Science questions not worth a thread I: I'm a moron!

[hobbsyoyo]

@peter grimes - Sorry, it's just that in my mind I'm only asking one question and expanding on that one question in order to help it make sense because I don't think I've been asking it very coherently.

I'm really asking the first question I posted and trying to get a satisfactory answer by expanding on that so that everyone can understand exactly what I'm asking. Maybe I'm wrong and it's been answered correctly already. However I think I have just been wording it very poorly as I lack the technical vocabulary in this subject, thus causing people to answer different but related questions.

 

[emzie]

Ah, but then how do you tell which genes are necessary to build a given species? All of the organisms within the species may have variations of these genes, but without a form or a functional form of the genes at all, they will have severe defects or will die or will not be of that species. There may well also be extraneous genes that are just there or are new mutations but are not prevalent or necessary for the species.

How do you tell with a limited sample which genes are necessary? How do you tell what the 'basic' version of a gene is so that you may then label some variations mutations and so on?

The species is more or less defined by the genes necessary to make it. It's a bit circular, but is the same as saying that a Royal Flush is defined as 10-J-Q-K-A of the same suit. A royal flush is defined by its makeup.

I think you're making an old mistake of archetypes -- that there is an ideal rabbit that is thus defined (by a specific genome) that all rabbits compare to. There's no such thing. The closest you can get to that is an average, where most rabbits in a given set have X version of Y gene, but that no single rabbit has the most common variant of every gene in the gene pool. The most common version of a gene will shift through time depending on selection pressures.

To go further, there's no real "basic version" of a gene. There's a version of a gene that functions in a specific way, and another version of the gene that functions slightly differently.

 

[Souron]

Ah, but then how do you tell which genes are necessary to build a given species? All of the organisms within the species may have variations of these genes, but without a form or a functional form of the genes at all, they will have severe defects or will die or will not be of that species. There may well also be extraneous genes that are just there or are new mutations but are not prevalent or necessary for the species.

How do you tell with a limited sample which genes are necessary? How do you tell what the 'basic' version of a gene is so that you may then label some variations mutations and so on?

We don't. We don't know what individual genes or no-gene triggers in DNA do by sequencing.

The only thing you can do is not use animals with cancer as representatives of their species.

 

[peter grimes]

To go further, there's no real "basic version" of a gene. There's a version of a gene that functions in a specific way, and another version of the gene that functions slightly differently.

And to go yet further still, some genes appear to be highly conservative, while others are more free to mutate. I don't know specifics (I am but a humble Carpenter, by trade), but I'm pretty sure Dawkins talks a bit about this in Ancestor's Tale - which, by the way, is one of my favorite books. I've read it through 4 times now, and I can't wait to do it again.

Some genes that code for a very Important protein involved in animal metabolism may experience a rate of mutation several orders of magnitude slower than a gene for, say, skin coloration.

@hobbs - I wasn't intending to spank you, just indicating that this is a rich enough line if inquiry that we could devote a whole thread to it

 

[dutchfire]

It sounds perfectly reasonable to me that a fraction of 0 of all numbers is prime.

But there is also a fraction 0 of all numbers that belongs to the empty set, and there are clearly more primes than numbers that belong to the empty set

 

[dutchfire]

And to go yet further still, some genes appear to be highly conservative, while others are more free to mutate.

Really? I wouldn't expect that.

(Unless you mean, certain mutations are very likely to kill you).

 

[hobbsyoyo]

Really? I wouldn't expect that.

(Unless you mean, certain mutations are very likely to kill you).

Canines are well known for having genetic codes very prone to duplication events and other mutations that allow them to morph into different breeds and such very quickly (quickly as in few generations). They are really interesting because on the genetic level they are perfectly suited to the genetic engineering we've been subjecting them too for thousands of years. They were the original lab rats.

 

[Michkov]

On that note, did we manage to produce a breed of dog which are a new species in itself (so that they cant reproduce with other dogs)?

