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Brews & Views Bulletin Board Service * Brews and Views Archive 2003 * September 2, 2003 * Genetic code and stability of strain properties? < Previous Next >

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Fredrik (213.114.44.237)
Posted on Monday, August 11, 2003 - 12:19 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

One question just struck me. Perhaps someone who knows more about microbiology or genetics has some ideas.

If exceptions are made for wine and champagne yeast as well as some belgian strains, most brewing yeast as far as I know all are Saccharomyces Cerevisae, which I have the impression has a unambigious genetic code - DNA? Is that correct so far?

Then, considering how frequently yeast reproduce, what gives rise to the different properties of the numerous brewing strains if then basically are the same - same genetic material?

The only thing I've come up with is that the cell strain during it's life (not individual cells) do to environmental conditions has acquired custom levels of various substances (not sure what - enzymes?) that distribute throughout the cells during budding. However with this explanation alone it seems to be that the "properties" of the strains, like ester profiles and so on would decay pretty damn quick?

This has been bothering me. I would be interesting to know if someone else thought of this and has an explanation. Maybe I just missed some factor here?

/Fredrik
 

Billy Wight (66.27.65.243)
Posted on Monday, August 11, 2003 - 01:22 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Fredrik-

I think the DNA for white labs california ale goes something like this:

AGTCGGACTGCTGAGAATCGTCGTAGCCGATCGGGTCGCATTCGATTCGATTCG...CGGTTACGAT

-Billy
 

Fredrik (62.20.8.148)
Posted on Monday, August 11, 2003 - 11:11 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Also with the same logic you make any yeast colony to go bananas, right? Though it may require a trained yeast psychologist.

/Fredrik
 

Magnus Graham (148.177.161.211)
Posted on Monday, August 11, 2003 - 11:44 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Try Origin of Species by C Darwin. Much of the first few chapters cover domestic and wild plants (yeast is eukareotic and can be thought of as a plant) and animals and the selection of desirable characteristics by breeders of pigeons and dogs (not with one another).
Brewers are the main environmental pressure on yeasts.
With suggessive subculture, yes yeasts will become "wild" again and the individuals with the selected/desired taste characteristics will become lost in the overall population.

Mr Darwin explained it a lot better.

Mag
 

Fredrik (62.20.8.148)
Posted on Monday, August 11, 2003 - 11:46 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

I could not resist coming up with this.

The master brewer brings his most precious yeast slurry to the psychologist.

[Master Brewer]: My yeast is going bananas, what is wrong?
[Psychologist]: Is that so?
[Master Brewer]: Yes
[Psychologist]: Do you feed it properly?
[Master Brewer]: Yes, give it 1.2 lbs of bananas each morning mashed 30 mins @ 160F.
[Psychologist]: How sweet!
[Master Brewer]: Yes
[Psychologist]: Your yeast is probably trying to identify itself with the banana.
[Master Brewer]: Oh! My baby, what have I done. What must I do?
[Psychologist]: Stop feeding it with bananas and run it through a hose at least 40 minutes each day and it'll be fine in a couple of weeks.
[Master Brewer]: Thank you very much!

/Fredrik
 

Magnus Graham (148.177.161.211)
Posted on Monday, August 11, 2003 - 11:49 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Think of how different breeds of dog look very distinct but if they cease to be subjected to breeder selection activities (dont allow the nice looking ones to breed) they soon start to lose the breed characteristics. Thay are still dogs though.

Mag
 

Fredrik (62.20.8.148)
Posted on Monday, August 11, 2003 - 11:49 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Thanks Magnus. I'll look into that!

/Fredrik
 

Fredrik (62.20.8.148)
Posted on Monday, August 11, 2003 - 12:03 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Magnus, forgive me if I mix this up but isn't what you suggest (evolution) some kind of mutation? Then the DNA changes doesn't it? I will have improve my understanding on this topic. The exact mechanism of this seems quite relevant after all. I think you made me realize where to look. Thanks!

