Dear Gert :
Many thanks for contacting me. You have done a very good objective job in
reviewing our book. The best and most comprehensive we have seen thus far
from a "general reader" (although it is clear from your deep grasp of the
subject matter you are more than just a general reader). For your
information we have yet to see anything like this from a professional
within the somatic hypermutation or experimental molecular evolution fields.
Every so often we say to ourselves " wouldn't it be nice to have all our
published work evaluated on the basis of the evidence". You have really
attempted to do this, and largely succeeded - on behalf of the authors of
"Lamarck's Signature" please accept our sincere thanks.
Given that there is so much molecular data to integrate to truly appreciate
why the title of our book appropriately represents our position ("the
somatic pattern is written into the germline DNA ", even for non-antibody
genes, below) it is gratifying that you made such a detailed effort to come
to grips with the problem.
We do have a few things to comment on and these are listed below.
- In the second paragraph of your review you highlight the real enigmas
presented by the apparent pristine "open reading frame" structure of the
chicken V-pseudogenes as well as the recombination process and the
"integration footprint" (ie.the Weiller signature predicted by cDNA
retrotranscipts of pieces of rearranged pre-mRNA of V genes acting as gene
conversion donors (is there another simple rational explanation?). Further
on you highlight the difference between the "germline configuration" and
the "somatic configuration" - and our comment would be, that without this
stark molecular difference the soma-to-germline analysis would be wellnigh
impossible. But in paragraph 2 you also state:
" Some of the steps of this mechanism (from somatic RNA to germline DNA)
do occur in organisms and are mentioned in the textbooks. For example some
pseudogenes are thought to have arisen by reverse transcription from mRNA,
followed by insertion into the chromosome."
It should be pointed out that the words "some pseudogenes" grossly
understates the situation for non-immunoglobulin "housekeeping" genes.
Thus for example in W-H Li and D Graur's "Fundamentals of Molecular
Evolution" (1991 Sinaure & Associates) you will note in Table 2 entitled
"The number of retropseudogenes and the number of parental functional genes"
that pretty well most single-copy/limited-copy "house keeping genes"
examined (as to 1991!) have as their counterparts multiple copies of
retropseudogenes (discussed and cited on pages 200-202 of "Lamarck's
Signature"). Further, in any extended chromosomal locus (eg. humans) you
might randomly select, and which has been completely sequenced, you will
find that retroelements of all types dominate the DNA sequence landscape
(eg. Rowen et al The Complete 685-Kilobase DNA Sequence of the Human
ß T Cell Receptor Locus
in Science vol 272 , June 21 1996).
- In paragraph 2 you then go on to state :
"What is not 'proven' is that these individual steps occur together"
Our comments are two fold. All the DNA sequence structural evidence
directly implies that the steps must have occurred together. This deduction
is identical to all conclusions on retrogenes, pseudo or otherwise viz.
evidence for RNA intermediate structures such as a lack of introns and
polyA tails written into DNA. The additional "retro" feature we add is the
documentation of the evidence for 'somatic selection' (at the intact
antibody protein level!) of germline V sequences.*
- The section entitled : "Revolutionary genetics: genes that don't behave"
You ask via way of a question mark whether our detailed analysis of "the
genetics and evolutionary uniqueness of the immune system" may have been
"unintentional?". Not at all, this was quite intentional - because if these
facts are fully grasped old fashioned and rigid views of genetics
(neo-Darwinian or otherwise) have to be abandoned. This then allows the
emergence of a new set of operational genetic rules which might be dubbed
the "New (Retro-) Genetics".
- The section entitled : "Should 'Darwin's Natural Selection Paradigm' be changed?"
At the end of the first paragraph you cite an anonymous reviewer (ref 13)
and say " The indirect evidence is interesting, but open to other interpretations".
Our response is blunt : If there are other interpretations we would like to
hear them - to this point plausible alternative genetic explanations have
not been advanced (And it is for this reason that we rhetorically contrast
our explanations with the non-scientific 'divine intervener').
We have read the review at this Website and in particular the use of the
"anonymous" comments (which we should point out have been added recently to
this Website review - they were not in the original review of Dec 1998-Jan
1999). This is a shallow attempt to explain some of the data. Large
tracts of data are ignored or not understood at all (see footnote *).