 

[peter grimes]

Really? I wouldn't expect that.

(Unless you mean, certain mutations are very likely to kill you).

No, it doesn't mean that specifically. It's more like some genetic elements exhibit a higher mutation rate independent of selection than others:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899115/

A gene’s intron gain rate shows a highly significant negative correlation with the coding-sequence evolution rate; intron loss rate also significantly, but positively, correlates with the sequence evolution rate. Correlations of the opposite signs, albeit less significant ones, are observed between intron gain and loss rates and gene expression level. It is proposed that intron evolution includes a neutral component, which is manifest in the positive correlation between the gain and loss rates and a selection-driven component as reflected in the links between intron gain and loss and sequence evolution.

and

http://europepmc.org/abstract/MED/519760/reload=0;jsessionid=kRxnw3vlvkJ1lEx6andt.20

the alpha gene is interrupted by two intervening sequences at precisely homologous positions, suggesting that these interruptions were present and have been preserved throughout vertebrate evolution.

[after some 'research']:

Umm, so these things may not actually say what I think they're saying. I'm having a tough time finding things that I thought were readily findable.

The gist of my earlier comment is that evolution, selection, and mutation don't all operate at the same rate across the entire genome of an organism. There are areas that are called non-coding DNA that were thought to not do anything, and these experience a higher mutation rate than other areas because they're blind to the culling effect of selection. The discovery of the mechanism of DNA methylation has called this interpretation into question.

But even among coding regions of DNA - introns - mutation is not necessarily observed to happen with equal probability at all sites independently of selection. This is the claim I'm having trouble sourcing, so definitely don't take my word for it. There's a good chance I've completely misunderstood something along the way, since I'm not finding support for my statement on PLOS or anywhere else.

 

[emzie]

On that note, did we manage to produce a breed of dog which are a new species in itself (so that they cant reproduce with other dogs)?

Kinda and no.

No, since if I take the semen from a miniature poodle, I could artificially inseminate a Great Dane bitch. Kinda, because I think our strict breeding restrictions have created a ring species effect where a Great Dane and a miniature poodle are not going to reproduce together, but they each would reproduce with other dogs that, in a chain, would link both individuals. Without the strict breeding lines and without geographic separation, eventually dogs would probably all turn into something like a dingo.

edit: auto-censor kicked in when it shouldn't've so I bypassed it because that's the correct term, damn it. Moderator Action: Clever and OK

 

[MCdread]

Really? I wouldn't expect that.

(Unless you mean, certain mutations are very likely to kill you).

No, it doesn't mean that specifically. It's more like some genetic elements exhibit a higher mutation rate independent of selection than others:

On one hand mutations in certain genes produce more dramatic effects than in others. As dutchfire says it doesn't mean that a specific string of base pairs is intrinsically more mutable. Mutations in so-called essential genes, for example, constitute a big problem. By definition, an essential gene is a gene without which the organisms can't grow, so there is a strong selective pressure to keep that gene relatively unchanged*. The lower mutation rate of these genes is therefore due to the fact we are sampling from individuals whose fitness hasn't been badly affected (i.e., we are sampling from what natural selection lets organisms get away with).

On the other hand, there are other effects that cause certain regions or nucleotide base-pairs in the DNA to mutate more. For example, some bases (the 4 'letters' in DNA) are more prone to mutation than others, and the transition probability of, say a mutation from A to G, is different than that of A to T, and so on.
Cells have ways of correcting some of these errors, but sometimes the mechanisms of repair also introduce a bias in the relative abundance of the bases, and are more likely to let some specific mutations pass than others.
Although I'm only vaguely familiar with it, another possible example is chromosomal recombination: there are some regions on the genome (and respective genes) that are more likely to be a target of recombination (recombination hotspots).


