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Author Topic:   Mendel wasn't entirely right
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 46 of 65 (194345)
03-25-2005 2:52 AM
Reply to: Message 38 by paisano
03-24-2005 5:27 PM


In actuality scientific ideas are usually developed incrementally by a cast of thousands, and the Big Names more often than not are individuals who were in the right place at the right time to make a major synthesis.
In Mendel's defense, his research was both groundbreaking and conducted largely solo. I'd say he's definately a Big Name, you know? And he deserves it, particularly since his contributions were unknown in his own lifetime.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 47 of 65 (194372)
03-25-2005 6:03 AM
Reply to: Message 44 by commike37
03-24-2005 11:38 PM


The idea here is that if this study proves true to a much larger scale for mutation in general, the effects could be enormous.
The effects would be enormous, so much so that if that were true we would already know it. The point I have made repeatedly is that this mechanism is clearly not in action at a larger scale for mutation in general. There have been enough genetic cross studies in a wide variety of organisms done for this to be readily apparent.
You are making a number of totally unwarranted assumptions about the prevalence, consistency and effects of this mechanism.
TTFN,
WK

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Ooook!
Member (Idle past 5815 days)
Posts: 340
From: London, UK
Joined: 09-29-2003


Message 48 of 65 (194374)
03-25-2005 7:02 AM
Reply to: Message 43 by commike37
03-24-2005 11:08 PM


And this is simply off-topic. Leave these little cheeky attacks out of your analysis
OK. I’ll stop the sniping (in this and the other thread) — it was born out of frustration. Suffice to say that the offer still stands — I’ll be happy to debate the ‘non-scienceness’ of ID any time: I’ll even start a fresh topic for you to defend your position if you are willing.
Sure, creationism has some religious dogma, but it is nowhere near the dogmatic position of evolution today scientifically speaking.
I find this statement very hard to accept. Creationism starts out with an unsupported assumption and then goes out to try and prove it whilst ignoring all evidence to the contrary. That’s almost the definition of dogmatic.
For example:
From the ICR website:
quote:
The Institute for Creation Research bases its educational philosophy on the foundational truth of a personal Creator-God and His authoritative and unique revelation of truth in the Bible, both Old and New Testaments.
and the CRS:
quote:
Membership in the Society requires agreement with the CRS Statement of Belief. Members of the society include research scientists from various fields of scientific accomplishment who are committed to full belief in the Biblical record of creation and early history.
Statement of belief!!! That’s not just some small religious aspect on the sidelines, that’s got dogma running through it like a stick of rock.
Contrast this to the way real science is carried out, where the confidence of any statement made is directly related to the amount of evidence that is around. If you have access to the article that WK posted then have a look at the language used. It’s full of might represent This strongly implies and results presented here indicate It’s all tentative — and goes some way to explaining why scientists sometimes have trouble writing non-scientifically. On top of this there is a paragraph devoted to previous studies into non-Mendalian genetics. It is not a new way of thinking or a rare challenge to a sacred scientific law — and this this is the way all science works and isi precisely what stops it from turning into dogma.
So when you say:
I don't every remember learning any explanation to the theory of life in science class besides evolution. And even when ToE has been refined and/or changed over the years due to "tentative" aspects, it's still been evolution in one form or another. There certainly is some dogma attached to evolution.
it simply is not true. Evolution is the only game in town because nothing else even comes close to fitting with the facts. It’s not dogma, it’s just blooming well supported.
I suspect that a large section of this post is quite far OT (especially considering there are other would-be thread starters keen to discuss the technical aspects of it), but I think I can ask an on-topic question:
What aspect of the study made you think that it was a paradigm busting paper?
This message has been edited by Ooook!, 25-03-2005 12:03 PM

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paisano
Member (Idle past 6422 days)
Posts: 459
From: USA
Joined: 05-07-2004


Message 49 of 65 (194380)
03-25-2005 8:26 AM
Reply to: Message 46 by crashfrog
03-25-2005 2:52 AM


The point was that this "If you can't trust Mendel, how can you trust Darwin" line of argument is fallacious in that it reveals a fairly unrealistic picture of how the scientific process works.
The point wasn't to disparage Mendel, but to point out that even if his ideas need modification this has no bearing on the scientific process in general or "what Big Name can't you trust now".

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paisano
Member (Idle past 6422 days)
Posts: 459
From: USA
Joined: 05-07-2004


Message 50 of 65 (194382)
03-25-2005 8:30 AM
Reply to: Message 47 by Wounded King
03-25-2005 6:03 AM


You are making a number of totally unwarranted assumptions about the prevalence, consistency and effects of this mechanism.
It's yet another example of how even a relatively intelligent creationist leaps at a perceived Silver Bullet that he thinks will bring down the edifice of evolution and vindicate his already preconceived dogmas.

