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Neo-Darwinism: The Current Paradigm
What'sNEW (More new items follow subtopis below!"
Will mutations produce wings like in angels, in a human being? If you wanted to develop a race
of angels, would it be possible to select for a pair of wings? Theodosius Dobzhansky
I could try! Peter Medawar (1)
Charles Darwin championed the theory of common
descent and eolution by natural selection amon!
descendants with sli!ht ariations on the ancestors"
features# The concept of natural selection sprin!s from
artificial selection$ a procedure breeders use to enhance
desired characteristics such as stamina$ color$ size$ yield$
and so forth$ in animals and plants# Darwin thou!ht that a
similar process happens in nature# There is nothin! to
disa!ree with here# %atural selection can brin! about
eolution in a fashion similar to artificial selection# &ut
animal breeders and plant breeders hae always known
that artificial selection has limits# 'holly new
characteristics neer emer!e from artificial selection(
they will neer breed a do! with antlers# The same kind
of limit applies to all natural selection operatin! on the
aailable !enetic material#
#enetis
Neo-Darwinism is an attempt to reconcile endelian genetics, which says that organisms do not
change with time, with Darwinism, which claims they do! )ynn Mar!ulis (*)
Darwin$ courtesy of the +enry ,# +untin!ton
)ibrary and -rt .allery
Darwin actually knew ery little about !enetics# The !reat pioneer of that field was
.re!or Mendel$ whose work was contemporary with Darwin"s# %ow the theory of
eolution incorporates Mendel"s !enetics into Darwin"s framework( the combined
theory was called /neo0Darwinism#/ (1ecently$ that cumbersome term is bein!
replaced by the simpler /Darwinism/#)
-ccordin! to this paradi!m$ eolution is drien by chance# Chance mutations affect one or a few
nucleotides of D%- per occurrence# &i!!er chan!es come from recombination$ a !enetic process
in which lon!er strands of D%- are swapped$ transferred$ or doubled# These two processes$
mutation and recombination$ create new meanin! in D%- by lucky accidents# -ccordin! to the
preailin! paradi!m$ this is the mechanism behind eolution#
2ne problem with this story is that it is implausible (tidak masuk akal)# 3t is analo!ous to sayin!
that a !reat work of literature such as oby Dick could emer!e from lesser pree4istin! books$ if
there were enou!h typos and swappin! of para!raphs alon! the way# The trouble is$ when this
process is actually attempted with te4t$ it neer succeeds# 2nly with !uidance can random
processes lead to meanin!ful sentences or para!raphs# &ut plausibility in the current paradi!m of
eolution is apparently unnecessary# 'e are told by 1ichard Dawkins$ /The !eneral lesson we
should learn is neer to use human 5ud!ment in assessin! such matters/ (6)#
2rdinary people are under the impression that there are e4amples in nature which proe that
chance mutation and recombination can create new meanin! in !enetic code new !enes# 7et
the alle!ed e4amples of the phenomenon do not actually e4emplify it# Consider the ability of
bacteria to become resistant to antibiotics# 8alador )uria and Ma4 Delbr9ck proed in 1:;6 that
the resistant bacteria descended from pree4istin! strains( the !enes for the resistance were
already aailable in the !ene pool# -lthou!h some hae disputed this interpretation of their
e4periments$ it is now well established# -nd today we know that bacteria often ac<uire whole
new !enes conferrin! resistance to antibiotics( the !enes are imported on /resistance plasmids/
(6#=)#
-nother e4ample of similar /eolution/ in eukaryotic cells is described in 1enato Dulbecco"s
"he Design of #ife# This time the !enes for the new characteristic are already present in the
or!anism (;)>
###Trypanosomes ?are@ small eukaryotic parasites that in -frica cause sleepin! sickness in humans and some animals#
The animal responds by producin! special protein moleculesantibodies that bind to the coat of the parasite and
