Tandem repeats and morphological variation

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bull terrier

All of us mammals have pretty much the same set of genes, yet obviously there have to be some significant differences to differentiate a man from a mouse. What we currently think is the major source of morphological diversity is in the cis regulatory regions; that is, stretches of DNA outside the actual coding region of the gene that are responsible for switching the gene on and off. We might all have hair, but where we differ is when and where mice and men grow it on their bodies, and that is under the control of these regulatory elements.

A new paper by Fondon and Garner suggests that there is another source of variation between individuals: tandem repeats. Tandem repeats are short lengths of DNA that are repeated multiple times within a gene, anywhere from a handful of copies to more than a hundred. They are also called VNTRs, or variable number tandem repeats, because different individuals within a population may have different numbers of repeats. These VNTRs are relatively easy to detect with molecular tools, and we know that populations (humans included) may carry a large reservoir of different numbers of repeats, but what exactly the differences do has never been clear. One person might carry 3 tandem repeats in a particular gene, while her neighbor might bear 15, with no obvious differences between them that can be traced to that particular gene. So the question is what, if anything, does having a different number of tandem repeats do to an organism?

Continue reading "Tandem repeats and morphological variation" (on Pharyngula)

23 Comments

Before someone else says it: “That’s just more evidence for design in nature.”

Reed, If you want some *real* evidence for design, check this out:

Science, Vol 306, Issue 5705, 2202-2203 , 24 December 2004

Danielle A. Garsin*

Bacteria are not isolated solitary organisms, but actively “speak” to one another by sending and receiving transmissions in the form of chemical signals. In a process called “quorum sensing,” bacteria measure the concentration of these signaling molecules in order to assess the size of the bacterial population. Once a “quorum” is reached, certain biological programs–such as sporulation, or the production of light, biofilms or virulence factors, depending on the species and context–are activated synchronously throughout the population. There are also examples where the chemical transmissions of one species can be detected by another, suggesting that these signals may be used for intraspecies as well as interspecies communication. Coburn et al. (Science, Vol 306, Issue 5705, 2270-2272 , 24 December 2004) reveal a remarkable example of a bacterial quorum-sensing molecule that is used not only for bacterial communication but also for direct detection of eukaryotic target cells.

How long are you guys going to keep turning a deaf ear to what is before your very eyes?

Charlie Wagner http://enigma.charliewagner.com

charlie:

While that’s very interesting material, and also quite excellent evidence for design, it is no superior to everything else ever noticed by anyone, all of which is equally excellent evidence for design.

How long are you guys going to keep turning a deaf ear to what is before your very eyes?

I don’t know what you mean.

But I do know that quorum sensing is not a new idea in microbiology. So I’m not sure why you’re so pumped about it.

Perhaps you’d like to email Dr. Zusman at UC Berkeley and ask him whether this research is relevant to proving the existence of an all-powerful committee of aliens who once designed and created all of the life forms that existed and/or continue to exist on earth, as opposed to those life forms arising from some other process (e.g., evolution).

Dr. Zusman has been studying fruiting body formation in Mxyococcus xanthus for years. He has an excellent sense of humor, I can assure you.

http://mcb.berkeley.edu/faculty/BMB/zusmand.html

Be sure to let us know how he responds, Charlie!

“He has an excellent sense of humor, I can assure you.”

And he’s a bit of an odd fellow, as I recall.

You’ll note that if you look at the systems involved in quorum sensing, a lot of the parts look awfully similar to parts in other regulatory & sensing systems. Looks like recycling or co-option…

Social amoebas a.k.a. slime molds

Interesting critters for sure. These little guys have presumably been around since the dawn of time. They’re the fittest creatures to ever grace the planet then or now by any measure - in every environment imaginable, diversity, number, biomass - pick any fitness metric and they win it anytime anywhere. If life started from Adam & Eve, single celled organisms would’ve eventually evolved from them if mutation/selection is operational across phyla boundaries. If the earth exploded tomorrow they’d be the only survivors. If they weren’t already on the Moon and Mars they are now as well as on their way out of the solar system on Voyager. They’re in us, in the air we breathe, the water we drink, on the space station, etc. There’s just no escaping them.

