One Evolution Question

[Mtgman]

I don’t have eleven like Ben, and I’ll be much less technial with mine, but I’ve recently seen something that evolution has yet to explain.

In a nutshell, the human genome is much smaller than evolutionary theories expected.

For an organism to evolve from a single-celled bacterium into a macro-organism the size and complexity of a human being would have taken billions and billions of genetic mutations. Given a growing population, we can understand that many of these mutations happened in parallel and the time would have been reduced from billions and bilions of years to millions and millions of years, but there is still one thing that seems wrong. If the human organism is truly made up of a great many miniscule changes in the genetic code, each of these changes would be unique and only when taken as aggregate would they combine to form a human being. This means there would be a seperate gene which accounts for eye color than there would be which accounts for the thickness of the lens in the eye. Complex genes, one which could specify both lens thickness and determine color would be much less likely to occur by random mutation. There have been many studies and a great deal of research done to estimate how many individual genes there must be in the human genome to be able to create a complete human being. These estimates range from 100,000 individual genes all the way up to 140,000+ genes.

With me so far? Here is where it gets sticky. The human genome was recently mapped, correct? The scientists found approximately 30,000 genes.

This finding is being questioned http://news.bbc.co.uk/hi/english/sci/tech/newsid_1426000/1426702.stm

but even the new estimates(based off of a much larger sample base of genetic databases) are still well under the calculated estimates based on known mutation rates. Essentially, microevolution acting over time, which is observable, would have produced humans with much higher gene counts than the current human species. The true number, the article says, is likely to be between 35,000 and 70,000. Still barely 2/3 of the minimum expected, even if all the areas which could be genes turn out to truly be genes(which the human genome project denies).

Anyone have an ideas or have read anything on theories to bridge this gap?

Please don’t take this chance to attack me on a creationist/evolutionist basis. My beliefs aren’t in question here, (indeed I have not mentioned my position, nor do I intend to, but I’m reasonably sure you would be wrong if you tried to guess). This is the Straight Dope right? The question is, how can a complex organism like a human be composed of only 30,000 genes if the microevolution process is correct?

Steven

[Mangetout]

I asked a related question here:
DNA - Holographic?

The OP assumes that a single gene is responsible for a single function in the organism when (Ben might correct me on this) genes are actually just the recipes for proteins; those proteins quite likely have more than one job to do.

[edwino]

I had a post ready, and Netscape crashed. Screw.

Welcome to SDMB. You have a good question with a nice new take, IMHO. I would like to reassert that the 30,000 gene number was arrived on after sequencing of the majority of the euchromatin and used a gene predictor algorithm which may be faulty. It could well be 100,000+ genes if we start finding lots of new genes in unexpected places.

First, the obligatory cite request. I am pursuing a doctorate in genetics and I have never heard of the theory that you need 100,000 to 140,000+ genes to construct a human. Not that you are wrong, I just want to educate myself.

Second, I see a number of problems in your reasoning. I will try to point them out. These mainly focus on your assertion that complex genes are not likely to form during evolution.

1. The first reason I believe complex genes are quite likely to form is that function is often conserved in evolution. Examples include homeobox-containing proteins involvement in body segmentation, Pax6 genes involvement in eye development, Atonal/Math5 genes involvement in neural fates throughout evolution. A function is often conserved, even if the system is increased in complexity (for instance the eye of a planaria versus the eye of a mouse is specified by a very similar Pax6 gene).

2. In cases where direct function is not conserved, whole systems are used for many different functions. Look at second messenger systems throughout nature. The tyrosine kinase receptor system and the cyclic AMP second messenger system is used in innumerable places in nature for innumerable functions. This can be explained easily microevolutionarily (if you insist on using that term). I can think of two off of the top of my head – first that an ectopic expression with selection for other pathway members, and second is a duplication with descent and divergence.

3. Many of the important genes that I concern myself with are “master control” genes. One gene, if expressed incorrectly, can turn on a whole huge developmental pathway (as seen in 1, and perhaps leading to a case like 2). While genes function in multipartite networks, one mutation in a master controller can cause an entire system to be utilized in a new way.

4. Proteins are much more complex than you give them credit for. This is caused by splicing, differential transcription and translation, RNA editing, posttranslational modification, protein and message stability, and differential degradation causing complex expression of multi-domain, multi-functional proteins. Mechanisms to this are also quite well researched from an evolutionary viewpoint – things like duplication with divergence, exon shuffling, mutation of splice sites, in frame fusions, partial deletions, and other random mutation can lead a simple protein to adopt new functions and forms.