stop its !rowth#### &ut when the antibodies hae almost !ained control$ parasites with a different coat make their
appearance#### 'hen the new antibodies are produced$ the second wae of parasites disappear$ but yet another kind
emer!es$ with coat molecules different from the first two#
The study of this phenomenon has uncoered an amazin! or!anization in the parasite"s D%-# 1adioactie probes ###
hae reealed that a hundred or more !enes are deoted to coat ariation$ each !ene specifyin! one kind of coat
molecule#### 2nly one is actie at a time#
The moth that has eoled to blend in with the sooty walls and treetrunks of modern industrial
cities is another e4ample of eolution in our time# -!ain$ the !enes for darker colorin! in the
moth were already aailable in the !ene pool# 7es$ there are a few documented e4amples in
which a simple mutation in a bacterium brin!s about antibiotic resistance$ but in these cases it
Mendel
does so by reducin! or eliminatin! the affected !ene"s function$ not by creatin! a new function#
-mon! iruses$ mutations can een alter a coatin! protein and thereby temporarily dis!uise the
irus (;#=)# &ut a!ain$ no new function is created# 8uch mutations could not drie the
eolutionary pro!ress we obsere in the fossil record#
2f course$ there are many e4amples of !enes that hae mutated sli!htly in the course of
eolution without losin! their ori!inal functions# -nd other e4amples$ fewer in number$
apparently indicate that !enes may mutate sli!htly and ac<uire different but closely related
functions# The !lobin family of !enes are in this cate!ory# -nd in a third cate!ory$ a handful of
e4amples may indicate that a !ene mutates sli!htly and ac<uires a wholly new function# These
finally seem to be e4amples in which mutations create new meanin!$ but we are not sure this
third account is accurate# The number of chan!ed essential nucleotides in new !enes that
supposedly arose this way is still in the dozens at least$ whereas the number of possible !enes
that would differ from a !ien aera!e0size !ene by only half0a0dozen essential nucleotides is
enormous$ on the order of 1AB1;# &lindly traersin! een this short distance in se<uence space so
lar!e re<uires incredible luck#
%eo0Darwinism can rebut this line of criticism in two ways> 1) almost any !ene
will work a /many0worlds/ theory of biolo!y$ or( *) there is a !uided
mutational pathway$ as Manfred ,i!en described in 1:CD (=)$ leadin! from the
first set of primitie !enes to all of the !enes subse<uently used in biolo!y# &ut$
since 1:CD$ ,i!en"s model has not been fleshed out# Eurthermore$ that kind of
eolution would be ultra0!radual$ unlike what we see in the fossil record# %either
of these two alternaties has any analo! in the world of other codes such as te4t or
computer pro!rams# - theory that aoids these difficulties should be considered#
The $rigin of %ntifree&e Protein #enes
"he notothenioid trypsinogen to $%&' conversion is the first clear e(ample of how an old
protein gene spawned a new gene for an entirely new protein with a new function! )ian!biao
Chen$ -rthur )# DeFries and Chi0+in! C# Chen! (G)
The -pril 1=$ 1::D issue of 'roc! Natl! $cad! )ci! *)$ contains a report with stron! eidence
se<uence similarities linkin! two !enes with different functions in a common -ntarctic fish#
2ne !ene codes for trypsino!en$ an enzyme produced in the pancreas# The other codes for a
protein called antifreeze !lycoprotein (-E.P) that keeps the fish"s blood from freezin!#
The related se<uences are so similar that the biolo!ists$ from the Hniersity of 3llinois$ Hrbana$
date the dier!ence of the se<uences as only fie to 1; million years a!o# This timin! coincides
with the independently estimated time when the -ntarctic 2cean was frozen# /8electie
pressure/ would hae faored the creation of an antifreeze !ene then# The report makes a stron!
case that the antifreeze !ene eoled from the trypsino!en !ene by a series of steps includin!
