × 10−11 = 6.5 × 10−10, or 650 parasites at the peak.  Each of those gains the second mutation at 8.2 × 10−11 per generation, which is 5.3 × 10−8 per patient per generation.  Over an assumed three generations at the peak that is 1.6 × 10−7 per patient, or one event per 6 × 1018 parasites.  Allowing either order and two alternative second sites multiplies the rate by four, giving one event per 1.6 × 1018.  A third specific mutation in the same lineage multiplies the cost by 1 ÷ (6.5 × 10−10), giving about 1028.  The eight generations of growth and the three generations at the peak are assumptions. ↩ ↩ ↩ ↩ ↩

  5. 5.

    Wootton, John C. et al.  “Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum.”  Nature 418:320–323.  Jul 18, 2002.  Read in abstract only, from the Europe PMC record.  The full text is behind a paywall and was not obtained.

    1. 5a.

      Section Abstract:  “Using 342 highly polymorphic microsatellite markers from a genetic map, here we show that the level of genetic diversity varies substantially among different regions of the parasite genome, revealing extensive linkage disequilibrium surrounding the key CQR gene pfcrt and at least four CQR founder events.” ↩ ↩

    2. 5b.

      Section Abstract:  “This disequilibrium and its decay rate in the pfcrt-flanking region are consistent with strong directional selective sweeps occurring over only approximately 20-80 sexual generations, especially a single resistant pfcrt haplotype spreading to very high frequencies throughout most of Asia and Africa.” ↩ ↩

  6. 6.

    Summers, Robert L. et al.  “Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite's chloroquine resistance transporter.”  Proceedings of the National Academy of Sciences 111(17):E1759–E1767.  Apr 29, 2014.  Read from the publisher PDF;  page numbers are the printed folios.  The PDF text flattens the superscript strain names, written here as PfCRT-HB3 and PfCRT-Dd2 in notes.  CQ is chloroquine, CQR chloroquine-resistant.  Mirror:  PMC

    1. 6a.

      Page E1759:  “mediates saturable CQ transport, whereas the wild-type form of the protein from CQ-sensitive (CQS) strains does not”.  Said of the mutant protein from the resistant strain Dd2. ↩

    2. 6b.

      Page E1759:  “These haplotypes all contain a mutation at position 76—the replacement of the positively-charged lysine (K) with an uncharged residue, usually threonine (T)—but are otherwise diverse, containing at least 4 and up to 10 mutations (13).” ↩ ↩

    3. 6c.

      Page E1759:  “CQR parasites that have arisen independently in Columbia, Peru, Papua New Guinea, the Philippines, and Southeast Asia (Fig. 1A) have distinct PfCRT haplotypes.”  The spelling of Colombia is the paper's. ↩

    4. 6d.

      Page E1759:  “We measured the ability of more than 100 variants of PfCRT to transport CQ when expressed at the surface of Xenopus laevis oocytes.”  “A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity.”  “Moreover, the attainment of full activity followed a rigid process in which mutations had to be added in a specific order to avoid reductions in CQ transport activity.” ↩ ↩

    5. 6e.

      Page E1760:  “Nevertheless, introduction of K76T or N75E into PfCRT HB3 (D38 and D39, respectively) did not result in significant uptake of CQ.  However, the addition of both mutations to PfCRT HB3 produced modest but significant CQ transport activity (D32; ∼19% of PfCRT Dd2).”  HB3 is the unmutated protein of a sensitive strain.  The strain names are superscripts in the original.  The second route, K76T with N326D, gave about 45% of the activity of the Ecuadorian protein. ↩ ↩

    6. 6f.

      Page E1763:  “Moreover, the fact that PfCRT Dd2 (but not PfCRT D28 or PfCRT E2) increased the CQ IC50 in HB3 parasites indicates that the extent to which mutant PfCRT alters the parasite's sensitivity to CQ is dependent on its capacity for CQ transport.”  D28 carries N75E, K76T and N326S.  E2 carries K76T, N326D and I356L.  The test genes were added on a plasmid beside the parasite's own unmutated gene, so this is weaker evidence than a gene replacement. ↩

    7. 6g.

      Page E1761:  “Given that all known PfCRT haplotypes contain either N75E/D or N326D (13), these results indicate that PfCRT acquires the ability to transport CQ via one of two main mutational routes, both of which entail the introduction of K76T plus the replacement of an asparagine (N75 or N326) with an acidic residue.” ↩

  7. 7.

    Gabryszewski, Stanislaw J. et al.  “Combinatorial Genetic Modeling of pfcrt-Mediated Drug Resistance Evolution in Plasmodium falciparum.”  Molecular Biology and Evolution 33(6):1554–1570.  2016.  Open access, CC BY-NC.  Read from the Europe PMC full text, which has no page numbers, so places are given by section.  CQR is chloroquine resistance and md-CQ is the drug's main breakdown product.  Mirror:  PMC

    1. 7a.

