Life will find a way

Creationists sometimes try to argue that what we consider straightforward, well-demonstrated cytological and genetic events don't and can't occur: that you can't get chromosome rearrangements, or that variations in chromosome number and organization are obstacles to evolution, making discussions of synteny, or the rearrangement of chromosomal material in evolution, an impossibility. These are absurd conclusions, of course—we see evidence of chromosomal variation in people all the time.

For example, A friend sent along (yes, Virginia, there is a secret network of evilutionists busily sharing information with one another) a remarkable case study of a radical chromosome arrangement in a mother and daughter. When you see how these chromosomes are scrambled, you'll wonder how they ever managed to sort themselves out meiotically to produce viable offspring…but life will find a way.

First, here's a partial karyotype to show the affected chromosomes 6, 9, 11, and 20. These are four pairs of chromosomes, and in a normal karyotype, each member of the pair should be basically identical to the other; here you can see that they're of different lengths, and even the pattern of bands shows some variations that are difficult to make out.

(a, b) Partial high-resolution GBG-banded karyotypes showing the rearranged chromosomes 6, 9, 11 and 20 of mother (a) and daughter (b).

After a fair amount of work, the investigators sorted out what was wrong. There were 12 breakpoints in these four chromosomes, and the fragments had been scrambled about to form these rearranged chromosomes, color-coded to help sort out who is who.

Summary of all breakpoints after completion of all mapping efforts. The chromosome fragments are drawn to scale.

This is amazing stuff. This is what cells do, though: when chromosomes are damaged, there are repair enzymes that struggle to put them back together. These enzymes are not smart or guided in any way, so they just do the best job they can…and sometimes that means they are reassembled so they can function, but it may not be the usual order of things.

Now the mother in this pair had the above arrangement of chromosome bits. The father's chromosome set was normal (as was that of the woman's parents), except that he did have a small deletion (again, these kinds of minor variations in chromosomes are common). In meiosis, when the woman produces haploid eggs, one step requires that chromosomes pair up—both orange chromosomes line up together, as do both blue ones, both green ones, and both yellow ones. Then they separate in an orderly fashion to guarantee that each egg receives exactly one orange chromosome, one blue, one green, and one yellow.

Umm, wait a minute…both orange chromosomes? In this woman, the orange chromosome is scattered in fragments across four chromosomes. How could this woman's cells arrange and sort out their contents in a well-distributed way?

Well, one way is for the chromosomes to contort themselves into strange yoga positions that allow most of the color-coded bits to pair up appropriately. Here, for example, is the most likely solution that allows the majority of the chromosomal homologs to pair up in meiosis. That's impressive.

(bâd) Putative pachytene configurations in meiosis. (b) One
possible pachytene configuration could consist of two tetravalents.

Even more impressive is a truly maximal pairing that allows all of the homologous portions to be in register, a structure called an octavalent that brings all 4 pairs of chromosomes together in a very specific tangle. This is an optimal arrangement for pairing, but is less likely to have occurred simply because getting that many chromosomes into an ideal arrangement is difficult.

(c) Possible octavalent pachytene figure allowing more regions to
synapse. (d) An alternative octavalent figure allowing even more
regions to synapse.

The real test of whether this can happen, of course, is that the woman successfully reproduced. It was difficult, and she had three miscarriages first—probably a result of occasions when her chromosomes did not sort out properly, and so her egg had an unbalanced arrangement—but on the fourth try she had a healthy daughter. The daughter had some developmental abnormalities, developmental delays, some retardation (although she did graduate from school), and later was diagnosed with diabetes. These problems are not a direct consequence of the chromosome arrangement, however, since the mother had the same arrangement without the developmental problems. Both mother and daughter shared one unusual trait, the prolonged expression of fetal hemoglobin, which could be correlated with one of the breakpoints.

This is an extreme example of a scrambled chromosome; lesser variations, like single translocations or fusions, are far less problematic.

Fauth C, Gribble SM, Porter KM, Codina-Pascual M, Ng BL, Kraus J, Uhrig S, Leifheit J, Haaf T, Fiegler H, Carter NP, Speicher MR (2006) Micro-array analyses decipher exceptional complex familial chromosomal rearrangement.
Hum Genet 119(1-2):145-53.


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Thank you for this. I've been on the lookout for a good example of chromosomal rearrangement that I could share for a quite a while. The public needs to see how pliable the evolutionary mechanisms can be.
Thanks again.