whole !ene duplication( the deletion$ insertion$ duplication$ and amplification of smaller
se<uences( and a frameshift mutation#
,i!en
Proc. Nat. Acad. Sci., USA
The work is undeniably interestin!# Perhaps the most interestin! part$ noted in commentary by
Iohn M# )o!sdon$ Ir# and '# Eord Doolittle$ is that /the noel portion of the -E.P !ene
(encodin! for the ice0bindin! function) deries from the recruitment and iteration of a small
re!ion spannin! the boundary between the first intron and the second e4on of the trypsino!en
!ene/ (D)# Thus$ accordin! to the report$ a se<uence without inte!rity or meanin! in the first !ene
fortuitously became a critical se<uence in the new !ene# 3s this the e4ample that has been lackin!
of the creation of a new !eneJ 8o it seems# &ut problems remain#
3t is possible to estimate the likelihood of creatin! a new !ene this way# 2ne could estimate the
actual rate at which the steps listed aboe occur in the fish !ermline cells and the fish population
at the time when the -ntarctic 2cean was freezin!# Erom there one could strai!htforwardly
calculate the appro4imate number of trials of new !enes that could hae occurred$ durin! a
reasonable time window$ to produce an antifreeze protein !ene in the fish# 2ne could also
estimate the number of different actual !enes that would code for antifreeze proteins# 2ther work
by the same authors in the same issue (C) makes this estimation seem possible# Einally$ a
mathematician could$ with little trouble$ count the number of possible different !enes that could
be created from the trypsino!en !ene and other possible precursor !enes by the steps listed
aboe# These estimates would enable one to calculate the probability that an antifreeze !ene
would be found by trial and error in the time aailable#
The last estimate$ howeer$ turns out to be lethal to our chances# The number of possible
different !enes that could be created by only a handful of steps from the list aboe is enormous#
Eor e4ample$ consider a !ene of *$=AA nucleotides$ allowin! a D=K error rate (G*= essential
nucleotides#) The number of possible different !enes that could be created by deletin! a sin!le
essential nucleotide and insertin! it elsewhere in the same !ene$ fie successie times$ is 1AB*C#
'hen se<uences for insertion into the tar!et !ene can be any len!th$ and can come from any of
thousands of other !enes$ the possibilities <uickly approach the theoretical ma4imum in this
e4ample ;BG*= or about 1AB6DA# 8o the proposed mechanism does not increase the probability of
arriin! at a wholly new !ene by chance# 3t"s still monkeys writin! 8hakespeare$ only now they
hae word processors with /cut and paste/ functions#
The authors are aware of this problem and postulate other roles for !enetic intermediates
between the two !enes# +oweer$ they seem to realize that this speculation is inade<uate$
because they conclude ?the second article@ by sayin!$ /The selection of an appropriate
permutation of three codons### was likely shaped by the structural specificity re<uired for
antifreeze ice interaction to take place#/ This sounds like teleolo!y#
-fter the careful analysis by Chen et al!$ one mi!ht understand if a neo0Darwinists lost patience
at this point in the discussion and simply asserted that it must hae happened as they describe#
-ny reasonable person would admit that !enetic se<uences may !radually dier!e oer time$ as
in the antifreeze !ene e4ample# Cosmic -ncestry does not dispute that !enetic se<uences can
!radually dier!e oer time$ and that !enetic recombination occurs# &ut for the discoery of
len!thy new se<uences with new meanin!$ the math in the e4ample still doesn"t work# -nd a
model for this process in te4t$ without !uidance$ will not succeed#
3f the antifreeze !ene was composed by the process Chen et al! describe$ perhaps antifreeze
actiity is so non0specific that /almost any !ene will do$/ as considered aboe# &ut if the precise
antifreeze se<uence was re<uired (allowin! only normal error tolerance)$ the composition
process would hae to hae been !uided somehow# %eo0Darwinism allows !uidance by a chain
of hypothetical intermediate steps (but not by teleolo!y)# Cosmic -ncestry would e4plain such
!uidance only by other instructions already in the !enome( howeer$ this concept is
undeeloped#
Puntuated E'uilibrium
"he usual procedure is to forget the difficulties, never to talk about them, and to proceed as if
the theory were without fault! Paul Eeyerabend (:)
Darwin wrote that eolution was a !radual process$ with infinitesimal chan!es accumulatin!