      Section Results, Effect of pfcrt Combinatorial Alleles on In Vitro Parasite Growth:  “Notably, in this genetic background, PfCRT K76T was insufficient for CQR and had a deleterious impact on parasite growth that was exacerbated by CQ.” ↩ ↩

    2. 7b.

      Section Results, Effect of pfcrt Combinatorial Alleles on In Vitro Parasite Growth:  “As compared with the 7G8 GC03 parasite line, our isogenic, pfcrt-modified parasites exhibited various degrees of in vitro fitness (range of mean s values: −0.26 to 0.11), with the majority of pfcrt alleles conferring comparable (s = 0) or inferior (s < 0) relative fitness”.  The selection coefficient s is per 48-hour generation, measured over ten generations of growth in competition.  The line name is printed with a superscript in the original. ↩ ↩

    3. 7c.

      Section Discussion, paragraph 1:  “Our simulations revealed pronounced biological constraints associated with the evolution of Ecu1110 pfcrt, a prototypical CQ-resistant allele comprised of four mutations, the smallest number required for resistance”.  “Among the pathways based on the sequential accumulation of single mutations leading to the Ecu1110 allele, the maximum realization probabilities for CQ and md-CQ resistance were, respectively, ∼5 × 10−7 and ∼10−6”.  The same paragraph gives about 3 × 10−4 for the four-step path in the pyrimethamine gene, from Kumpornsin and colleagues 2014. ↩ ↩ ↩

    4. 7d.

      Section Discussion, paragraph 2:  “As the fixation of pfcrt alleles bearing one to three mutations has not been documented in the field, we hypothesize that pfcrt-mediated CQR arose through mutational bursts with brief periods of intervening growth, whereby one or more mutations were acquired and expanded during a short time window prior to the acquisition of additional mutations.  Based on our combined IC50 and growth data, the most likely scenario would be the near-simultaneous emergence of three to four mutations.”  The source prints IC50 with a subscript. ↩ ↩ ↩

  8. 8.

    Lozovsky, Elena R. et al.  “Stepwise acquisition of pyrimethamine resistance in the malaria parasite.”  Proceedings of the National Academy of Sciences 106(29):12025–12030.  Jul 21, 2009.  Read from the publisher PDF as archived by the Wayback Machine;  page numbers are the printed folios.  The paper codes each form as four digits for positions 51, 59, 108 and 164, so 0010 is S108N alone.  Mirrors:  PMC | Archive.org

    1. 8a.

      Page 12025:  “The coding sequence for dihydrofolate reductase (DHFR) from the malaria parasite Plasmodium falciparum was mutagenized, and tests were carried out in Escherichia coli under conditions in which the endogenous bacterial enzyme was selectively inhibited.”  “The most frequent pathway (S108N and then C59R, N51I, and I164L) accounts for more than half of the simulated realizations.” ↩ ↩

    2. 8b.

      Page 12026:  “Fig. 1 shows that 2 of the 4 possible single mutants (1000 and 0001) are about equally sensitive to pyrimethamine as the nonmutant allele 0000.  Thus, the first step in the evolutionary pathway toward pyrimethamine resistance is likely either 0010 or 0100.” ↩

    3. 8c.

      Page 12028:  “Just 3 pathways in Fig. 2 account for 87.5% of the pathways traversed at significant frequencies in the simulations.  All 3 of these pathways feature S108N as the first step, and the 2 most likely pathways include C59R as the second step.” ↩

    4. 8d.

      Page 12028:  “a strongly deleterious interaction between N51I and I164L occurs, with the result that the fourth mutation decreases the growth rate in the absence of pyrimethamine by 30%–40% (Fig. S1), even though it increases the IC50 value by 25%–50% (Fig. 1).”  “According to table 3 in ref. (6), relative to the nonmutant DHFR, the quadruple mutant shows an approximate 500-fold increase in Ki/Km at the expense of about a 6-fold decrease in kcat/KM.”  The growth rates were measured in bacteria carrying the parasite enzyme. ↩

    5. 8e.

      Page 12029:  “Elsewhere in the genome, a selective sweep associated with pyrimethamine resistance has been reported across a region of chromosome 13 (39).  It is an interesting, testable hypothesis that this region of chromosome 13 may include 1 or more mutations that also alleviate the deleterious fitness effects of DHFR resistance alleles.”  Reference 39 is Volkman and colleagues 2007. ↩

    6. 8f.

      Page 12028:  “In the absence of pyrimethamine, the growth rates of the strains bearing 0010 (S108N), 0110 (S108N + C59R), or either of the triple mutants are not manifestly impaired relative to the previous step or even the nonmutant allele (Fig. 3; Table S2).”  Measured in bacteria carrying the parasite enzyme. ↩ ↩

  9. 9.

    Lents, Nathan H.  “'Darwin Devolves' -- who's the one really going backward here?”  AIPT.  Feb 12, 2019.  Retrieved Sep 27, 2026.  Lents is a biologist at John Jay College.  The page as read in 2026 no longer discusses chloroquine.  The withdrawn passage survives as quoted by Luskin 2019.