/Fredrik
 

Ken Anderson (24.55.254.125)
Posted on Monday, August 11, 2003 - 12:19 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Fredrik! Stay focused! From CO2 molecule to DNA molecule is a pretty big jump. How many projects do you have going??? :)
Ken A.
 

Beerboy (81.134.85.22)
Posted on Monday, August 11, 2003 - 12:30 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Maybe we should make a model of Fredriks giant leaps of logic!
 

Fredrik (62.20.8.148)
Posted on Monday, August 11, 2003 - 12:31 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

I have discovered several years ago that all my projects sooner or later tend to converge to the one and same fuzzy core, and I am not talking about the meaning of life (but almost). I think some knowledge about genetics is not going to damage my CO2 logger. Beeing too narrow may sometimes be a mistake :) Of course the ultimate goal is crack the core open. I try to attack the core from as many relevant angles as possible.

/Fredrik
 

Ken Anderson (24.55.254.125)
Posted on Monday, August 11, 2003 - 01:08 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

This will help you get to the theory of everything. And of course, at that point, you will naturally make better beer. Don't forget the beer!
Ken A.
http://www.amazon.com/exec/obidos/tg/detail/-/0375708111/qid=1060606929/sr=8-1/ref=sr_8_1/002-7087160-4967227?v=glance&s=books&n=507846
 

Fredrik (62.20.8.148)
Posted on Monday, August 11, 2003 - 01:35 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

:) In my opinion those superstring theories are not an ultimate theory even if they solve the technical problems associated with them. They sure explain lots of things, like how all the elemeteray particles arise (beeing different energy modes of strings). But on the other hand they introduce something too much ad hoc stuff that makes even less sense to me at least than the newtonian absolute universe.

There are alot of excellent findings and excellent research in this area, no question about that, but in my opinon the string theories still conforms to old time thinking. I just don't like the idea to start with.

I think there is need for new thinking. Not new models conformant to the same old framework of thinking and philosophy.

Ken, you're not one of those superstring nerds are you? :)

/Fredrik
 

Drew Avis (209.226.137.107)
Posted on Monday, August 11, 2003 - 01:56 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Frederik, I'm not a microbiologist, but I play one in my brewery.

"Mutation" is actually quite rare in any species. Furthermore, most mutations are not favourable - that is, the mutated organism is usually less likely to survive than it's parent. Only in the very rare case where the mutation gives the organism some sort of advantage, or at least an equal footing, will the mutated organism survive to pass its new DNA on. In a homebrewing situation, you're talking about a few cells in a population of billions - not enough to make much of a difference.

When homebrewers say their re-pitched yeast has "mutated" and now makes bad beer, what they really mean is that the bacteria / wild yeast population in their slurry has increased to the point where it affects the beer.

To really start creating new strains, you'd have to isolate a single mutated yeast cell, then grow up a population, pitch it, and see what kind of beer it makes.
 

Ken Anderson (24.55.254.125)
Posted on Monday, August 11, 2003 - 02:48 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Drew, these boards are full of armchair microbiologists. I was recently told on rcb that if yeast are too quickly chilled, they will morph into petite mutants (or some such thing). I'm in your camp about the bacteria/wild yeast thing. As is the case with so many topics, folks just jump on the bandwagon and perpetuate what they believe to be the truth.
Ken A.
Oh! Don't forget the bacteria hiding in your plastic fermenter's scratches!
 

Fredrik (213.114.44.237)
Posted on Monday, August 11, 2003 - 05:14 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Ah darn, I realized my mistake. I was confused with the individual vs spieces. The DNA would only be 100% defined for an individual and not for a speice. I'm sorry for my confusion. Then the breeding makes sense and the stability of strains make sense.

Most of DNA is always the same (for S.Cerevisae), but some little fraction of the code is what make the difference between individual cells, right? Differences in this small part is what makes the strains?