oer the a!es to eentually yield ma5or differences in liin! thin!s# 3f eolution adances as
Darwin says it must$ only tiny steps would eer happen# +e states in "he +rigin of )pecies> /3f it
could be demonstrated that any comple4 or!an e4isted which could not possibly hae been
formed by numerous$ successie$ sli!ht modifications$ my theory would absolutely break down/
(1A)#
,idence from fossils does not bear out Darwin"s theory of !radual chan!e# 3nstead$ species
remain relatiely unchan!ed for lon! periods$ and then suddenly$ new kinds arise# Many bacteria
today hae apparently chan!ed ery little since they first appeared# 8ome archaebacterial species
appear to be as old as life on ,arth( they haen"t eoled ery far in almost four billion years# 'e
know that bacteria were the only inhabitants of the earth until about 1#D billion years a!o#
-pparently$ no ma5or eolutionary deelopments happened amon! the bacteria for the first two
billion years of lifemore than half of the time life has e4isted on ,arth#
&y contrast$ the entire Cambrian ,4plosion of about =DA million years a!o took only fie to nine
million years (11)# -ll kinds of multicelled creatures$ in astonishin! ariety$ seemed to come at
once out of nowhere (1*)# 2n the coer of "ime we read this synopsis of the Cambrian
,4plosion> /%ew discoeries show that life as we know it be!an in an amazin! biolo!ical frenzy
that chan!ed the planet almost oerni!ht/ (16)#
8imilar discontinuities can be seen on a finer scale in the indiidual histories of species# 3n fact$
the sudden appearance of new kinds of creatures$ without eidence of intermediate kinds$ is more
the rule than the e4ception# ,4amples of intermediate kinds$ such as the do!0sized Mesohippus
that preceded the horse are actually <uite rare# 8tephen Iay .ould calls this discrepancy between
the theory (!radualism) and the eidence (bi! steps) the paleontolo!ists" /trade secret#/
Today there is still considerable discord oer punctuated e<uilibrium# +ow real is stasis (the
period without appreciable chan!e)$ how !radual is punctuation$ and how can neo0Darwinists
account for themJ 2ne proposal is /species sortin!/ or /species selection#/ 3n !eneral$ the new
idea is that bi! eolutionary steps occur !radually in small$ isolated populations# 'hen the
eolutionary steps are complete$ the small population with its new adanta!e <uickly e4pands
and replaces the bi!!er population# Thus$ in the !eolo!ical record the chan!e looks
instantaneous# This solution has some appeal$ but it offers little more by way of e4planation than
that !radual eolution always takes place somewhere out of si!ht# 3n 1:61$ I#&#8# +aldane
foresaw this problem# /The paleontolo!ist can always postulate a slow eolution in some area
hitherto une4plored !eolo!ically$ followed by mi!ration into known areas/ (1;)# Perhaps
punctuated e<uilibrium is a clue that the !enetic mechanism underlyin! eolutionary pro!ress is
alto!ether different from the one currently in faor#
Coordinating #enes
We violate probability, by our nature! )ewis Thomas
1ichard Dawkins writes that the eye could eole easily$ by chance$ in tiny steps# 3n an article
entitled /The ,ye in a Twinklin!$/ he discusses how improements of only one percent each
could lead$ in only some ;AA$AAA !enerations$ to the eye of a fish (1=)# +e says eyes could hae
eoled many times$ as they must hae$ because there are about ;A different kinds of eyes#
3f eyes hae eoled as Dawkins describes$ by chance$ then the !enetic pro!ram to coordinate all
the embryolo!ical steps in the !rowth of an eye (of each type) would eole only after the !enes
for the steps themseles had eoled# 7et recently$ scientists learned that the same !ene
coordinatin! the embryolo!ical steps in eye0makin! works in wasps and miceL The coordinatin!