Now, the interesting question. Since they’re inarguably the fittest, most highly evolved life on the planet, and they’ve been around billions of years longer than any multicellular forms of life, and they sometimes gather in colonies and communicate with each other to accomplish important things, did they develop some kind of colonial intelligence during those billions of years? Maybe they designed us as the ultimate armored transport vehicle - 100% recyclable since when we’re no longer able to provide them with protection and locomotion they eat us.

LOL!

There are more things in heaven and earth, Horatio, than are dreampt of in your philosophy.

How long are you guys going to keep turning a deaf ear to what is before your very eyes?

Synesthesia?

How long are you guys going to keep turning a deaf ear to what is before your very eyes?

Grrrr. Mixed metaphors really make my blood stand on end.

DaveScot:

Social amoebas a.k.a. slime molds

Interesting critters for sure. These little guys have presumably been around since the dawn of time. They’re the fittest creatures to ever grace the planet then or now by any measure - in every environment imaginable, diversity, number, biomass - pick any fitness metric and they win it anytime anywhere. If life started from Adam & Eve, single celled organisms would’ve eventually evolved from them if mutation/selection is operational across phyla boundaries. If the earth exploded tomorrow they’d be the only survivors. If they weren’t already on the Moon and Mars they are now as well as on their way out of the solar system on Voyager. They’re in us, in the air we breathe, the water we drink, on the space station, etc. There’s just no escaping them.

Now, the interesting question. Since they’re inarguably the fittest, most highly evolved life on the planet, and they’ve been around billions of years longer than any multicellular forms of life, and they sometimes gather in colonies and communicate with each other to accomplish important things, did they develop some kind of colonial intelligence during those billions of years? Maybe they designed us as the ultimate armored transport vehicle - 100% recyclable since when we’re no longer able to provide them with protection and locomotion they eat us.

LOL!

There are more things in heaven and earth, Horatio, than are dreampt of in your philosophy.

Quite possibly this is true. So what? This has nothing to do with evolution or your lack of understanding of the theory of evolution, I’m afraid.

After all, there are more species of beetles than anything on the planet: perhaps the earth was designed solely for beetles and we’re a biological mistake. After all, we’ve only been here for an eye-blink of time compared to, oh, say, cockroaches. Or sharks.

DaveScot Wrote:

Social amoebas a.k.a. slime molds

Interesting critters for sure.  These little guys have presumably been around since the dawn of time.  They’re the fittest creatures to ever grace the planet then or now by any measure - in every environment imaginable, diversity, number, biomass - pick any fitness metric and they win it anytime anywhere. 

Um no, they don’t. Bacteria have slime molds and everything else greatly outclassed in terms of diversity, biomass, etc. Maybe you’ve got them confused?

Slime molds can be amoeboid, bacterioid, or fungoid. Social amoeba demonstrate the same type of behavior in chemical signaling for group activities such as spore formation as bacterial and fungal colonies. I just like the common name “Social Amoeba” because everyone that ever looked at pond water in a microscope has seen a live amoeba and adding “social” to it is just too cute. Maybe I took a little literary license with it. So sue me. In any case, I meant single celled organisms with species that demonstrate colonial behaviors in the general sense. There’s an estimated 4 million (if memory serves) different species of single celled organisms (maybe it’s 40 million) with fewer than 1 in 10 of them observed or documented. Lots of them defy placement in one phlya or another. Here’s a bit of light reading on amoeba taxonomy.

http://tolweb.org/accessory/Amoebae?acc_id=51

And the point still stands that single celled organisms were around for billions of years before any complex multicellular lifeforms emerged. They had much longer to evolve. The fact that they did not evolve into multicellular forms for so long is quite a testament to how fit they are for virtually every environmental niche imaginable - environments so harsh even humans don’t have the technology to inhabit yet.

No New Species of Dog

Humans have been artifically isolating and breeding dogs for specific traits for 20,000 years. In all that time, in all those isolated groups, where several hundred true breeding variations from Chihuahuas to Saint Bernards have been created, they’re ALL STILL DOGS and every one of them can readily breed with the common wolf ancestor.