Ah -- rearrangements! Interesting topic.

You may be interested in the following articles that I have organized in chronological order, beginning with the most recent. Every non-technical or semi-technical article is paired with corresponding technical articles written by the same researchers describing the research which was the basis for the non-technical articles.

These deal principally with genomic rearrangement, including:

1. the genomic differences in genomic structure which naturally exist in the human population and are not disadvantageous (in which similar differences of genomic structure within the populations of other species has undoubtedly facilitate adaptation and speciation during throughout the history of the evolution of life);
2. the causes of genomic rearrangement in terms of alternate DNA structures (Z-DNA and H-DNA) which place stress on the genome and result in breakages at specific points;
3. diseases (particularly cancer) which may result from such breakages;
4. the manner in which genomic rearrangement resulted in the mammalian radiation approximately 60 MYA;
5. the origins of this rearrangement and gene duplication potential in primarily in retrotransposons which are relics of retroviral infections over the past 150 MYA;
6. the apparent role of one class of retrotransposons (Type III LTR) in the regulation and orchestration of gene expression during embryonic development.

The last of these suggests that the evolution of life in eukaryotes and the pace at which it took place has been significantly influenced by the the endogenization of retroviruses and subsequent co-adaption of retroelements to the host genome in which at least one class of retroelements (the Type III LTR retrotransposons) regulatory roles in gene expression. One indication of the significance of this lies in the fact that while genes which are transcribed into proteins constitute only 1.5 percent of the human genome, Type III LTR retrotransposons (much of which may play a fairly significant role in the regulation of gene expression) constitute 30 percent.

All but one technical article ("Patchwork People" in "Nature") is accessible without subscription.


Chromosome rearrangements not as random as believed
Genetic predisposition may raise risk of rare disabling syndrome
Public release date: 16-Feb-2006

A palindrome-mediated mechanism distinguishes translocations involving
LCR-B of chromosome 22q11.2
Anthony L. Gotter, Tamim H. Shaikh, Marcia L. Budarf, C. Harker Rhodes
and Beverly S. Emanuel
Human Molecular Genetics, 2004, Vol. 13, No. 1 103-115

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

When Good DNA Goes Bad
Article Date: 15 Feb 2006 - 1:00am (UK)

Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells
Guliang Wang, and Karen M. Vasquez
Published online before print September 1, 2004, 10.1073/pnas.0405116101
PNAS | September 14, 2004 | vol. 101 | no. 37 | 13448-13453

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

Comparative chromosome study finds breakage trends, cancer ties
Article Date: 23 Jul 2005 - 0:00am (UK)

Insight Into DNA's 'Weakest Links' May Yield Clues To Cancer Biology
Posted: March 24, 2005

Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies
Comparative Maps
William J. Murphy,Denis M. Larkin,
Annelie Everts-van der Wind, Guillaume Bourque, Glenn Tesler,
Loretta Auvil, Jonathan E. Beever, Bhanu P. Chowdhary,
Francis Galibert, Lisa Gatzke, Christophe Hitte,
Stacey N. Meyers, Denis Milan, Elaine A. Ostrander, Greg Pape,
Heidi G. Parker, Terje Raudsepp, Margarita B. Rogatcheva,
Lawrence B. Schook, Loren C. Skow, Michael Welge,
James E. Womack, Stephen J. O'Brien,
Pavel A. Pevzner, Harris A. Lewin.
22 February 2005; accepted 1 June 2005,%202005%20…

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

'Junk' DNA May Be Very Valuable To Embryos
Posted: October 12, 2004

Retrotransposons Regulate Host Genes in Mouse Oocytes and
Preimplantation Embryos
Anne E. Peaston, Alexei V. Evsikov,
Joel H. Graber,1 Wilhelmine N. de Vries,
Andrea E. Holbrook, Davor Solter,
and Barbara B. Knowles
Developmental Cell, Vol. 7, 597606, October, 2004, Copyright 2004 by Cell Press…

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability
Versus Speciation
Shaying Zhao, Jyoti Shetty, Lihua Hou, Arthur Delcher, Baoli Zhu,
Kazutoyo Osoegawa, Pieter de Jong, William C. Nierman, Robert L.
Strausberg and Claire M. Fraser
Genome Research 14:1851-1860, 2004

Reconstructing large regions of an ancestral mammalian genome in silico
Mathieu Blanchette1, Eric D. Green, Webb Miller and David Haussler
Genome Research 14:2412-2423, 2004