    1. 9a.

      “Note: An earlier version of this article misrepresented Behe’s claims about the evolution of chloroquine resistance in malaria.  The author regrets the error.”  Printed at the foot of the article. ↩ ↩

  10. 10.

    Burgess, Robert W., and Martin D. Young.  “The development of pyrimethamine resistance by Plasmodium falciparum.”  Bulletin of the World Health Organization 20(1):37–46.  1959.  Read in abstract only, from the PubMed Central record.  The scanned article itself could not be downloaded.

    1. 10a.

      Section Abstract:  “Of seven cases observed after 25-mg treatment, five relapsed.”  “It is concluded that under the experimental conditions of this study resistance to pyrimethamine by P. falciparum may occur rapidly after a single dose of 25 mg, being manifested during relapses on the second challenge with the drug.  Increasing the drug dosage does not overcome the resistance.  The resistant character is readily transmitted by mosquitos.” ↩ ↩

  11. 11.

    Living wild land mammals:  bats are two-thirds of individuals and less than one-tenth of 20 million tonnes.50  One-tenth of 20 million tonnes is 2 × 109 kilograms.  At an assumed 10 grams per bat that is at most 2 × 1011 bats, and 2 × 1011 ÷ (2/3) = 3 × 1011 mammals.  At an assumed one generation a year for 2 × 108 years the total is 6 × 1019.  Wild marine mammals are large and few, and livestock are recent, so neither changes the order.  New mutations:  6 × 1019 births × 63 = 3.8 × 1021.51  Each specific substitution:  1.2 × 10−8 ÷ 3 × 2 copies = 8 × 10−9 per birth, and 8 × 10−9 × 6 × 1019 = 4.8 × 1011.  For the parasite:  8.2 × 10−11 × 1.5 × 1021 = 1.2 × 1011 and 8.2 × 10−11 × 7.5 × 1021 = 6.2 × 1011.4  Giving every mammal the human mutation rate and treating all mammals as one genome are both simplifications.  The published HIV article's statement that fewer than 1020 mammals have lived cites an anonymous 2014 Stack Exchange answer, and its footnote quotes only that answer's count of bacteria.  The answer does give a mammal figure:  an upper bound of 2.88 × 1025 mice over 200 million years, which it says is "probably about around 4-10 orders of magnitude less than this", so "probably something like 1020 total mammals ever existed".  That is about 1020, not fewer.  The figure here is derived independently. ↩ ↩ ↩

  12. 12.

    Dondorp, Arjen M. et al.  “Estimation of the total parasite biomass in acute falciparum malaria from plasma PfHRP2.”  PLoS Medicine 2(8):e204.  2005.  Open access, CC BY.  Read from the Europe PMC full text.  Mirror:  PMC

    1. 12a.

      Section Abstract:  “The estimated geometric mean parasite burden was 7 × 1011 (95% confidence interval [CI] 5.8 × 1011 to 8.5 × 1011) parasites per body, and was over six times higher in severe malaria (geometric mean 1.7 × 1012, 95% CI 1.3 × 1012 to 2.3 × 1012) than in patients hospitalised without signs of severity (geometric mean 2.8 × 1011, 95% CI 2.3 × 1011 to 3.5 × 1011; p < 0.001).”  The patients were adults.  Most African cases are young children, who have less blood. ↩

  13. 13.

    World Health Organization.  Malaria.  Dec 4, 2025.  Retrieved Sep 27, 2026.  Fact sheet.  The counts are for all malaria species.

    1. 13a.

      Section Key facts:  “Globally in 2024, there were an estimated 282 million malaria cases and 610 000 malaria deaths in 80 countries.”  “In 2024, the WHO African Region was home to 95% of malaria cases (265 million) and 95% (579 000) of malaria deaths.”  Section Overview:  “P. falciparum is the deadliest malaria parasite and the most prevalent on the African continent.” ↩

    2. 13b.

      Section Genetic mutations:  “In 2024, these mutated parasites were reported in 42 malaria endemic countries”. ↩

  14. 14.

    Payne, D.  “Spread of chloroquine resistance in Plasmodium falciparum.”  Parasitology Today 3(8):241–246.  Aug 1987.  Read in abstract only, from the Europe PMC record.  The full text is behind a paywall and was not obtained.

    1. 14a.

      Section Abstract:  “The drug was introduced in 1934, but was not in large-scale use until the early 1950s.  Anecdotal reports suggest that resistance emerged as early as 1957 both in Colombia and along the then Cambodia-Thailand border area.  But by 1960, resistance in these areas was confirmed - and may represent two separate events.” ↩ ↩ ↩

  15. 15.

    Bopp, Selina E. R. et al.  “Mitotic evolution of Plasmodium falciparum shows a stable core genome but recombination in antigen families.”  PLoS Genetics 9(2):e1003293.  2013.  Open access, CC BY.  Read from the Europe PMC full text.  Mirror:  PMC

    1. 15a.