How much time and experimentation do you boys think you’ll need to actually observe a new species evolving? I’m a patient man but 20,000 years wears even my patience down. LOL

The fact that they did not evolve into multicellular forms for so long is quite a testament to how fit they are for virtually every environmental niche imaginable - environments so harsh even humans don’t have the technology to inhabit yet.

Um, Dave, some of the ancestors of today’s bacteria did evolve into multicellular life forms. And some didn’t, for the reason you allude to.

And even the ones that “remained” single-celled have undoubtedly changed. If we could obtain the genome sequence of some ancestor of E. coli from 1 billion years ago, do you think it would be identical to today’s bacteria?

Yes, life is extraordinarily diverse. Isn’t it interesting? Can you imagine how big the brains of the aliens were that designed each of those unclassifiable amoeba-like creatures? I can’t. No brain could be that huge. Therefore, evolution must be the answer.

DaveScot:

There’s an estimated 4 million (if memory serves) different species of single celled organisms (maybe it’s 40 million) with fewer than 1 in 10 of them observed or documented. Lots of them defy placement in one phlya or another.

I learned that the phyla are taxonomic categories of metazoa. Single celled life (bacteria, eubacteria, archaea) are not metazoa. The Linneaen taxonomy doesn’t really apply to these. Bacteria and archaea are probably a poor fit for the metazoan categories like ‘species’.

The fact that they did not evolve into multicellular forms for so long is quite a testament to how fit they are for virtually every environmental niche imaginable

Probably true. Given a 3 billion year head start, these little suckers snagged all the prime real estate. Colony critters (which evolved into eukaryotes, and then into multicelled animals, plants and fungi) could almost be said to have been obliged to colonize a whole new planet.

Interesting stuff, of course. Do you have a point to make?

And I guess someone needs to do the boilerplate slogging, so I might as well put on the hair shirt…

No New Species of Dog

Humans have been artifically isolating and breeding dogs for specific traits for 20,000 years.

Interesting number. Can you tell us where you got it? I’m not saying it’s wrong, I’m just wondering how it may have been derived.

In all that time, in all those isolated groups, where several hundred true breeding variations from Chihuahuas to Saint Bernards have been created, they’re ALL STILL DOGS and every one of them can readily breed with the common wolf ancestor.

How much time and experimentation do you boys think you’ll need to actually observe a new species evolving? I’m a patient man but 20,000 years wears even my patience down. LOL

Multiple misunderstandings here, every one of them so predictable as to make one wonder whether some people EVER leave the creationist sites, which all copy one another…

Anyway, you clearly don’t know what a species is. A species is an intrabreeding population, which rarely breeds with a different breeding population. Not never, just rarely. Not *can’t* interbreed with another population, *doesn’t* breed with them. The number of species of animals unable to impregnate any other species is in the small minority. So species is a *population* description, not necessarily a strictly genetic description. I recently read about two species different only in color - one more red, the other more blue. These two were never observed to interbreed naturally. So experimenters put them into an environment where the light was filtered so that their eyes couldn’t tell red from blue – and they interbred immediately and the offspring were fully fertile! So the boundaries between species can be very arbitrary.

Now consider that for morphological reasons, two breeds of dogs cannot perform sex even if they wanted to. Is that enough to make them separate species? By every means of defining species I’ve ever encountered, they are different species. A LOT different than just coloration.

Next issue: Just how long does a speciation event take? This is generally measured in generations, and can take anywhere from thousands to millions of generations (some genomes seem far more variable than others, and some groups (like beetles) throw off new species furiously, while others almost never). For a large mammal, 20,000 years in the wild seems quite fast.

So DaveScot doesn’t know what a species is, doesn’t understand evolutionary time, and apparently doesn’t care to do even minimal reading about either one. He has apparently cribbed a lousy example from a creationist tract somewhere, but neither he nor his source has educated themselves enough to realize how foolish they look.

DaveScot writes: “Slime molds can be amoeboid, bacterioid, or fungoid.”