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gengar
Inactive Member


Message 51 of 65 (194418)
03-25-2005 11:07 AM
Reply to: Message 32 by Wounded King
03-24-2005 4:23 PM


Maternal effect
WK writes:
You are probably thinking of epigenetic markers such as methylation of DNA, methylation and acetylation of histones and a number of other not strictly genetic factors thought to be important in the development of the early embryo and not neccessarily perfectly reset in SCNT.
None of these are transcription factors, but you may be thinking of something completely different.
Indeed I was, but its not a surprise as I was relying on dim and distant memories of Cell Biology back in my first year at University. I think I was talking about the maternal effect - the phenotypic expression of maternal mRNA put into the egg cell. This has been shown to have a role in development of the embryo, for example in the development of the anterior-posterior axis of Drosophila (crude link but it was the first one which came up in Google).
Of course, I probably don't have to tell you about this stuff. But it does demonstrate something other than DNA passing genetic information on to the next generation.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 52 of 65 (194424)
03-25-2005 11:24 AM
Reply to: Message 49 by paisano
03-25-2005 8:26 AM


In that I absolutely agree. We shouldn't take Mendel's ideas, or anyone else's, as dogma simply because he's a scientific household name.

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judge
Member (Idle past 6443 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 53 of 65 (194600)
03-26-2005 4:14 AM
Reply to: Message 8 by Wounded King
03-24-2005 9:52 AM


quote:
The paper suggests that the mutation of HTH may greatly increase the frequency of an otherwise very rarely operating mechanism.
If a mechanism operates very rarely how is it selected for?
Is it just that even very rare use provides a very very small bias?

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pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 54 of 65 (194645)
03-26-2005 9:56 AM
Reply to: Message 53 by judge
03-26-2005 4:14 AM


off the top of my head...
quote:
The paper suggests that the mutation of HTH may greatly increase the frequency of an otherwise very rarely operating mechanism.
If a mechanism operates very rarely how is it selected for?
Look at the quote again - it is only rare in the presence of the HTH gene. One possibility that comes to mind is that the unknown "backup" mechanism was selected for prior to the arisal of the HTH gene.
Perhaps the backup mechanism made a species more fit for a part of its history/environment, but the same mechanism later reduced fitness - the HTH gene/system may have been selected for to "override" the "backup" system.
Hopefully that makes sense - the key is that we can't look at a fully intact modern organism and assume that a characteristic of interest evolved in an identical organism without that system. Instead, the characteristic may have evolved in a very remote ancestor species bearing no resemblance to the modern species and living under quite different conditions.

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 Message 55 by Wounded King, posted 03-28-2005 6:42 PM pink sasquatch has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 55 of 65 (195026)
03-28-2005 6:42 PM
Reply to: Message 54 by pink sasquatch
03-26-2005 9:56 AM


Re: off the top of my head...
I think Judge is justified in saying it is rare. If this were a frequent occurence in Arabidopsis in any number of mutant backgrounds, or in any plant or organism lacking the Hothead gene, then I can't see how it could have been failed to be noticed. An up to 10% discrepancy from the expected mendelian ratios would be pretty significant in the sorts of numbers commonly used in genetic studies.
TTFN,
WK

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 Message 56 by pink sasquatch, posted 03-29-2005 3:03 PM Wounded King has replied

  
pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 56 of 65 (195230)
03-29-2005 3:03 PM
Reply to: Message 55 by Wounded King
03-28-2005 6:42 PM


Re: off the top of my head...
I think Judge is justified in saying it is rare.
Of course he is, when describing modern Arabidopsis - I didn't say otherwise.
My comments referred to a potential evolutionary history of Arabidopsis; that is, that we don't know that the mechanism was always as specifically and rarely utilized in the species' evolutionary history as it is in modern Arabidopsis.
I don't see how you comments counter that point.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 57 of 65 (195361)
03-30-2005 2:56 AM
Reply to: Message 56 by pink sasquatch
03-29-2005 3:03 PM


Re: off the top of my head...
I disagree. For the mechanism to be maintained from that distant ancestral species it surely has to have continued to be selected. If it was no longer conferring an advantage then why would it not have degenerated through processe like drift. Perhaps the many constituent parts are involved in other processes but mechanism specific functions in some would surely have been lost.
Given that only one species of Arabidopsis has been studied yet it seems a bit pointless to be making up 'just so' stories out of thin air.
The mechanisms operation is rare in the wild type, even a rarely operating mechanism can be maintained provided the advantage it confers is substantial enough. I don't see why it ever needs to have been widespread, and even if it was at some point then Judges question about selection on rarelu utilised traits is still relevant since it has to have been maintained since becoming rare.
TTFN,
WK