We have found this to be a common mistake of neophyte critics - they focus on
one aspect of the data, without realizing that "Lamarck's Signature"
constitues a multifaceted set of genetic features all of which require a
rational explanation. In short, if the anonymous reviewer had understood
the data he/she would not have drawn the conclusions published on that
Website.
In the second paragraph you make the point "So the subtitle of his book is
a little bit misleading. Even if the soma-to-germline route would be
proven,it would not follow that other organs/tissues apart from the
immunological system could behave in the same way. It would not be a
general mechanism."
At the moment I suppose this is the legitimate and conservative position to
take - but it should be tempered and balanced by the realisation that
"retrogenes" (DNA sequences in the genome that have been processed by
reverse transcription via an RNA intermediate template sequence) are
general (not restricted to antibody genes) and widespread in the genome
(eg. see point 1 above: Table 2 in W-H Li and D Graur's "Fundamentals of
Molecular Evolution" [1991 Sinaure & Associates] and Table 2 in Rowen et al
in Science vol 272, June 21 1996).
- The point in the last paragraph of your review is well taken. We did
omitted defining (paradoxically!) "retrogenes". So an appropriate
definition is :
retrogenes : DNA sequences in the genome that have been processed by
reverse transcription via an RNA intermediate template sequence.
We will endeavour to clean up these blemishes if the book goes to a new edition reprint.
Before closing I would like to state that our data and analyses have been
peer reviewed and published in quite a few professional journals these past
few years ie. we have passed through many critical 'negative selection
gates' in science and as yet we have not been refuted by the professionals
in the field. Our most recent definitive paper which closely approximates
and underpins the book is:
Blanden RV, Rothenfluh HS, Zylstra P, Weiller GF
& Steele EJ 1998 The signature of somatic hypermutation appears to be
written into the germline IgV segment repertoire.
Immunological Reviews 162 : 117 - 132.
Publication here is by invitation only and is thus an
indicator of how the professional circle in this area of molecular
immunology (somatic hypermutation) view the plausibility of our work thus far.
I will sign off by bringing your attention to a a very important recent
development. Some direct independent proof of the reverse trancriptase
process in somatic hypermutation of antibody-related genes ( the genes that
encode the T cell receptor) has just been published in the Journal of
Immunology (Jan 15 1999) by A. Mellor's group at the Medical College of
Georgia, in Augusta, Georgia. An Abtstract of the paper is pasted below. ¶
It seems (as we have always suspected) that evidence like this would emerge
in the most unlikely of situations - and that is what appears to have
happened; in T cells, in vitro not in vivo ( note that for a couple of
years there has been evidence that T cell receptor V genes can hypermutate
in certain situations; and we predicted in 1993 that T cell receptor genes
should in fact hypermutate).
Their key concluding statement is : " Evidence is presented for the
presence of cDNA reverse transcripts of the TCR alpha-chain within the
hybridoma, suggesting a role for reverse transcriptase in the generation of
mutations."
We have read the paper carefully and cannot fault it. This represents
independent confirmation by a group of molecular immunologists new to the
somatic hypermutation field. They stumbled across the phenomemon by
accident, then described it meticulously.
So I hope I have commented on most of the relevant points in your book
review. Feel free to use any of this response in future e-mail
communications with other correspondents or on your Website.
Thanks again for contacting us and reviewing "Lamarck's Signature".
Ted Steele
Dr. Edward J Steele
Associate Professor
Department of Biological Sciences
University of Wollongong
Northfields Avenue
Wollongong NSW 2522
AUSTRALIA
Phone No. 61 (0)2 42 213434
Fax No. 61 (0)2 42 214 135
E-mail Address Ted_Steele@uow.edu.au
Copy :
Robert V Blanden ( Robert.Blanden@anu.edu.au )
Robyn A. Lindley ( Robyn_Lindley@uow.edu.au )
footnotes
¶ The full Abstract of that paper is :
Journal of Immunology 1999 Jan 15;162(2):871-7
Alternative splicing and hypermutation of a nonproductively rearranged TCR
alpha-chain in a T cell hybridoma.