I have been told there are no stupid questions. Even if there are I want to get rid of them as soon as possible :)

/Fredrik
 

Paul Gallagher (128.143.17.25)
Posted on Monday, August 11, 2003 - 05:48 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Frederik,

Now you've got it. There are published genomic sequences for a number of different plant and animal species, but those sequences (dna codes) are only based on a relatively few individuals within the species. For example, one of the original draft sequences of the human genetic code was based on only 5 people. The variation within a species is what makes different strains.
 

Magnus Graham (148.177.161.211)
Posted on Tuesday, August 12, 2003 - 11:44 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Also a lot was understood about genetics and inheritance long before DNA was identified as the material containing the genetic code.
As a micro graduate I have seen researchers go as far up their own arses as it is possible to get. This often confuses the casual observer and frequently the same researchers are unaware and/or incapable of relating their genetic work to the big picture of populations and mutations within populations and also the application of the theory they have just proved.
My belief is in microbial ecology. You can see your yeast culture (brew) as a population. This population will adapt to the environmental conditions. Adapting involves the proliferation of more suited individuals and the loss of the 'weak'. A beer culture may not be the best way of perpetuating the flavours we want. Successive use of the same yeast will allow the fast growers to proliferate perhaps at the expense of slower growing good yeasts (flavour profile etc).
From what I read, Lager yeasts are more pure culture than ales and are cultured from single colonies in the commercial environment.

If this bores you all, blame Fredrik, he started it.

Magnus
 

Drew Avis (209.226.137.108)
Posted on Tuesday, August 12, 2003 - 01:28 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Regarding the yeast population - that's true, Magnus, but it takes hundreds, if not thousands, of generations to see a serious change in the genetic makeup of a population, and we're talking maybe 5 - 10 generations per brew.

As for lager being "purer" than ale strains, I believe that's bunk. Both are cultured from single colonies in the labs. Perhaps some breweries re-pitch their ale slurry longer than lager slurry - I don't know. But when you buy the strain from a vendor, it's the pure stuff.
 

Magnus Graham (148.177.161.211)
Posted on Tuesday, August 12, 2003 - 04:15 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Yes, I may be as of going up my own arse here, it being theoretically possible for your yeast to lose its character. It may be possible to keep repitching willy nilly for 10-100 brews with no problems - I've never tried it.

Have any brewers here have repitched to destruction so to speak??

Mag
 

Chris Colby (66.25.197.116)
Posted on Wednesday, August 13, 2003 - 04:00 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Frederick,
Here's a link to a brief introduction to evolutionary biology. It gives a general idea of how populations evolve, although no specifics on how beer yeast strains differentiated.

http://www.talkorigins.org/faqs/faq-intro-to-biology.html

Chris Colby
Bastrop, TX
 

Fredrik (213.114.44.237)
Posted on Wednesday, August 13, 2003 - 05:02 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Thanks Chris, nice intro. I will read it!

By the way, I just found that physicists has dectected the amino acid glycine in interstellar molecular clouds in free space which is a little bit interesting.

http://www.physicsweb.org/article/news/7/8/7

I think I am getting it now. My main confusion was the DNA encoding of speices vs individuals. Beeing foreing to these fields I never gave any of this any thought until now.

/Fredrik
 

Fredrik (62.20.8.148)
Posted on Wednesday, August 13, 2003 - 11:32 am:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

I just noticed that Chris is the author :) Great paper Chris! I read it through quickly during my lunch break. As I mentioned I've never given this much thought before, but the evolution mechanisms are I belive closely to any learning mechanism that I would expect to see in a learning model. Just like who is most "fit" at the moment changes and has no absolute definition, knowledge is relative. I would be tempted to make parallells in such a way that the biological environment - that keeps changing, and dynamincally changes who is "fittest", are very analogous to the body of knowledge of an individual. What appears completely random to one obverver, may appear very predictably by another observer because two observers usually never has the same set of information. I don't think knowledge and predictive power are absolute. What I've been thinking of is a model that will handle an abstract flow of information. Out of this flow, an intelligence will in a way similar to evolution come up with ideas, discard the inconsistent onces and keep the consistent ones. Origin of spieces would be the analogue to orign of elementary particles. Actually our entire world is nothing but mindwork anyway. Elementary particles like electrons has appeared in mankinds struggle to process the flow of information. Clearly this idea has been pretty consistent and thus survived. These are some interesting things!
I believe that these ideas, can be formalized and modelled. This idea but applied mainly to physics rather than biology is another of my big projects that I've had laying around for some years.