      Section Abstract:  “Using these derived mutation rates for P. falciparum (1.0–9.7×10−9 mutations per base pair per generation), we can now model the frequency at which drug or immune resistance alleles will emerge under a well-defined set of assumptions.” ↩

  16. 16.

    Claessens, Antoine et al.  “Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of var genes during mitosis.”  PLoS Genetics 10(12):e1004812.  2014.  Open access, CC BY.  Read from the Europe PMC full text.  Mirror:  PMC

    1. 16a.

      Section Results:  “From these data we estimate mutation rates of 4.07×10−10, 3.63×10−10 and 3.78×10−10 SNPs per erythrocytic life cycle per nucleotide for 3D7, Dd2 and HB3 respectively (Table 1).” ↩

    2. 16b.

      Section Results:  “This means that in the Dd2 strain, for every 48-hour intraerythrocytic generation approximately 0.2% of parasites will have undergone a var exon 1 recombination event producing a new chimeric var gene.”  Section Abstract:  “the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved.”  At 0.2% of 1012 parasites, a heavily infected patient would produce 2 × 109 new chimeric genes per generation.  That figure is this article's arithmetic. ↩

  17. 17.

    Hamilton, William L. et al.  “Extreme mutation bias and high AT content in Plasmodium falciparum.”  Nucleic Acids Research 45(4):1889–1901.  2017.  Open access, CC BY.  Read from the Europe PMC full text, which has no page numbers.  ELC in the quotations means one erythrocytic life cycle of 48 hours, and BPS means base-pair substitution.  Mirror:  PMC

    1. 17a.

      Section Materials and Methods:  “the mean overall BPS rate per ELC per bp for all clone trees (2.45 × 10−10 BPS/ELC/bp)”.  Table 1:  Per-isolate means in units of 10−10:  3D7 2.10, HB3 2.95, Dd2 3.20, KH1-01 2.27, KH2-01 1.64.  A sixth isolate, W2, had too few clones for a rate.  In all, 279 clones were sequenced and 85 substitutions found. ↩ ↩

    2. 17b.

      Section Materials and Methods:  “we divided μ1 by the total genome size of P. falciparum (G), 2.33 × 107 bp”.  The source prints μ with a subscript 1. ↩ ↩

    3. 17c.

      Section Results:  “The 3D7 indel rate was extremely high, around 10-fold greater than the BPS rate, at 21.1 × 10−10 (95% confidence interval, CI, 13.2 × 10−10–28.9 × 10−10) indels/ELC/bp; i.e. about one in every 20 parasites (95%CI 15–33) would be expected to harbor a de novo indel per 48-h ELC, compared with one de novo BPS in every 175 parasites (95%CI 134–253) per ELC.” ↩

    4. 17d.

      Section Abstract:  “Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution”. ↩ ↩

  18. 18.

    Gardner, Malcolm J. et al.  “Genome sequence of the human malaria parasite Plasmodium falciparum.”  Nature 419:498–511.  Oct 3, 2002.  Free to read at the journal.  Read from the publisher PDF;  page numbers are the printed folios.

    1. 18a.

      Page 498:  “The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date.” ↩

    2. 18b.

      Page 506:  “The 3D7 genome contains 59 var, 149 rif and 28 stevor genes, but for each family there are also a number of pseudogenes and gene truncations present.” ↩

  19. 19.

    Sidhu, Amar Bir Singh et al.  “Chloroquine resistance in Plasmodium falciparum malaria parasites conferred by pfcrt mutations.”  Science 298(5591):210–213.  Oct 4, 2002.  Read from the author manuscript at PubMed Central, which has no page numbers.  Mirror:  PMC

    1. 19a.

      Paragraph 1:  “This safe and inexpensive 4-aminoquinoline compound accumulates inside the digestive vacuole of the infected red blood cell, where it is believed to form complexes with toxic heme moieties and interfere with detoxification mechanisms that include heme sequestration into an inert pigment called hemozoin (2–4).” ↩

    2. 19b.

      Section Abstract:  “Here, we provide conclusive evidence that mutant haplotypes of the pfcrt gene product of Asian, African, or South American origin confer chloroquine resistance with characteristic verapamil reversibility and reduced chloroquine accumulation.” ↩

  20. 20.

    Shafik, Sarah H. et al.  “The natural function of the malaria parasite's chloroquine resistance transporter.”  Nature Communications 11:3922.  2020.  Open access, CC BY.  Read from the Europe PMC full text.  Mirror:  PMC

    1. 20a.

      Section Abstract:  “We identify host-derived peptides of 4-11 residues, varying in both charge and composition, as the substrates of PfCRT in vitro and in situ, and show that PfCRT does not mediate the non-specific transport of other metabolites and/or ions.” ↩

  21. 21.

    Kublin, James G. et al.  “Reemergence of chloroquine-sensitive Plasmodium falciparum malaria after cessation of chloroquine use in Malawi.”  Journal of Infectious Diseases 187(12):1870–1875.  2003.  Read in abstract only, from the Europe PMC record.  The full text was not obtained.