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

Some 400 'Fragile Regions' Of Genome More Vulnerable To Evolutionary Breaks
New Theory Could Have Implications For Cancer Research
Posted: June 18, 2003

Genome Rearrangements in Mammalian Evolution: Lessons From Human and
Mouse Genomes
Pavel Pevzner and Glenn Tesler
Genome Research
Vol 13, Issue 1, 37-45, January 2003

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

"Jumping Genes" Create Ripples In The Genome - And Perhaps Species' Evolution
Posted: August 16, 2002

Human L1 Retrotransposition Is Associated with Genetic Instability In Vivo
David E. Symer, Carla Connelly, Suzanne T. Szak, Emerita M. Caputo,
Gregory J. Cost, Giovanni Parmigiani, and Jef D. Boeke
Cell, Vol 110, 327-338, 9 August 2002

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

(Said in teh manner of a clinching argument):

"But they're still humans!!

By Andy Groves (not verified) on 28 Feb 2006 #permalink

"Vary-a-shuns with-in ah ky-nd" say it in Southern Baptist just once for me...

By Jeffery Keown (not verified) on 28 Feb 2006 #permalink

I find these particular creationist arguments to be especially curious ("Mutations have NEVER produced additional DNA structures..." "The lightning in the early earth environment would more likely KILL the cute little amino acid than form it.." "It TAKES MORE FAITH to believe in evolution than creationism..." etc., ad nauseum). Their originators seem to think that matter sits around, waiting to be acted upon, and has to be cajoled, as it were, to interact--as if matter were a sulky teen-ager dawdling at the task of cleaning up his bedroom and must be yelled at 15 times by his father before he does it.

Perhaps there is a kernel of truth among the layers of BS in the argument that observing evolution involves more faith than does clinging to creationism, since it is the scientific mind that honors the awesome powers of matter, whereas the religious mind assumes matter merely to be--well, immaterial, unimportant, and impotent in itself. Religion seems to assume a pessimistic view of nature in the first place--and this, I've never understood. I shall never understand it.

Here are a few more articles related to rearrangements. In particular, in smaller populations, rearrangements may be more common which are slightly deleterious to the population, but which later become stablized through additional mutations and act as a positive, creative force in evolution.

Mutations, Population Size, and Near-Neutral Evolution

Fishing for the Origins of Genome Complexity
Deciphering a paradox of evolution( non-techical)
December 15, 2005

Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution
Adam Eyre-Walker, Peter D. Keightley, Nick G. C. Smith, and Daniel Gaffney
Mol. Biol. Evol. 19(12):2142?2149. 2002

The Origins of Genome Complexity
Michael Lynch and John S. Conery SCIENCE VOL 302 21 NOVEMBER 2003

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

In a previous post (currently on hold for approval) I listed a few articles on how retrotranspositions and rearrangements may be tolerated in smaller populations. In what follows, I have a couple more articles which may be of interest...

The view that genomic complexity is inversely related to population size is largely an outgrowth of the near-neutral theory of molecular evolution put forward by Tomoko Ohta, a student of Motoo Kimura, the originator of the neutral theory of evolution. While Kimura's theory is no longer considered a viable theory, it still provides a theoretical basis for the molecular clock and the null hypothesis through which we test for selection as opposed to mere drift. To learn more about Ohta's near neutral theory, you may wish to see her article:

Near-neutrality in evolution of genes and gene regulation
Tomoko Ohta
PNAS | December 10, 2002 | vol. 99 | no. 25 | 16134-16137…

I tend to focus on on combinatorial regulation, particularly as it is closely related to one of my interests -- how viruses in general and retroviruses in particular are an important engine in the evoluition of eukaryotic life. However, this should be balanced with a recognition of the importance of downstream regulation, particularly in terms of the evolutionary change in introns. You may want to check:

Intron evolution as a population-genetic process
(exon shuffling|genome complexity|genome evolution)
Michael Lynch

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

That was really amazing! Thanks. I was struggling a bit at first (a lot of technical terms that weren't in my ken) but when the coloured diagrams appeared it all became very clear.

I'd never really understood before what things go wrong to cause a miscarriage. That was very informative, and helped to slide a few more things into place.

I don't really know cos I didn't take high school biology, but is this kind of thing ever covered at that stage? I don't necessarily mean in as much technical detail, but the diagrams and the concepts are still comprehendible.

Fascinating posting, I'm passing it on to my biologist housemate who will no doubt demonstrate that i don't understand it at all.