* May look a bit circular a definition, but there are other properties that define these sets of genes. For example, the products (proteins) of many of the essential genes are required more often than others and therefore must exhibit less expression noise (variation of abundance levels). That is precisely what is observed in vivo. Furthermore, in higher organisms, it is common that they are located in regions of open chromatin (i.e., they're more readily accessible by the machinery that reads them out and produces mRNA). Otherwise they'd exhibit noisy bursts of production.

In bacteria, they tend to be found near the origin of replication site (the site where replication of their circular chromosome begins), which causes a similar effect.

 

[PlutonianEmpire]

If Earth had happened to form as a circumbinary planet, and the geologic history remained mostly the same (including keeping our moon), and was still able to support life (and eventually us), how might things be different? And, how much might human culture and other aspects of human civilization been influenced by evolving on a circumbinary?

 

[Meteor Man]

If Earth had happened to form as a circumbinary planet, and the geologic history remained mostly the same (including keeping our moon), and was still able to support life (and eventually us), how might things be different? And, how much might human culture and other aspects of human civilization been influenced by evolving on a circumbinary?

That...is certainly an interesting question. No doubt the presence of two suns would influence the religious beliefs of ancient civilizations. I wonder how our circadian rhythms would be affected...

 

[PlutonianEmpire]

That...is certainly an interesting question. No doubt the presence of two suns would influence the religious beliefs of ancient civilizations. I wonder how our circadian rhythms would be affected...

Yeah, those are some of the things I was curious about, but also, how time- and calendar-keeping would turn out.

 

[emzie]

That's such a complex question that you could write an entire sci-fi series based on it.

 

[Bluemofia]

If Earth had happened to form as a circumbinary planet, and the geologic history remained mostly the same (including keeping our moon), and was still able to support life (and eventually us), how might things be different? And, how much might human culture and other aspects of human civilization been influenced by evolving on a circumbinary?

Well, for this to happen, you'd probably have the two stars orbiting close together, rather than far apart and the planets clustered close to one of them. (So circadian rhythms will not be affected) This is because orbiting farther apart is much more dangerous in terms of gravitational perturbations, as it exhibits resonances with some orbits which will destabilize more easily than if they were clustered close together. I think there would be either more mass extinctions in geologic past, and/or Late Heavy Bombardment (which, was caused by the 4, possibly 5, gas giants migrating around in the real life solar system and gravitationally perturbing everything) would last longer or be more intense.

To start, we would probably believe in a heliocentric universe much much sooner. The two stars moving in front of each other every once in a while (in order to maintain the disk-like formation of the solar system along the orbital plane for stability) will give it away soon enough if they look different, else a bit of math would discover it quickly enough.

It is possible that the two stars will be treated like a mother and a father figure, rather than the moon be the mother figure. I don't know what the moon would be representative of, but it might even be possible that it would be the fatherly figure, while the two suns are the two motherly figures, and encourage polygamy since early in human history the adult gender ratio was roughly 2:1 female to male.

All in all, there's too much uncertainty in how people would interpret things, and which one of those happens to gain enough followers to be able to successfully win wars and spread that belief. It's a crap-shoot.

 

[Gigaz]

But there is also a fraction 0 of all numbers that belongs to the empty set, and there are clearly more primes than numbers that belong to the empty set

Yes but I mean this is a pretty common thing when you deal with infinity. The number of primes is exactly the same as the number of whole numbers or numbers which can be divided by 7. But if you ask 'which fraction of natural numbers has this feature?' you'd always get a different result.

 

[salty mud]

Here's one that's been annoying me for a while now.

Is each of the chromosomes in an organism (assume we're talking eukaryote here, since most prokaryotes have a singular chromosome) unique or are they all replicas of each other? So for a human's 46 chromosomes, are they all identical or does each chromosome hold completely different genetic information? I am thinking it's the latter.

 

[hobbsyoyo]

They're all coded to contain different information.

 

[salty mud]

As I expected. Thanks for the clarification.