    1. 21a.

      Section Abstract:  “The prevalence of the chloroquine-resistant pfcrt genotype decreased from 85% in 1992 to 13% in 2000.  In 2001, chloroquine cleared 100% of 63 asymptomatic P. falciparum infections, no isolates were resistant to chloroquine in vitro, and no infections with the chloroquine-resistant pfcrt genotype were detected.” ↩

  22. 22.

    Batten, Don.  “Clarity and confusion.”  Journal of Creation 22(1):28–33.  Apr 2008.  Retrieved Sep 27, 2026.  A review of Behe's book by a scientist on the staff of Creation Ministries International.  Read from the publisher's web page, which does not mark the journal's page breaks.

    1. 22a.

      Section Clarity:  “For example, chloroquine resistance in Plasmodium is due to a fault in a transport protein that moves the poison into the organism’s vacuole.” ↩

  23. 23.

    Behe, Michael J.  “A Key Inference of The Edge of Evolution Has Now Been Experimentally Confirmed.”  Evolution News.  Jul 14, 2014.  Retrieved Sep 27, 2026.  The site is published by the Discovery Institute and now carries the name Science and Culture Today.

    1. 23a.

      Paragraph 7:  “The bottom line is that the need for an organism to acquire multiple mutations in some situations before a relevant selectable function appears is now an established experimental fact.” ↩

    2. 23b.

      Paragraph 6:  “(Interestingly, one of the two mutations I discussed in The Edge of Evolution as possibly required, at position 76 of the protein chain, is in fact one of the two that Summers et al. proved to be needed.  But the other one I discussed, at position 220, isn’t.” ↩

  24. 24.

    Luskin, Casey.  “So, Michael Behe Was Right After All; What Will the Critics Say Now?”  Evolution News.  Jul 16, 2014.  Retrieved Sep 27, 2026.  Luskin was then a staff member of the Discovery Institute.

    1. 24a.

      Paragraph 4:  “It can no longer be denied that the critics were dead wrong: chloroquine resistance does not arise at all until two mutations or more are present.”  Paragraph 6:  “His argument was based upon an empirically observed data point from public health studies which found that chloroquine resistance arose in about 1 in every 1020 organisms.” ↩

  25. 25.

    Myers, PZ.  “Quote-mined by Casey Luskin!”  Pharyngula.  Jul 17, 2014.  Retrieved Sep 27, 2026.  Myers is a developmental biologist at the University of Minnesota Morris.

    1. 25a.

      Paragraph 3:  “That the malaria parasite needs two mutations was never a point of contention, nor was it particularly worrisome.  What was wrong with Behe’s work is that he naively claimed that the two mutations had to occur simultanously in the same individual organism, so that the probability that could happen was the product of multiplying the two individual probabilities.  That’s ridiculous.”  The spelling is the original's. ↩

  26. 26.

    Behe, Michael J.  “An Open Letter to Kenneth Miller and PZ Myers.”  Evolution News.  Jul 21, 2014.  Retrieved Sep 27, 2026.  Exponents were read from the page's HTML.

    1. 26a.

      Paragraph 5:  “From the sequence and laboratory evidence it’s utterly parsimonious and consistent with all the data — especially including the extreme rarity of the origin of chloroquine resistance — to think that a first, required mutation to PfCRT is strongly deleterious while the second may partially rescue the normal, required function of the protein, plus confer low chloroquine transport activity.”  Paragraph 6:  “It’s also entirely reasonable shorthand to characterize such a situation as needing “simultaneous” or “concurrent” mutations, as has been done by others in the malaria literature, even if the second mutation actually occurs separately in the recent progeny of some sickly, rare cell that had already suffered the first, harmful mutation.” ↩

  27. 27.

    Miller, Kenneth R.  Edging towards Irrelevance, part 3: Parasites and Drugs.  2014.  Retrieved Sep 27, 2026.  Miller is a cell biologist at Brown University.  The page is undated;  part 2 of the series refers to Behe's posts of 14 and 21 July 2014.

    1. 27a.

      Section Parasites and Drugs:  “But Behe was dead wrong about it being “strongly deleterious.”  In fact, it seems to have no effect on transport activity at all.  A neutral mutation like this can easily propagate through a population, and field studies of the parasite confirm that is exactly what has happened.  In fact, a 2003 study recommended against using the K76T mutation to test for chloroquine resistance since that same mutation was also found in 96% of patients who responded well to chloroquine.”  Miller does not name the 2003 study and it was not identified.  In the field K76T is found only inside forms carrying four to ten mutations, so its presence in patients who recovered does not show that it spreads alone. ↩

    2. 27b.

      Section Parasites and Drugs:  “To put it clearly, the problem with the logic of The Edge isn’t the specific figure of one chance in 1020, but the way in such probabilities are multiplied.  In fact, it doesn’t really matter if chloroquine resistance emerges at a probability of one chance in 1020, one in 1015, or even one chance in 1010.” ↩

  28. 28.