/Fredrik
 

Chris Colby (66.25.197.116)
Posted on Wednesday, August 13, 2003 - 03:20 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Hey Fredrik,
If you're interested in modelling -- now where would I get that idea? 8-) -- as it applies to biology, find a college library and check out a book on population genetics. (Hartl and Clark's book is good, so is Nagylaki's if your math skills are pretty good.) "Pop gen" is the mathematical theory of how the genetics of populations change over time (i.e. how they evolve).

This theory has been piling up since the 1930's. "Recently," with the discovery of DNA sequencing technology, biologists have found vast amounts of data to use in sorting out which theories are promising and which need to get the boot.

I feel like I should include something about brewing here 8-) So, I'll mention that I brewed a "dark white" beer last night. The beer my interpretation of a Belgian wit with some added dark grains (Carafa III) to bring the color to about 17 SRM. I'm going to spice it with coriander, orange peel and dried lavender flowers.

Chris Colby
Bastrop, TX
 

Denny Conn (63.114.138.2)
Posted on Wednesday, August 13, 2003 - 07:17 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Wow, that sounds like a really interesting beer, Chris! Hey, Fredrik, have you ever thought about brewing something??? :)
 

Fredrik (213.114.44.237)
Posted on Wednesday, August 13, 2003 - 09:07 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Yes Denny, I am actually going to brew this weekend! :) I haven't decided yet what pitching rate to use though. Since I am really out of beer I consider to not gamble too much with this batch. Unlike some other batches this will be dedicated for consumption :) But I am not sure. I feels almost like a waste to brew an entire batch and not add an element of experiment. I'll see what I do. I will probably use the same pitching rate and same method as my stuck batch, but with another yeasy and extract. Unfortunately my logger will be busy until that batch left primary so I wont be able to do any other experiments meanwhile.

/Fredrik
 

Denny Conn (63.114.138.2)
Posted on Wednesday, August 13, 2003 - 09:13 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Fredrik, I'm stunned _nearly_ speechless! You're...actually...brewing...to..make...beer??? I just can't get my mind around that concept! :)
 

Chris Colby (66.25.197.116)
Posted on Wednesday, August 13, 2003 - 09:42 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Thanks Denny, I hope my "Scwartz Wit" turns out good. One of the members (Steve Williams) of the homebrew club I belong to (the Austin ZEALOTS) was a brewer for Celis when the Austin plant was operating. So, I should be able to get a good critique.


Chris Colby
Bastrop, TX
 

Denny Conn (63.114.138.2)
Posted on Wednesday, August 13, 2003 - 09:45 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Schwarz wit...I LOVE it! PLease let us know how it turns out!
 

Fredrik (213.114.44.237)
Posted on Monday, August 18, 2003 - 04:35 pm:   Edit Post Delete Post View Post/Check IP    Ban Poster IP (Moderator/Admin only)

Fascinating reading! Biology has indeed been a "missing chapter" to me, or rather I have ignored it drewling over other stuff, so I bought a Stryers biochemistry and started reading. I am fascinated how the abstraction pattern from other sciences repeat. Just like particle diversity and the big bang in physics. There are similar ideas here. Niether of this seems relevant to me before I started to consider yeast. Apart from the DNA encoding itself it's interesting just because of the abstraction pattern used. Now I think the next DNA revolution is that we find that each single individual has each own pattern of abstraction and learning. Evolution of intelligence and the genetic coding of learning algoritms.

Until then, I'm glad I got into brewing :) I am ejoying watching by bubble counter. I am currenly at 12044 bubbles, which should be about the 6% progress. I'm excited to see if I get a dip this time!

/Fredrik

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