One little request though, is it by any chance possible to have diagrams that are clickable for enlargements? or even just gif/png compression on the flat colour diagrams? it would make the annotations a little easier to read for those of us on high resolutions.


I hope that no one minds the links. I figure they are relevant enough, though, and will provide some interesting additional reading.

However, back to the paper, in humans, chromosomal anomalies occur in roughly 6 out of 1000 births. Approximately half of these are not clinically significant. In smaller populations, they more easily become widespread simply as the result of genetic drift. In anycase, when they are not clinically significant, they may be regarded as a kind of genomic polymorphism which nevertheless results plasticity and contributes to the evolvability of the species. Even when the chromosomal anomalies are initially slightly deleterious, if the species is fragmented into smaller populations, this would undoubtedly be a significant causal factor in allopatric speciation.

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

Nice. Going into a bookmark file for my anthro friend who also has a strong interest in evolutionary science (yes, those nasty cultural anthropologist who are always asking uncomfortable questions about your studies often get _some_ grounding in biology).

It was groovy trying to remember how meiosis works.

WOW. Never mind meiosis, how does this woman manage mitosis without major problems? Her cells must be replete with aneuploidy... I'm completely thrown.

In mitosis the rearranged chromosomes only pair with copies of themselves after S phase. Why do you think there'd be a problem?

Funny, I somehow expected the Wagnerian Inquisition to make an appearance here. I'm sure Larsson will point out that my expectation of the Wagnerian Inquisition was just the problem.

Maybe the journal linking spree up there scared the little tyke off.

Dustin wrote:

Funny, I somehow expected the Wagnerian Inquisition to make an appearance here. I'm sure Larsson will point out that my expectation of the Wagnerian Inquisition was just the problem.

His chief weapon is stupidity
... and the drool dripping from his chin.

His two chief weapons are stupidity, the drool dripping from his chin
... and the overwhelming, nauseating bordom which he induces in his enemy.

His three chiefs weapons are...

By Timothy Chase (not verified) on 28 Feb 2006 #permalink

Very rarely, someone will wind up with a damaged Y chromosome so they turn out female instead of male despite being XY. Even more rarely, they'll retain some fertility.

There's at least one known example of a girl who inherited her X chromosome from Dad and her Y chromosome from Mum.

By Peter Ellis (not verified) on 28 Feb 2006 #permalink

Dustin, Timothy,

LOL! You made my day a good one. Even if I too expect the Wagnerian Inquisition, always...

By Torbjorn Larsson (not verified) on 01 Mar 2006 #permalink

Timothy- what a great collection of links. Thank you very much.

By Steve LaBonne (not verified) on 01 Mar 2006 #permalink

Torbjorn Larsson wrote:

Dustin, Timothy,

LOL! You made my day a good one. Even if I too expect the Wagnerian Inquisition, always...

The truly inspired idea was Dustin's. I just added to it a little in the way of a response.

Incidentally, Kent Hovind inspired a non-technical piece Thoughts on the Intelligent Design Inference a while back. Currently, I am working up to being able to write something semi-technical. Gathering information, organizing notes.

And oddly enough, the Wagnerian opera/comedy(?) which we keep getting treated to (does seem a bit ad lib for an opera -- doesn't it?) has given me the inspiration for a semi-technical piece which might be something I could write at this point. Not sure how much the fellow who inspired it will be able to follow -- may be a wee bit over his head if I manage to get it done...

By Timothy Chase (not verified) on 01 Mar 2006 #permalink

PZ --

I personally didn't know specifically about the enzymes which are responsible for piecing back together the fragments of chromosomes. Essentially, what I had thought was simply that there exist transposons which are responsible for breaking chromosomes up, or at least for removing pieces of them, then integrating them into other chromosomes. Likewise, there are also retrotransposons which duplicate and then integrate segments into different places in the same chromosome or into other chromosomes.

Although there is very little information (from what I have been able to gather so far), a likely origin for transposons appears to be infection by DNA viruses. However, there appears to be a great deal of evidence that retroelements have their origin in the endogenization of retroviruses. For example, retrotransposons are more or less simply the proviral form of retroviruses which have lost their envelope gene.

Now I realize, for example, that the enzyme telomerase (which exists on chromosome 5 in humans) is responsible for the lengthening of telomeres which is essential for meiosis. Moreover, the enzyme telomerase is essentially functionally homologous to reverse transcriptase and the template for a telomere. Moreover, in at least one species of eukaryote (drosophila, I believe) there is considerable structural homology between the reverse transcriptase found in some species of retrovirii and the telomerase employed by this eukaryote.