    Moran, Laurence A.  “Taking the Behe challenge!”  Sandwalk.  Aug 2014.  Retrieved Sep 27, 2026.  Moran is a biochemist, emeritus at the University of Toronto.  His post treats the blood-stage parasite as carrying two copies of the genome.  It carries one.

    1. 28a.

      “The bottom line is that mutation to chloroquine resistance is going to be rare even if only two mutations are required and they occur sequentially.  If four mutations are required for substantive chloroquine resistance then it's not at all surprising that so few resistant strains have been observed.  There's no need to invoke simultaneous mutations and no need to assume that one of the mutations is deleterious.”  Near the end of the post. ↩

    2. 28b.

      “What this means is that if you start with an infection by a cell that has none of the required mutations then you will only get the right pair of mutations once in one million infected people.”  A million patients at 1012 parasites each is 1018 parasites.  Moran used a mutation rate of 2.5 × 10−9, ten times the rate measured since. ↩

  29. 29.

    Lents, Nathan H. et al.  “The end of evolution?”  Science 363(6427):590.  Feb 8, 2019.  A review of Behe's Darwin Devolves.  Read from the text posted on the journal's book blog, by way of the Wayback Machine.

    1. 29a.

      “Behe doubles down on his claim that the evolution of chloroquine resistance in malaria by random mutations is exceedingly unlikely because at least two mutations are required, neither of which is beneficial without the other.  His calculations have already been refuted (5), and it has long been known that neutral and even deleterious mutations can provide stepping stones to future adaptations.” ↩

  30. 30.

    Luskin, Casey.  “On Chloroquine Resistance, Nathan Lents Severely Misrepresents Behe's Arguments.”  Evolution News.  Feb 19, 2019.  Retrieved Sep 27, 2026.

    1. 30a.

      “Behe never says that chloroquine resistance is too complex to evolve.  As was explained previously, he observes that it does evolve and he cites public health data showing that it arises in approximately 1 in 1020 cells.” ↩

  31. 31.

    Miller, Kenneth R.  Edging towards Irrelevance, part 5: Been There, Done That.  2014.  Retrieved Sep 27, 2026.

    1. 31a.

      Section Been There, Done That:  “In reality, none of the criticisms took issue with that number at all.” ↩

  32. 32.

    Nair, Shalini et al.  “A selective sweep driven by pyrimethamine treatment in Southeast Asian malaria parasites.”  Molecular Biology and Evolution 20(9):1526–1536.  2003.  Read in abstract only, from the Europe PMC record.

    1. 32a.

      Section Abstract:  “Pyrimethamine resistance is generally assumed to have evolved multiple times because the genetic basis is simple and resistance can be selected easily in the laboratory.  Yet our data clearly indicate a single origin of resistant dhfr alleles sampled over a large region of SE Asia.” ↩

  33. 33.

    Roper, Cally et al.  “Intercontinental spread of pyrimethamine-resistant malaria.”  Science 305(5687):1124.  Aug 20, 2004.  Read in abstract only, from the Europe PMC record.

    1. 33a.

      Section Abstract:  “Here we present molecular evidence demonstrating that malaria parasites bearing high-level pyrimethamine resistance originally arrived in Africa from southeast Asia.” ↩

  34. 34.

    Pearce, Richard J. et al.  “Multiple origins and regional dispersal of resistant dhps in African Plasmodium falciparum malaria.”  PLoS Medicine 6(4):e1000055.  2009.  Open access, CC BY.  Read from the Europe PMC full text.  The senior author is Cally Roper.  Mirror:  PMC

    1. 34a.

      Section Introduction:  “In east Africa, mutations at codons A437G and K540E of dhps, together with the triple mutations of dhfr were shown to be a significant predictor of SP treatment failure in Kenya, Malawi, and Uganda”. ↩ ↩

    2. 34b.

      Section Abstract:  “We used microsatellite polymorphism flanking the dhps gene to determine which resistance alleles shared common ancestry and found five major lineages each of which had a unique geographical distribution.”  “Resistant dhps has emerged independently in multiple sites in Africa during the past 10–20 years.” ↩

  35. 35.

    Looareesuwan, Sornchai et al.  “Clinical studies of atovaquone, alone or in combination with other antimalarial drugs, for treatment of acute uncomplicated malaria in Thailand.”  American Journal of Tropical Medicine and Hygiene 54(1):62–66.  1996.  Read in abstract only, from the Europe PMC record.  This is the clinical study behind Behe's statement that resistance to atovaquone appears in every third patient, which he cites through a 1999 review by White.

    1. 35a.

      Section Abstract:  “However, irrespective of the duration of therapy, overall cure rates were approximately 67%.  In vitro sensitivity studies on parasites taken from patients prior to treatment and at the time of recrudescence showed a marked decrease in susceptibility to atovaquone in the recrudescent parasites.” ↩

  36. 36.