Marshall B, Schulz R, Zhou M, Mellor A
Institute of Molecular Medicine and Genetics, Program in Molecular Immunology,
Medical College of Georgia, Augusta 30912-3175, USA. marshall@immag.mcg.edu
[Medline record in process]
Like Ig genes, TCR genes are formed by somatic rearrangements of noncontiguous
genomic V, J, and C regions. Unlike Ig genes, somatic hypermutation of TCR V
regions is an infrequent event. We describe the occurrence of spontaneous
hypermutation in a nonproductively rearranged TCR alpha-chain gene in a clonal
T cell hybridoma that had lost its productively rearranged alpha-chain. The
mutating hybridoma was eventually supplanted in culture by a nonmutating
variant that had restored an open reading frame in the nonproductively
rearranged TCR alpha-chain through the use of cryptic splice sites in the V
alpha region. Evidence is presented for the presence of cDNA reverse
transcripts of the TCR alpha-chain within the hybridoma, suggesting a role for
reverse transcriptase in the generation of mutations.
PMID: 9916710, UI: 99113748
Other footnotes are
*In general :
- a] they display a significant deficit of stop codons and point
mutation-generated pseudogenes below numbers expected from random point
mutation;
- b] codon-by-codon analysis of the V coding segments shows an excess of
amino acid replacement changes in the "antigen contact" CDR regions yet
amino acid silent changes in framework (FW) regions;
- c] the highly non-random distribution and type of insertion deletion
events - within coding regions there are insertions or deletions of triplet
codons or multiples therepf ( which preserve the translational reading
frame, even in chicken pseudogenes) and in the flanking non-coding regions
there are variable length insertions and deletions clustered around the
transcription start site, within the leader (L-V) intron and immediately
downstream of the 3' (righthand) edge of the V coding segment;
- d] heavy chain V chicken pseudogenes contain 3' (righthand end) terminii
with pieces of D sequence, all in the preferred reading frame and the 3'
ends of both the H and L chain V pseudogenes show evidence of nucleotide
additions and trimmings diagnostic of somatic V(D)J rearrangement ( thus
implying the reverse transcription-coupled soma-to-germline flow of genetic
information, a conclusion reached independently of us by the molecular
evolutionist M. Nei and his group (Ota T & Nei M 1995 Evolution of
immunoglobulin VH pseudogenes in chickens, Mol. Biol Evol 12 : 94-1002; this
is cross referenced in: Rothenfluh HS, Blanden RV & Steele EJ 1995
Evolution of V genes : DNA sequence structure of functional germline genes
and pseudogenes Immunogenetics 42 : 159-171);
- e] dendrogram analysis of 5' flanking sequences compared with the
transcription unit or V coding region segments indicates that the flanking
and coding regions are evolving indepently ( implying hyper recombination
events targetted to transcription/V coding units);
- f] recombination
analysis using the Phylogenetic Profiles algorithm ( also called the
Weiller Algorithm after Georg Weiller who developed it) within familes of
mouse (VH186.2-related) and human (Vk) germline V segments shows that major
sites of recombination coincide with the borders of the L-V intron, the
transcription start site and the 3' end of the V segment ( logically
deduced and interpreted as the predicted homologous recombination events of
soma-to-germline integration predicted by the particular species of V(D)J
retrotranscripts generated (say) by the hypothesised reverse
transcriptase-coupled somatic hypermutation process)**
** See recent J. Immunol paper by Marshall et al, above¶
Return-Path: Ted_Steele@uow.edu.au
Date: Fri, 12 Mar 1999 11:40:16 +1100 (EST)
X-Sender: ejsteele@sci-pop.uow.edu.au
To: Gert Korthof
From: Ted Steele Ted_Steele@uow.edu.au
Subject: Addendum
Dear Gert :
Can I make an Addendum to what I sent you yesterday. I overlooked your
reference 5*) - a good point because you only ask this question(s) if you
have really understood the modus operandi of the immune system.
We think the evolutionary value is in "genetic housekeeping" as we outline
on page 185 of "Lamarck's Signature" ie. maintenance of a functional V
repertoire (irrespective of specific V sequences) over evolutionary
time.
Best regards
Ted
These email comments reference my review version 2.2. In version 3.0 corrections are added.
*) Reference 5 is now included in the text: 'the philosophy of the immune system is
"to prepare for the unknown".' [gk]
"The Independent" newspaper (London, UK) Saturday May 8 1999 "Comment" page
Genetic Notes - Embarrassment of the neo-Darwinists
by Edward J. Steele, Robyn A. Lindley and Robert V. Blanden
Fifty years before Charles
Darwin's seminal Origin of Species the French
biologist Jean Baptiste de Lamarck published his view on how animals
evolved. A core idea , uniformly accepted by his peers, was that organisms
adapting to a changing environment altered their bodily and behavioural
characteristics and passed these acquired characteristics to their progeny.