Given this, I was wondering whether the enzymes responsible for reconstituting the chromosomes after breakages (due to weaknesses in Z/H-DNA, etc.) are at least functionally homologous to either the enzymes of DNA viruses, or to the integrase of retroviruses? Are there significant differences between the integration enzymes from one species to another, such that some of these enzymes may have originated in DNA viruses, whereas others are far more likely to have arisen in retroviruses?

By Timothy Chase (not verified) on 01 Mar 2006 #permalink

Steve LaBonne wrote:

Timothy- what a great collection of links. Thank you very much.

No problem. Just trying to piece things together for myself, and maybe at some later point an article. What these sources would be for however is a little beyond my current level of understanding, but they might help others, and they did seem relevant.

Part of what is slowing me down right now is the lack of the appropriate writing environment. I had created something a while back, a program I called BrainStorm. It was on a Mac. It wound up helping me organize over two thousand pages of material -- on a different subject. Currently I am working on recreating it on a PC, this time written in C-Sharp, only bigger, badder. It is now to the point that I can begin to use it for organizing my notes (hierarchically, with cross-referencing within a dynamic structure) and structuring larger papers. When the program is sufficiently polished, I will make it available for free. Might help others with their personal studies, learning and more.

By Timothy Chase (not verified) on 01 Mar 2006 #permalink

"The truly inspired idea was Dustin's. I just added to it a little in the way of a response."

Yes. But I'm a simple mind, so I enjoyed both. And as is abundantly clear, it started in a similar vein, was a ripoff, and dumbed down to fit the reduced bandwith of the web. (The original sketch contrasts dialog and action.)

Crackpots are fascinating in their odd behaviour, and I see I'm not the only one who sometimes get stimulated by them. Unfortunately for them, the stimulation isn't quite as they envision...

By Torbjorn Larsson (not verified) on 01 Mar 2006 #permalink

An Alternative to Reverse Transcriptase in Drosophilia

Since I mentioned the fact that telomerase includes a reverse trascriptase a little earlier on, I thought people might be interested in these two articles regarding an interesting alternative to the usual telomerase/telomere system employed by most multicellular organisms -- in the drosophilia. (It involves two retrotransposons. PZ might have mentioned it at some point, but even then it is worth mentioning as some might have missed it.)

TAHRE, a Novel Telomeric Retrotransposon from Drosophila melanogaster, Reveals the Origin of Drosophila Telomeres
José . Abad, Beatriz de Pablos, Kazutoyo Osoegawa, Pieter J. de Jong, Antonia Mart�Gallardo and Alfredo Villasante
Mol. Biol. Evol. 21(9):1620-1624. 2004

Annual Review of Genetics
Vol. 37: 485-511 (Volume publication date December 2003)
First published online as a Review in Advance on August 6, 2003
Mary-Lou Pardue and ?P.G. DeBaryshe?…

By Timothy Chase (not verified) on 02 Mar 2006 #permalink

As for the reverse transcriptase in most eukaryotic telomerase complexes, you may wish to check:

Telomeres and telomerase
Elizabeth H. Blackburn
UC San Francisco
University of California
Year 2004 Paper 366…

The telomerase reverse transcriptase: components and regulation
Genes and Development
Vol. 12, No. 8, pp. 1073-1085, April 15, 1998
Constance I. Nugent, and Victoria Lundblad

By Timothy Chase (not verified) on 02 Mar 2006 #permalink

This may also be of interest:

Reversing Time: Origin of Telomerase
Cell, Vol. 92, 587-590, March 6, 1998
Toru M. Nakamura and Thomas R. Cech
Howard Hughes Medical Institute
Department of Chemistry and Biochemistry
University of Colorado
Boulder, Colorado 80309-0215

By Timothy Chase (not verified) on 02 Mar 2006 #permalink

Timothy Chase: Any chance you'll release your new program as Open Source for us Linux & BSD weenies? And yeah, that's an awesome mass of data -- possibly enough for a textbook (hint, hint ;-) ).

By David Harmon (not verified) on 16 Mar 2006 #permalink

Fascinating! Thank you very much. I have often wondered how descendant species could have different numbers of chromosomes, since it would seemingly be a barrier to reproduction. Now I begin to understand. I knew there must be a solution, since it obviously happened. :-)