Great white shark genome decoded

[scd]

sure. but dont forget to involve natural selection.

[swamidass (S. Joshua Swamidass)]

@scd if we start with a limited number of genes, say 1000, and we can’t make more, then we can loose more than 1000 genes. Therefore there is a limit to how many genes you can loose.

Please admit defeat.

Oh. Natural selection happens too (involved).

[John_Harshman]

@scd

there is no real limitation for the rate of gene loss when we are dealing with millions of years

Shall we agree that millions of years is not the same as infinite time? There is a limit to the rate of any process.

@scd

say that many of human genes became unnecessary or even disadvantage (about 10,000 of them). all we need is to remove them from the genome. since natural selection can be involve, and say that we only need a single deletion to delete a gene, we only need about 10,000 deletions. in 7 millions years we can get much more then that.

Say that three equals five. I can show you all manner of things with that. It is impossible that 10,000 humans genes would become unnecessary over the course of 7 million years.

[evograd (Blogging Graduate Student)]

@scd

say that many of human genes became unnecessary or even disadvantage (about 10,000 of them).

That’s a pretty substantial first premise. I think you’d have trouble making the argument that such a thing would be possible. By all means, give it a go.

@scd

we only need about 10,000 deletions. in 7 millions years we can get much more then that.

To completely delete 10,000 genes in such a short period of time would require them to bestow a significant fitness disadvantage, and then you have the problem of the other 10,000 genes to replace them.

[John_Harshman]

@evograd

bestow a significant fitness disadvantage

And they would have to retain this disadvantage even after being deactivated and/or present only in fragmentary form. Odd.

[scd]

@John_Harshman

Shall we agree that millions of years is not the same as infinite time?

sure.

@John_Harshman

It is impossible that 10,000 humans genes would become unnecessary over the course of 7 million years.

im not sure about that. If I remember correctly many genes (or even most of them) are unnecessary in some species (im still searching for a reference). if its true then there is no real problem with my scenario.

[John_Harshman]

@scd

If I remember correctly many genes (or even most of them) are unnecessary in some species (im still searching for a reference).

I await the results of your search.

[scd]

meanwhile i found this:

Towards a compendium of essential genes – From model organisms to synthetic...

take a look at table 1.

[John_Harshman]

You’re thinking about the wrong thing. It’s not just essential genes that won’t be lost. Any gene whose loss would be selected against won’t be lost. Note also that the figure is for genes essential to the survival of cancer cells; nothing to do with the whole organism.

[evograd (Blogging Graduate Student)]

You also have to consider that deleting gene A might not be lethal, and deleting gene B might not be lethal, but deleting both can be. Now think of this on the scale of 10,000 genes.

[scd]

@evograd

You also have to consider that deleting gene A might not be lethal, and deleting gene B might not be lethal, but deleting both can be. Now think of this on the scale of 10,000 genes

its possible. but if its true then why they published their result in the first place?

[scd]

@John_Harshman

the figure is for genes essential to the survival of cancer cells; nothing to do with the whole organism.

the table also mention other creatures. and they indeed talking about the whole organism:

“Essential genes are defined as genes that are required for sustaining life”

[evograd (Blogging Graduate Student)]

@scd

but if its true then why they published their result in the first place?

Because it’s good data about what they’re testing. They’re careful to define what their claim about the data is - they don’t say something like “these data prove that we could delete 90% of genes, leave 10% behind, and the organism would A: survive, and B: be just as fit as the wild-type.”

That interpretation is something you’re imposing on their results, because you haven’t read the paper and are generally uninformed about genetics.

[scd]

you know what? lets take it to the extreme. say that human will have no genes at all. in this scenario we can claim that this creature somehow evolved by an unknown process. remember that in darwin days they knew nothing about genetics, and yet they believed that all creatures evolved somehow.

[John_Harshman]

You’re not making a lot of sense there. If humans had no genes but presumably had some completely different method of inheritance, we could definitely conclude that something very weird was going on, and one obvious conclusion would be that we weren’t related to all the other life on earth. Then again, that would conflict with all the other data, from fossils, morphology, physiology, etc. It would be extremely puzzling, but we couldn’t fit it into any evolutionary scheme.

Fortunately, your hypotheticals are not the case. Instead, we are only slightly different from other apes, and are separated from chimpanzees by only 40 million mutations, a tiny number in a huge genome. The real question is what we should make of that.

[T_aquaticus]

@scd

you know what? lets take it to the extreme. say that human will have no genes at all. in this scenario we can claim that this creature somehow evolved by an unknown process. remember that in darwin days they knew nothing about genetics, and yet they believed that all creatures evolved somehow.

They believed life evolved because of the evidence. In 1882, George Romanes wrote an essay listing the evidence that supported evolution. Those evidences were classification, morphology or structure, geology, biogeography, and embryology. You should give the essay a read to get a feel for the evidence that led to the scientific community accepting the theory:

http://www.gutenberg.org/files/19922/19922-h/19922-h.htm

[scd]

@John_Harshman

It would be extremely puzzling

extremely puzzling yes. but evolution will be just fine.

[John_Harshman]

@scd

but evolution will be just fine.

I will point out that you are arguing for something that we don’t see. Better you should address what we do see.

[scd]

its a theoretical situation to show why evolution cant be falsified. but let’s agree to disagree.