This is Lamarckian inheritance and is probably one of the most emotive
issues in contemporary science (apart from the metaphysical issue of
whether an all-powerful "God" exists).
Historical ironies abound. Both Charles Darwin and his grandfather Erasmus
accepted Lamarckian modes of inheritance. The notion is overt in all of
Charles Darwin's evolutionary analyses. Thus in 1868 he published his
theory "Pangenesis" to explain the origin of genetic variations in nature
because his evolution theory assumed the pre-existence of such genetic
variation in populations of plants and animals, which are then subjected to
natural selection to sort out the parents for the next generation - a
process which the philosopher Herbert Spencer coined the term "survival of
the fittest". Therefore Darwin considered that, during a somatic, or
bodily, change necessary for a particular adaptation, the body cells of the
excited target organ would emit genetic material or "gemmules" (also termed
"pangenes") which were considered to be minute representations of each
normal or altered bodily component. These were discharged from the active
organ into the bloodstream , thus allowing them to enter the germ cells
(eggs and sperm) and be genetically transmitted to the next generation.
Darwin's late-19th-century and 20th-century followers, the neo-Darwinists,
have been particularly embarrassed by his genetic speculations and have,
where possible, expunged them from the scientific record. Lamarck's
contribution to modern genetics has been demonised; many interesting
acquired inheritance phenomena have been suppressed.
It began in earnest in 1885 when August Weismann erected his now famous
conceptual barrier protecting germ cells from any genetic changes within
the soma or body of the organism and thus forbidding any form of acquired
inheritance. Despite the intellectual efforts of heavy weight critics such
as Arthur Koestler and Sir Fred Hoyle, neo-Darwinism sustained by
Weismann's genetic chastity belt has reigned supreme throughout the 20th
Century, a development which would have mystified if not horrified Darwin.
We have all been witnesses therefore to the triumph of the "Darwinian
dogma", that evolution proceeds only by the natural selection of chance
events. In this century we have the tragic story of the Austrian biologist
Paul Kammerer wonderfully told by Arthur Koestler in his 1971 book The Case
of the Mid-Wife Toad and then the bizarre aberration of the so-called
Lamarckian theory promulgated by Joseph Stalin's head of Soviet agriculture
T.D. Lysenko (who, in the course of a ruinous 30 year career destroyed
Soviet agriculture, biology and genetics).
So at the end of a turbulent and violent century neo-Darwinism apparently
remains impregnable - much like Communism just prior to its dramatic
implosion. Are neo-Darwinism and Weismannism, which reached their zenith
during the Cold War, on the verge of a similar collapse?
We have marshalled and analysed the available molecular evidence on the
functioning and evolution of the antibody genes of the immune system in a
new book. Without a Lamarckian soma-to-germline gene feedback process it
is difficult , if not impossible, to explain a large number of striking
features of the DNA sequence structure of these genes. The challenge is for
those other scientists, who really understand these data , viz. molecular
immunologists, to come up with a better scientific explanation .We don't
think there is one - outside of course those non-scientific propositions
evoking an "intelligent gene manipulator" or, if you will a " divine
intervener" as playing a role in evolution.
Edward J Steele, Robyn A Lindley and Robert V Blanden are the authors of
'Lamarck's Signature : How retrogenes are changing Darwin's natural
selection paradigm ' ( Allen & Unwin).
|
From: John.Hoyland@rbi.co.uk
Mime-Version: 1.0
Date: Wed, 19 May 1999 11:46:21 +0100
Subject: Re: Letter Steele,Lindley & Blanden?
To: Ted Steele <Ted_Steele@uow.edu.au>
Cc: Maggie.McDonald@rbi.co.uk
Status:
Thanks for your message. I'm afraid my advice was not to run your
letter.
Yours sincerely, John Hoyland (Letters)
______________________________ Reply Separator
Subject: Letter Steele,Lindley & Blanden?
Author: Ted Steele <Ted_Steele@uow.edu.au> at INTERNET
Date: 19/05/99 09:49
Dear Sir/Madam::
On or about April 22 we submitted the letter below via your Sydney
(Australia) office (via e-mail). We have noted that as the May 15 issue of
New Scientist the letter has not been published and we were wondering if a
decision "yes" or "no" has been made by your office to publish our letter.
We would greatly appreciate a response as soon as you are able.