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pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 58 of 65 (195486)
03-30-2005 3:12 PM
Reply to: Message 57 by Wounded King
03-30-2005 2:56 AM


contextintent
I disagree. For the mechanism to be maintained from that distant ancestral species it surely has to have continued to be selected.
You can't really disagree with me on that point because I never made that argument.
I don't see why it ever needs to have been widespread,
Again, I never claimed it was widespread, not even in speculation.
Given that only one species of Arabidopsis has been studied yet it seems a bit pointless to be making up 'just so' stories out of thin air.
My intent was not to try to explain away the finding's impact on evolution with speculation. My intent was to try to explain to judge that we can't assume that a mechanism evolved intact in the biological context we now see it; in other words to counter the same sort of argument that many attempt to use to show irreducible complexity.
Perhaps I would have better served this cause using a better-documented example such as the blood clotting cascade; however, I'm not sure why you are so intent on argument to the point that you are arguing against statements I have not made.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 59 of 65 (197406)
04-07-2005 8:19 AM


I think it is very interesting that there is such a pronounced parental bias in this phenomenon.
While the authors show that reversion re-establishes the paternally inherited, by whatever means, ancestral HTH allele they don't provide quite such strong evidence in the maternal case.
In their experiments showing the paternal origin of revertants they find no revertants in similar experiments with a hth/hth mother. In fact the only evidence of a maternal reversion is a couple of HTH/HTH genotype plants. They say...
In fact, in this experiment we also detected rare double revertant HTH/HTH embryos, which must have inherited one of their two wild-type HTH genes from the maternal parent and therefore could not have been the result of outcrossing.
I'm not sure this follows. They may have some sequence data which determines the parental origin of the HTH alleles, but if so it isn't presented. There is no clear evidence of when this mechanism operates is it during germ cell production or in the zygote? The fact that they find more HTH/hth genotypes than wild type phenotypes is interpreted as being due to reversion in the embryonic tissues which do not form part of the adult plant, which may suggest that reversion occurs after fertilisation rather than during germ cell production.
If reversion does take place in the zygote or early embryo then it may be that both revertant alleles come from the paternal line. Crosses of hth/hth lines of Columbia and Landsberg would presumably allow this to be determined, provided the rare double revertants turn up.
I am fascinated as to the possibility of a store of genetic memory as dsRNA. Is this maintained at specific levels? How many copies of each gene from each generation are there? Are there stores of all of these dsRNAs in all cells? Surely not, if there were wouldn't RT-PCR experiments in Arabidopsis thrown up many bizzare results and false positives?
How are these copies established? Are highly transcribed mRNAs better represented in the 'store' than infrequently transcribed ones? Are mRNAs which are highly transcribed specifically in the tissues of the developing germ cells preferentially stored? Do microRNAs play a part in this process?
Are many revertants highly mosaic? If they can occur only in non-contributing embryonic tissues can they occur later in particular cell lineages? I am not sure that their genomic blot would neccessarily show up differences due to mosaicism, and I'm sure the PCR would be unlikely to, especially since they themselves note a number of apparently revertant genotypes without a revertant phenotype.
Does the reversion occur earlier in the developing germ cells themselves? This might be consistent with the much higher rates of paternal to maternal reversion. I think it would be interesting to syudy the DNA of pollen and ovules and see if they show allelic variation in Hothead.
There are so many more possibilites as well. I hope that they are well on the way to a further publication on this topic, it is one of the most fascinating phenomena in years.
There is an article referenced in the latest Tnagled Bank which suggests that the phenomenon may simply be due to revertants due to mutation being selected by virtue of improved fertility of HTH pollen. The author suggests that a hth/hth background leads to general genetic instability ather than any targeted mehcanism, and that subsequent selection leads to the reappearance of the ancestral allele.
There is no evidence presented which suggests that their other markers of genomic instability actualy represent ancestral alleles rather than simply novel polymorphisms. There is however some evidence along these lines, in that they saw reversion of the Erecta(er) phenotype in hth/hth er/er crosses at a similar frequency.
Anyone have any feeling on the comparative merits of the original paper's or the critique's explanations of the phenomenon? I prefer the original papers explanation, but It seems a bit early to tell one way or another, I'm not sure that the selection based model really fully explains the results.
TTFN,
WK

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pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 60 of 65 (197427)
04-07-2005 10:37 AM
Reply to: Message 59 by Wounded King
04-07-2005 8:19 AM


mosaicism?
Does the reversion occur earlier in the developing germ cells themselves? This might be consistent with the much higher rates of paternal to maternal reversion.
"What about the germ cells?" was my first thought on reading their conclusion. Separate of reversion, does it make sense that mosaicism restricted to germ cells could be inherited?
Pollen-based studies are fairly routine in Arabidopsis, since some have used it is as a way to simplify genetic analysis by looking at haploid genomes. I see no reason that an allele that exists in 10% of pollen couldn't be rather easily detected, even just by a simple PCR.
Intuitively, germ cell mosaicism is a more plausible explanation to me than a back-up dsRNA genome, which as you say should have sent up some sort of flag with expression analysis - though perhaps the back-up is restricted to the germ cells, and I'm not sure what kind of expression analysis has been done in germ cells (particularly pollen).
Lots of unanswered questions -

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