!ene must hae come first# /The obseration that mammals and insects$ which hae eoled
separately for more than =AA million years$ share the same master control !ene for eye
morpho!enesis indicates that the !enetic control mechanisms for deelopment are much more
uniersal than anticipated/ (1G)# 3n March$ 1::D$ a !roup of scientists at the %ational ,ye
3nstitute in &ethesda$ Maryland and the Hniersity of &asel in 8witzerland reported that a !ene
controllin! eye deelopment is shared by fruitflies$ mice$ and s<uid (1D)# These startlin!
deelopments hae made theorists reconsider how eyes eoled (1C)#
- coordinatin! !ene that works the same way in ery different animals is not confined to the eye#
+omeotic !enes in Drosophila (the fruitflies often used to study !enetics) are known to control
the e4pression of at least twenty of the fly"s !enes# +omeotic !enes can be identified by the
presence in them of a se<uence 1CA nucleotides lon! called a homeobo4# /The bi! surprise
concernin! homeobo4es came in 1:C; with the discoery of a homeobo4$ ery similar to the
Drosophila ones in a ertebrate$ the toad ,enopus laevis# 8oon afterwards the first mammalian
homeobo4es were located###/ (1:)# Coordinatin! !enes appear to be standardized across a broad
ran!e of multicelled animals# -nd in March$ 1::D$ biolo!ists from the Iohn 3nnes Centre for
Plant 8cience 1esearch in %orwich$ ,n!land and Caltech found impressie similarities between
homeotic !enes in the fruitfly and a flowerin! plant (*A)#
3t is difficult for neo0Darwinism to e4plain the appearance of embryolo!ical coordinatin! !enes
before the appearance of the embryolo!ical steps they coordinate# 3t"s like sayin! that the
blueprints for automobile manufacturin! plants were on hand before the inention of
automobiles#
Con(ergent E(olution
Doubts, additional -uestions, argument and criticism contribute to the strength, not the
weakness, of scientific thought! 1obert Macchiarelli$ paleontolo!ist$ Hniersity of Poitiers
(*A#=)
/Coner!ent eolution/ has been obsered since the time of Darwin# 3t is the name !ien to
apparent coincidences in eolution$ such as the physical similarity between sharks (fish) and
dolphins (mammals)$ or the parallelism in the cochlea of birds and mammals# - strikin! e4ample
is the resemblance between the Tasmanian wolf$ which is an -ustralian marsupial /do!$/ and
mammalian do!s common on other continents# -lthou!h the two would be ery far apart on a
phylo!enetic tree$ it takes a skilled zoolo!ist to distin!uish them by anatomical features like the
skeleton# -nd e4amples of coner!ence also appear at the molecular leel$ as in similar antibody
proteins carried by camels and nurse sharks# -s "he New .ork "imes obseres$ /The more
scientists look$ the more e4amples of coner!ence they find/ (*1)#
%eo0Darwinism accounts for the phenomenon by supposin! that eolutionary options are often
seerely restricted by circumstances# /Coner!ences keep happenin! because or!anisms keep
wantin! to do similar thin!s$ and there are only so many ways of doin! them$/ says molecular
biolo!ist 1udolf -# 1aff of 3ndiana Hniersity (**)# 8o the phenomenon has been named /the
principle of coner!ence/ or /coner!ent eolution#/ &ut namin! the problem doesn"t mean it
has been e4plained# The renowned +arard biolo!ist 8tephen Iay .ould beliees that sli!ht
differences in the course of eolution should lead to totally different outcomes# 3f so$
coner!ence is bafflin!# - discernin! witness is 5ustified in wonderin! if neo0Darwinism
ade<uately e4plains coner!ence$ or if another theory mi!ht account for it better#
Does Miroe(olution E)plain Maroe(olution*
icroevolution / $ change in the gene pool of a population over a sucession of generations!