    Korsinczky, Michael et al.  “Mutations in Plasmodium falciparum cytochrome b that are associated with atovaquone resistance are located at a putative drug-binding site.”  Antimicrobial Agents and Chemotherapy 44(8):2100–2108.  2000.  Read from the PubMed Central page, which has no page numbers.  Mirror:  PMC

    1. 36a.

      Section Abstract:  “A single amino acid mutation was detected in parasites isolated from a recrudescent patient following atovaquone treatment.”  Section Results:  “The TM93-C1088 isolate (Y268S) showed a 9,354-fold-higher IC50 than the K1 parent line.”  The source prints IC50 with a subscript. ↩ ↩

  37. 37.

    Fisher, Nicholas et al.  “Cytochrome b mutation Y268S conferring atovaquone resistance phenotype in malaria parasite results in reduced parasite bc1 catalytic turnover and protein expression.”  Journal of Biological Chemistry 287(13):9731–9741.  2012.  Open access.  Read from the Europe PMC full text.  Mirror:  PMC

    1. 37a.

      Section Abstract:  “The Y268S mutation is shown to confer a 270-fold shift of the inhibitory constant (Ki) for atovaquone with a concomitant reduction in the Vmax of the bc1 complex of ∼40% and a 3-fold increase in the observed Km for decylubiquinol.”  The source prints Ki, Vmax, bc1 and Km with subscripts. ↩

  38. 38.

    Price, Ric N. et al.  “Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number.”  Lancet 364(9432):438–447.  2004.  Read from the author manuscript at PubMed Central, which has no page numbers.  Mirror:  PMC

    1. 38a.

      Section Summary:  “In 1984 mefloquine was introduced as treatment for uncomplicated falciparum malaria, but substantial resistance developed within 6 years.”  “Amplification in pfmdr1 is the main cause of resistance to mefloquine in falciparum malaria.” ↩

  39. 39.

    Ariey, Frédéric et al.  “A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.”  Nature 505:50–55.  Jan 2, 2014.  Read from the author manuscript at PubMed Central, which has no page numbers.  The senior author is Didier Ménard.  ART is artemisinin.  Mirror:  PMC

    1. 39a.

      Section A candidate molecular marker of ART resistance:  “The ART-resistant F32-ART5 parasite line was selected by culturing the ART-sensitive F32-Tanzania clone under a dose-escalating, 125-cycle regimen of artemisinin for 5 years”.  “Subsequent PCR analysis of the PF3D7_1343700 locus detected the M476I mutation after 30 drug-pressure cycles”.  Section Emergence and spread of K13-propeller mutants in Cambodia:  “This analysis reveals overall 17 mutant alleles, including three high-frequency (> 5%) alleles (C580Y, R539T and Y493H).”  PF3D7_1343700 is the gene for kelch13. ↩ ↩

  40. 40.

    Takala-Harrison, Shannon et al.  “Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.”  Journal of Infectious Diseases 211(5):670–679.  2015.  Read from the PubMed Central page.  The senior author is Christopher Plowe.  Mirror:  PMC

    1. 40a.

      Section Abstract:  “Haplotype analysis revealed both population-specific emergence of mutations and independent emergence of the same mutation in different geographic areas.” ↩

  41. 41.

    Uwimana, Aline et al.  “Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda.”  Nature Medicine 26:1602–1608.  2020.  Open access, CC BY.  Read from the Europe PMC full text.  Mirror:  PMC

    1. 41a.

      Section Abstract:  “While cure rates were >95% in both treatment arms, the Pfkelch13 R561H mutation was identified in 19 of 257 (7.4%) patients at Masaka.  Phylogenetic analysis revealed the expansion of an indigenous R561H lineage.  Gene editing confirmed that this mutation can drive artemisinin resistance in vitro.” ↩

  42. 42.

    Balikagala, Betty et al.  “Evidence of Artemisinin-Resistant Malaria in Africa.”  New England Journal of Medicine 385(13):1163–1171.  Sep 23, 2021.  Read in abstract only, from the Europe PMC record.  The senior author is Toshihiro Mita.

    1. 42a.

      Section Abstract:  “The independent emergence and local spread of clinically artemisinin-resistant P. falciparum has been identified in Africa.”  The study was done in northern Uganda.  The mutations were A675V and C469Y, which differ from the Rwandan one. ↩

  43. 43.

    Birnbaum, Jakob et al.  “A Kelch13-defined endocytosis pathway mediates artemisinin resistance in malaria parasites.”  Science 367(6473):51–59.  Jan 3, 2020.  Read in abstract only, from the Europe PMC record.  The senior author is Tobias Spielmann.

    1. 43a.

      Section Abstract:  “Parasites with inactivated Kelch13 or a resistance-conferring Kelch13 mutation displayed reduced hemoglobin endocytosis.  ARTs are activated by degradation products of hemoglobin.  Hence, reduced activity of Kelch13 and its interactors diminishes hemoglobin endocytosis and thereby ART activation, resulting in parasite resistance.” ↩

  44. 44.