5. Leading into #4 is a concept which I often see tossed out by people not in the biological sciences. This is the idea that a random mutation necessarily is a minute, inconsequential thing. This I believe comes from equating random mutations with point mutations. Point mutations can cause drastic changes and random mutations are more than just isolated point mutations. Point mutations in humans lead to resistance to malaria and AIDS. Point mutations in the fruitfly can lead to legs growing where antennae normally are. And, random mutation includes things like transpositions, duplications, inversions, translocations, deletions, and other large genetic changes which can rapidly cause large scale rearrangement of genomes. These can be on the scale of just a few nucleotides to whole chromosome arms.

Also, I’d just like to point out that we are not that much more complex than fruit flies, who have around 12,000 genes. While you may find this hard to believe at first, we share many of the same core concepts of multicellular life, and we just expand on many of the same themes. They have complex body patterning, locomotion, and nervous, digestive, circulatory, and integumentary systems.

I hope this answers a few of your questions. In short, I think that complex proteins are easily formed during evolution and that we should have little problem making due with only 30,000 (which is still a tremendous amount of research to do…)

[GIGObuster]

My impression is that more research is needed to pinpoint the actual number of genes, even the private labs are concerned that indeed they could have missed many genes, however if the number of genes is “low” the question is: compared to what? I would not be surprised to find out in the near future that a similar reduction in the number of genes will be the result of the genome mapping of other creatures.

But a low count of genes could also mean that nature does not throw things away when it can reuse the pieces, I remember many examples in nature of adaptations in organs that do other tasks, one example is the panda’s thumb. At the gene level a similar “reuse” of genes could be at play:

http://199.97.97.16/contWriter/yhd7/2001/02/14/medic/3525-0116-pat_nytimes.html

Steve Fodor, chief executive of Santa Clara’s Affymetrix Inc., said the relative scarcity of genes doesn’t simplify drug discovery. If anything, it intensifies the challenge, because the gene mappers showed that many human genes make several proteins.
Fodor, whose firm makes glass chips used to study gene activity in sick cells, said it won’t be enough to understand which genes are involved in a disease. Researchers must also need to know which variations of the genes are implicated.
We know of one gene that makes 12 different proteins,'' Fodor said. One of these proteins causes cells to commit suicide. A different protein variant of the gene stops the suicide process. The perception that things get simpler (with fewer genes) is wrong,’’ Fodor said.

Looking at the original article:

Arguments over how many genes it takes to build a human being look set to continue. A gene sweepstake set up by scientists attending the Cold Spring Harbor Genome Meetings in the United States is still taking entries. To date, there have been 165 bets, ranging from 27,462 to 153,478 human genes. So far, the money is on 61,710.

So there is still lots of research to be done, but one thing is clear, that “minimum expected” is around 27,462 to 61,710 (using the original article) your count of “100,000 individual genes all the way up to 140,000+ genes” is coming from relatively old ESTIMATES of some companies:
http://www.wired.com/news/topstories/0,1287,21882,00.html

12:00 p.m. Sep. 22, 1999 PDT
Human beings may have twice as many genes as previously thought, researchers at a biotechnology company said Tuesday – a suggestion that would have big implications for scientists racing to map all the genes.
Palo Alto, California-based Incyte Pharmaceuticals says it estimates humans have 140,000 genes. The company says it has sequenced most of these genes, and has added what it has found to publicly available data on genes to come up with the figure.

All that still needs to be verified and compared with the current results in other companies and labs around the world.

the nematode worm with 18,000 (genes) and the fruit fly with 13,000.

Macro evolution is not the only factor in our evolution, but nature does indeed make humans with the 61,710 genes that according to the article is the best estimate, again more research is needed, but the most probable counts are indeed larger than the ones in simpler life forms.

The implication that the low number of genes disproves macroevolution is premature.

[JonF]

There’s some reason to believe that evolutionary processes tend to come up with “rich” solutions that a human designer never would generate. I really like the example of An evolved circuit, intrinsic in silicon, entwined with physics (click on the “PDF” near the upper right corner to see the full paper). The evolved circuit used far fewer gates than a human designer would, and we can’t figure out how it works. Several gates are not nominally connected to the rest of the circuit but are critical to the function of the circuit. They’re coupled in by parastitic capacitance or something similar. No human designer would do that, or even investigate the chip to try to find such effects. If the manufacturer changes the chip masks, the circuit would probably stop working; this illustrates the fact that evolutionary algorithms tend to find a local optimum and have no vision of the future.