acroevolution / 0volutionary change on a grand scale, encompassing the origin of novel
designs, evolutionary trends, adaptive radiation, and mass e(tinction! %eil -# Campbell (*6)
,rnst Mayr"s 1:CC classic$ "oward a New 'hilosophy of 1iology$ asks the <uestion$ /Does
Microeolution ,4plain MacroeolutionJ/ (*;)# The issue came into sharper focus after %iles
,ldred!e and 8tephen Iay .ould introduced the concept of /punctuated e<uilibrium/ into the
discussion of eolution# Microeolution would occur durin! stasis$ and macroeolution at the
punctuation points# This scenario is inconsistent with neo0Darwinian !radualism$ accordin! to
which macroeolution is simply cumulatie microeolution oer lon! periods of time# The
<uestion challen!es standard neo0Darwinism at its heart#
3n our opinion$ neo0Darwinism ade<uately accounts for microeolution# Chan!es in e4istin!
allele fre<uencies are already known to cause microeolution such as the darkenin! of the
,n!lish moth"s win!s# - sin!le nucleotide substitution can alter a irus"s protein coat into one
that the host"s immune system doesn"t reco!nize# The insertion or deletion of a sin!le nucleotide
causes a nonsense mutation that would disable$ for e4ample$ a promoter or repressor se<uence$
thereby switchin! other whole !enetic pro!rams off or on#
Macroeolutionary pro!ress such as the eolution of photosynthesis$ on the other hand$ re<uires
wholly new !enes with len!thy new instruction se<uences# 'hereas a new !ene can be activated
by a sin!le point mutation$ as mentioned aboe$ there is scant eidence that new !enes can be
composed by Darwinian random point mutations and recombination eents# ,4amples
supportin! this composition method are ery few and weak#
%otice the term /pro!ress/ in the precedin! para!raph# -ny si!nificant adance in eolution
re<uires new !enes# &ut loss of function$ of course$ can occur without new !enes# 8o$
macroeolutionary loss of function is not hard to e4plain# The real <uestion is$ /Does
microeolutionary pro!ress e4plain macroeolutionary pro!ressJ/
-n e4cellent e4ample of microeolutionary pro!ress was discoered in 1:::$ by !eneticists and
ophthalmolo!ists at Hniersity Colle!e )ondon# Erom se<uences of opsin !enes they hae
deduced a plausible way for trichromatic ision in the howler monkey to hae eoled from
dichromatic ision by neo0Darwinian !ene duplication and random mutation# Their analysis of
the control re!ions of the !enes$ which are upstream of the codin! re!ions$ confirms the
duplication# 3nterestin!ly$ of the appro4imately CA nucleotides from the codin! re!ion of the two
!enes that were compared$ only one nucleotide was not identical# This plausible mutation causes
a sin!le amino acid substitution in the second howler opsin that chan!es its color sensitiity# The
chan!ed !ene makes 60color ision possible (*=)# 3n a recently discoered closely related
e4ample only two amino acid substitutions account for the blue0shifted ision of coelacanths
(*G)#
The howler monkeys" ac<uisition of trichromatic ision represents eolutionary pro!ress$
un<uestionably# &ut the same neo0Darwinian microeolutionary mechanism has not been shown
to be capable of manufacturin! the wholly new !enes necessary for macroeolutionary pro!ress#
'e beliee that another source for these new !enes is necessary#
+ummar,
!!!$ considerable part of Darwinism is not of the nature of an empirical theory, but is a lo!ical
truism# Marl 1# Popper$ 1:D* (*D)
-rtificial selection neer produces wholly new characteristics# 'ithout the input of new !enes$
there is no eidence that natural selection does either#
The notion that mutation and recombination can compose new !enes is implausible#
There is scant eidence that mutation and recombination can compose functional new !enes
that differ from any known predecessor by more than$ say$ a dozen essential nucleotides#
The eolution of antifreeze !lycoproteins in -ntarctic cod presents problems for both
Darwinism and Cosmic -ncestry#
,olution does not appear to be !radual$ contrary to Darwin"s firm prediction#
The standard theory cannot e4plain why the coordinatin! !enes that control the deelopment of
embryos and ma5or features are often ery similar across totally different species#
Coner!ent eolution is a surprise not well0e4plained by neo0Darwinism#
Macroeolutionary pro!ress is not accounted for by neo0Darwinian microeolution#