Slime molds are protists (eukaroytes). Mxyococcus xanthus, which the Zusman lab studies, are bacteria. Interestingly, the fact that members of slime mold populations undergo terminal differentiation during some phases suggests a precursor to multicellularity. Additionally, some cyanobacteria like Anabaena form heterocysts which are terminally differentiated forms.

See: http://www.expasy.org/spotlight/bac[…]t_or_n.shtml

DaveScot writes: “Slime molds can be amoeboid, bacterioid, or fungoid.”

Slime molds are protists (eukaroytes). Mxyococcus xanthus, which the Zusman lab studies, are bacteria. Interestingly, the fact that members of slime mold populations undergo terminal differentiation during some phases suggests a precursor to multicellularity. Additionally, some cyanobacteria like Anabaena form heterocysts which are terminally differentiated forms.

See: http://www.expasy.org/spotlight/bac[…]t_or_n.shtml

Tim

My bad.

Corrected: “Slimes can be amoeboid, bacterioid, or fungoid.”

Expanded: “Amoeboid or fungoid are slime molds while bacterial slimes are also called biofilms.”

Is that better?

Great White said:

“If we could obtain the genome sequence of some ancestor of E. coli from 1 billion years ago, do you think it would be identical to today’s bacteria?”

Well since we can’t obtain the ancestral E. coli genome the hypothesis of it being dissimilar is not falsifiable. Thus it isn’t science and deserves no further consideration.

How’s the view on that petard?

David Springer, proud owner of “waterfront property” and an ignorant crank, tries to hide from the noxious fumes of his smoldering arguments:

Well since we can’t obtain the ancestral E. coli genome the hypothesis of it being dissimilar is not falsifiable. Thus it isn’t science and deserves no further consideration. How’s the view on that petard?

Whose petard?

Are you suggesting that it isn’t plausible for me to hitch a ride on a “mysterious” alien’s time machine and perform the analysis? I guess only you and your fellow cranks are entitled to such privileges.

I was merely trying to straighten you out about how evolution works. I realize now that’s a hopeless task given your belief that scientists are conspiring to hide their bad data from self-proclaimed geniuses like you who managed to pass a marine biology class.

So, it turns out that VNTRs are a brilliantly designed mechanism for determining variation within a species. Is the purpose of pandasthumb to convert people to ID? It sure seems that way.

So, it turns out that VNTRs are a brilliantly designed mechanism for determining variation within a species. Is the purpose of pandasthumb to convert people to ID? It sure seems that way.

Fortunately, the PandasThumb is intended for readers intelligent enough to recognize your “begging the question” when they see it.

Others, not so bright, might take away a different message.

DaveScot writes: Well since we can’t obtain the ancestral E. coli genome the hypothesis of it being dissimilar is not falsifiable. Thus it isn’t science and deserves no further consideration.

If we were able to look at the parent of E. coli from a billion years ago, we know that it would be quite different from the E. coli of today. The preferred habitats of E.coli are the intestines of mammals which weren’t around that long ago. E. coli’s nearest species relation is something like Salmonella enterica and that split seems to have happened about 100 million years ago.

We know that the natural strains of E. coli can display variations of up to a million base pairs (Measured chromosome lengths range from 4.5 - 5.5 Mb. There is probably even greater variation that we simply haven’t seen yet). So that’s about a 20% difference among living samples of the genome. These differences can represent significant changes in the host ranges and biochemical capabilities of the various strains. Additionally it appears that E. coli has “sampled” large chunks of DNA via horizontal transfer. Howard Ochman’s research in comparative genomics and the evolutionary dynamics of bacterial chromosomes suggests that about 1.6 Mb of horizontally transferred DNA has passed through the E. coli genome since its divergence from S. enterica about 100 million years ago.

Ochman’s PNAS paper here: http://www.pnas.org/cgi/content/full/95/16/9413

Another interesting reference on the dynamics of E. coli genome evolution: http://www.nature.com/cgi-taf/DynaP[…]filetype=pdf

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This page contains a single entry by PZ Myers published on January 3, 2005 12:18 PM.

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