[tracer]

Ooh! Ooh! Mista Kotta!
I have an evolution question too!

What’s the currently favored model for how viruses evolved?

[andros]

Oh, please, tracer, you know very well that viruses are hyperintelligent alien invaders.

[Ben]

*Originally posted by Mtgman *
**There have been many studies and a great deal of research done to estimate how many individual genes there must be in the human genome to be able to create a complete human being. These estimates range from 100,000 individual genes all the way up to 140,000+ genes.
**

Cite?

-Ben

[Mangetout]

*Originally posted by andros *
**Oh, please, tracer, you know very well that viruses are hyperintelligent alien invaders. **

Silly Andros, viruses were created by a loving and benevolent God (not sure which of the six days this was though)

[Mtgman]

*Originally posted by Ben *
**

*Originally posted by Mtgman *
**There have been many studies and a great deal of research done to estimate how many individual genes there must be in the human genome to be able to create a complete human being. These estimates range from 100,000 individual genes all the way up to 140,000+ genes.
**

Cite?

-Ben **

I hesitate to do this because you’ve been openly contemptous of research done by others in the past which didn’t support your position. But here are a couple of articles and a quote or two.

http://www.feedmag.com/templates/default.php3?a_id=1630&page_num=2

The science behind the original estimate was largely based on a standard model in genetics that one gene transcribes one type of RNA, which then produces just one protein. “It’s been ingrained since the 1950s,” says Barabara Hanson, “that one gene makes one protein, and because we have so many different proteins in our body [nearly 100,000], that we had one gene for each of those proteins.”

http://www.sscnet.ucla.edu/geog/gessler/167-2001/genome.htm

Their principal discovery is how few human genes there seem to be. Textbooks have long pegged the number of human genes at around 100,000, but with the sequence of human DNA units in hand the two teams have found far fewer than expected. Dr. Venter says he has identified 26,588 protein-coding genes for sure and another 12,000 possible genes. The consortium says there are 30,000 to 40,000 human genes. Both sides prefer the lower end of their range, since their methods of gene discovery tend to predict more genes than they believe exist.
…
Despite these face-saving efforts, human self-esteem may be in for further blows as genome analysis progresses. Dr. Venter said he could find only 300 human genes that had no recognizable counterpart in the mouse. The mouse, though a fellow mammal, last shared a common ancestor with people 100 million years ago, time in which many more genetic differences might have been expected to develop.

And maintaining my neutral position on this topic, here is a article which tells about theories which predicted low gene counts from the beginning.

http://www.skincarephysicians.com/eczemanet/july.html

The finding of a surprisingly small number of human genes supports studies in evolutionary genetics indicating that many genes carried by humans (1) developed early in evolution and, (2) were preserved and “recycled” through increasingly complex organisms up to and including humans. The conservation, recycling and adaptation of genes that were “road tested” for survival value over millions of years may have been a good evolutionary strategy as organisms became more complex. An analysis of protein families (proteins are a major product of genes) supports the concept that most human genes were conserved from a distant evolutionary past when there were no organisms more complex than bacteria, fungi and yeasts: of the 1,278 protein families specifically identified with human genes, only 94 are specific to vertebrates (animals with a backbone). [Baltimore D. Our genome unveiled. Nature 2001; 409:815-816.]

As I have said, I am neutral on this topic, I will claim neither camp as my own.

I would like to remind creation scientists that evidence is more important than rhetoric, but time will be allowed for theories to develop to explain the evidence. Theories will be expected, science can not exist on faith alone.

I would remind evolutionists that your understanding of how humans work is still being shaken with findings like these. Do not think you are ready to put nails in the coffin of creation theory.

Steven

[Ben]

*Originally posted by Mtgman *
**I hesitate to do this because you’ve been openly contemptous of research done by others in the past which didn’t support your position.

**

Could you provide an example? I don’t feel I’ve been contemptuous of any research presented here.

-Ben

[tracer]

andros wrote:

**Oh, please, tracer, you know very well that viruses are hyperintelligent alien invaders. **

Aw, c’mon, guys, you mean you’re going to make me look this up myself?!

Oh, very well …

<tracer goes to the Talk.Origins archive search page>

Darn it, I still can’t find anything. All I can find is a few articles about how sexual reproduction evolved as a possible defense against viruses. I wanna know where the viruses came from in the first place! Waaaaaaah! Mooooommmm!!