    Feleke, Sindew M. et al.  “Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia.”  Nature Microbiology 6:1289–1299.  2021.  Open access, CC BY.  Read from the Europe PMC full text.  The senior author is Jonathan Parr.  RDT is rapid diagnostic test.  Mirror:  PMC

    1. 44a.

      Section Abstract:  “we estimate that HRP2-based rapid diagnostic tests would miss 9.7% (95%CI 8.5-11.1) of P. falciparum malaria cases owing to pfhrp2 deletion.”  “We propose a model in which pfhrp3 deletions have arisen independently multiple times, followed by strong positive selection for pfhrp2 deletion owing to RDT-based test-and-treatment.” ↩

  45. 45.

    Roberts, David J. et al.  “Rapid switching to multiple antigenic and adhesive phenotypes in malaria.”  Nature 357:689–692.  Jun 25, 1992.  Read from the author manuscript at PubMed Central, which has no page numbers.  Mirror:  PMC

    1. 45a.

      Section Abstract:  “Our data show that antigens at the parasitized cell surface undergo clonal variation in vitro in the absence of immune pressure at the rate of 2% per generation with concomitant modulations of the adhesive phenotype.” ↩

  46. 46.

    Stubbs, Janine et al.  “Molecular mechanism for switching of P. falciparum invasion pathways into human erythrocytes.”  Science 309(5739):1384–1387.  Aug 26, 2005.  Read in abstract only, from the Europe PMC record.

    1. 46a.

      Section Abstract:  “We show that switching from sialic acid-dependent to -independent invasion is reversible and depends on parasite ligand use.  Expression of P. falciparum reticulocyte-binding like homolog 4 (PfRh4) correlates with sialic acid-independent invasion, and PfRh4 is essential for switching invasion pathways.” ↩

  47. 47.

    Nair, Shalini et al.  “Adaptive copy number evolution in malaria parasites.”  PLoS Genetics 4(10):e1000243.  2008.  Open access, CC BY.  Read from the Europe PMC full text.  CNP is copy number polymorphism.  Mirror:  PMC

    1. 47a.

      Section Abstract:  “Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2–11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs.”  “We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification.”  “These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function.”  Section Results:  “The simplest explanation is that the 2.2 kb, 8.7 kb, and >11 kb amplicon share the same origin, and that the 1.7 kb and 7.3 kb amplicons have evolved independently.” ↩

  48. 48.

    Volkman, Sarah K. et al.  “A genome-wide map of diversity in Plasmodium falciparum.”  Nature Genetics 39(1):113–119.  Jan 2007.  Read in abstract only, from the Europe PMC record.  The abstract does not name the chromosome.  Lozovsky and colleagues, who cite this paper, place the region on chromosome 13.

    1. 48a.

      Section Abstract:  “We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites.” ↩

  49. 49.

    Amino-acid changes in the most changed form of each gene:  PfCRT 10,6 DHFR 4,8 DHPS 2,34 cytochrome b 1,36 kelch13 1.39  Total 18.  Each amino-acid change needs at least one nucleotide change, so 18 is a floor.  The alternative forms in other lineages, which include 17 kelch13 forms and several PfCRT forms, were not counted one by one.  The figure of 100 is a round upper limit for them and is an estimate.  Low end:  18 ÷ 7.5 × 1021 = 2.4 × 10−21.  High end:  100 ÷ 1.5 × 1021 = 6.7 × 10−20.  The denominators are from the ledger.3  For HIV, the published article gives no more than 5,000 constructive changes among 6 × 1022 particles, and 5,000 ÷ 6 × 1022 = 8 × 10−20. ↩

  50. 50.

    Greenspoon, Lior et al.  “The global biomass of wild mammals.”  Proceedings of the National Academy of Sciences 120(10):e2204892120.  2023.  Open access.  Read from the Europe PMC full text, which has no page numbers.  The paper does not print a total count of individuals in its main text.  Mirror:  PMC

    1. 50a.

      Section Abstract:  “We present a detailed assessment, arriving at a total wet biomass of ≈20 million tonnes (Mt) for all terrestrial wild mammals (95% CI 13-38 Mt), i.e., ≈3 kg per person on earth.”  Section Results:  “Bats (Chiroptera), for example, comprise one-fifth of species and two-thirds in terms of individual mammals, but only contribute less than one-tenth of the total biomass of wild land mammals”. ↩ ↩

  51. 51.

    Kong, Augustine et al.  “Rate of de novo mutations and the importance of father's age to disease risk.”  Nature 488(7412):471–475.  Aug 23, 2012.  Read from the author manuscript, which has no journal page numbers.  The senior author is Kari Stefansson.  Mirror:  PMC

    1. 51a.

      Section Abstract:  “Here we show that in our samples, with an average father’s age of 29.7, the average de novo mutation rate is 1.20×10−8 per nucleotide per generation.”  Section Results:  “a total of 4,933 de novo mutations, or an average of 63.2 per trio, were called.”  A trio is two parents and a child, so 63.2 is the count per child. ↩ ↩