Thanking you
Dr. EJ Steele
LETTER TO EDITOR, NEW SCIENTIST - submitted 22.4.99
Dear Sir,
The review of our book "Lamarck's Signature" by Laurence D. Hurst,
New Scientist, April 17, 1999, PP 60-61, entitled "Cut off their tails" is
a mixture of ignorance and misrepresentation. As far as we are aware,
no-one in our discipline area (Molecular Immunology) has commented like
Hurst, possibly because they don't have a viable alternative explanation
for the mass of data published in the scientific literature that we have
used to underpin the discussions in our book. Furthermore, since
publication of the book, cDNA intermediates predicted by our reverse
transcriptase model of somatic hypermutation of immunoglobulin and T cell
receptor genes have been found by Marshall et al (Journal of Immunology,
1999, 162:871-877), adding further weight to our analysis. If Hurst had
read and understood the references cited in the book he may not have
written such an ignorant review. Finally we must confess our astonishment
at Hurst's obsession with the amputation of rat's tails. His notion that
we should have seriously considered the possibility that rats might
deliberately bite their tails off is truly astounding. We are not aware of
any record of spontaneous self-mutilation by animals. It seems that only
humans indulge in such things, both physically and mentally.
Yours sincerely
E. J. Steele, R. A. Lindley (Wollongong University)
and R. V. Blanden (Australian National University)
Communicating author:
Dr. EJ Steele
Associate Professor
Department of Biological Sciences
University of Wollongong
Northfields Avenue
Wollongong NSW 2522
AUSTRALIA
Phone No. 61 (0)2 42 213434
Fax No. 61 (0)2 42 214 135
e-mails : Ted_Steele@uow.edu.au
& coauthors : Robert.Blanden@anu.edu.au,
Robyn_Lindley@uow.edu.au
Date: Mon, 26 Feb 2001 09:33:58 +1100
To: Gert Korthof
From: Ted Steele ejsteele@uow.edu.au
Subject: Re:Changed URL
Dear Gert :
My first book should have been cited and/or either one of two experimental
papers I published with Gorczynski.(see below)
- Steele, E.J. Somatic Selection and Adaptive Evolution : On the Inheritance of Acquired Characters. First Edition. Williams-Wallace, Toronto, 1979: Croom-Helm, London, 1980.2nd Edition. Revised with an author's Postscript , University of Chicago Press, Chicago, 1981.
- Gorczynski, R.M. and E.J. Steele (1980). Inheritance of acquired immunologic tolerance to foreign histocompatibility antigens in mice. Proc. Natl. Acad. Sci. (USA)77: 2871-2875.( Communicated by Howard M. Temin).
- Gorczynski, R.M. and E.J. Steele (1981). Simultaneous yet independent inheritance of somatically acquired tolerance to two distinct H-2 antigenic haplotype determinants in mice. Nature 289: 678-681.
However these events occurred a long time ago. Those who know the field
are aware of the priority - it is cited in many of my publications, and in
letters published by me and colleagues during and after a
plagiarism/priority dispute with Prof John Cairns in the late 1980s
(references to these letters are also pasted below) which was followed by a
News & Views in Nature by Howard Temin(1989) (see ref on
pages 193-196 and page 270 of "Lamarck's Signature" ).
- Steele, E. J. (1989) Immunol. Cell Biol. 67 : 151-152 and the letter by
Blanden RV, Fenner, F, Both GW, Reed K and Rolfe BJ published along side it
in the same issue.
- Steele , E.J. (1989) Mechanism of directional mutations ? Molec. Reprod. Develop. 1 : 231-232.
- Howard Temin (1989) "Retrons in Bacteria", Nature 339: 254-255.
- Steele, E. J. and J. Cairns (1989) Dispute resolved. Nature 340 : 336.
I will try to get to that issue of Nature - but it seems to me it does not
add anything new to what we have known for over 20 years now on generalised
reverse transcription - there is a lot of unbelievable American hype and
rubbish being published right now on the human genome. To get an accurate
picture of the important microvariability you would need to sequence
thousands of human genomes (clearly impossible). The important job is to
interpret what we have against a back drop of biological principles that
have been, and are, being discovered on a smaller scale.
Thanks again.
Ted
Dr. EJ Steele
Associate Professor
Molecular Immunology & Evolution Laboratory
Department of Biological Sciences
University of Wollongong
Northfields Avenue
Wollongong NSW 2522
AUSTRALIA
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