Humans cause yeast to become multicellular, a threat to ID?

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Re: Humans cause yeast to become multicellular, a threat to

#46

Post by Bill McEnaney » Fri Jan 27, 2012 8:38 pm

"It means we can actually observe the process of evolution, of a leap from single-celled to multi-cellular organisms, something that creationists have long held to be impossible due to the lengths of time often involved."
What did the cells form a new organism or only a clump? Bacteria form colonies when they grow on agar in a petri dish, but I don't of any microbiologist who believes that a bacterial colony is an organism rather than a collection of organisms.

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Re: Humans cause yeast to become multicellular, a threat to

#47

Post by MarcusOfLycia » Fri Jan 27, 2012 9:15 pm

They haven't even studied the DNA. I'm not a biologist, but I would think that if I were one, I wouldn't make such radical claims until I had inspected the DNA and determined it had changed significantly enough to be another species.
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Re: Humans cause yeast to become multicellular, a threat to

#48

Post by Ivellious » Fri Jan 27, 2012 10:03 pm

To everyone on the site criticizing the paper: I understand your points, but a little clarification. I've talked with one of the professors on the job with a few fellow students, and here's what I got: Genetic testing is currently underway at a lab at the University of Minnesota (where the original research took place). The paper, complete with the results of the genetic testing and several follow up experiments, is expected to be submitted to a peer reviewed journal once the experiment is complete in that regard. The reason it was submitted to the PNAS (a non-peer reviewed material), was to get the research out there, apparently. I admit, it kind of sounds like an attention grab, but the purpose being just to garner interest in their work. I can't comment on the reputations of the researchers in question, though I hope this clears a little bit up.

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Re: Humans cause yeast to become multicellular, a threat to

#49

Post by Canuckster1127 » Fri Jan 27, 2012 10:12 pm

At the very least it would seem to be fair to suspend final judgment for or against until it's out in a peer reviewed context.
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Re: Humans cause yeast to become multicellular, a threat to

#50

Post by sandy_mcd » Fri Jan 27, 2012 11:21 pm

zoegirl wrote:Is PNAS not peer-reviewed?
http://www.pnas.org/site/misc/iforc.shtml#submission wrote:Direct Submission. The standard mode of transmitting manuscripts is for authors to use Direct Submission. Authors must recommend three appropriate Editorial Board members, three NAS members who are expert in the paper's scientific area, and five qualified reviewers. The Board may choose someone who is or is not on that list or may reject the paper without further review. Authors are encouraged to indicate why their suggested editors are well qualified to handle the paper. A directory of PNAS member editors and their research interests is available at http://nrc88.nas.edu/pnas_search. The editor may obtain reviews of the paper from at least two qualified reviewers, each from a different institution and not from the authors' institutions. For Direct Submission papers, the PNAS Office will invite the reviewers, secure the reviews, and forward them to the editor. The PNAS Office will also secure any revisions and subsequent reviews. The name of the editor, who is to remain anonymous to the author until the paper is accepted, will be published in PNAS as editor of the article. Direct Submissions are published as “Edited by” the responsible editor and have an identifying footnote.

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Re: Humans cause yeast to become multicellular, a threat to

#51

Post by Ivellious » Fri Jan 27, 2012 11:33 pm

So basically the PNAS is reviewed, but you get to pick your reviewers (and I'm presuming the PNAS editorial committee makes sure your reviewers are legit experts in the field). That is different in the sense that most peer-reviewed journals get the submission and the lead editor selects scientists to review the work. Good to know.

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Re: Humans cause yeast to become multicellular, a threat to

#52

Post by sandy_mcd » Sat Jan 28, 2012 12:14 am

It's standard in a number of journals to suggest possible reviewers. The main editor may or may not follow these suggestions, in part no doubt based on familiarity with the research.

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Re: Humans cause yeast to become multicellular, a threat to

#53

Post by zoegirl » Sat Jan 28, 2012 12:03 pm

Gotcha, didn't know about the details of that particular journal.

Ultimately what we have here is simply a selection experiment for yeast cells to have stronger binding to each other. Considering that they are known to do this already, it seems that this is taking a character trait that already exists and selection for it. The differentiation claim seems sketchy and a reach, but it is intriguing.

Remember that if these cells can already do this, then selecting for yeast that have more binding proteins or stronger binding proteins does not merit the jubilation that seemed to accompany this experiment. There are plenty of unicellular protists that can exist as colonies and yet not perform like a true multi-cellular organism.

Just seems to be that things like this are welcomed all too easily as solid foundation, the bullwark of evidence needed. What's fascinating is that being critical of an experiment like this seems to immediately warrant the label "anti-evolution". Seems that this is exactly what science always needs, skepticism. Remember, we should always be developing strong experiments that can withstand scrutiny and welcome that scrutiny. Something that seems to be absent in the press of this experiment. Hmm, a little bias, don't you think? :ewink: We *like* this result of this experiment and therefore it is all good. First thing that any good researcher should do in response to the scrutiny should be "you're right, further experiments need to be done". (which seem to be taking place).

Like most articles concerning evolutionary theories, the pop media takes it and runs with it, where hopefully the real story should be more cautious.
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Re: Humans cause yeast to become multicellular, a threat to

#54

Post by zoegirl » Sat Jan 28, 2012 1:31 pm

For instance,

Think about what has to happen, at the least, for unicellular organisms to become multicellular

1. Cells to adhere to each other, to which this experiment seems to lend evidence.

2. -Differentiation (what causes the differentiation? ...the cells communicate and change the expression of their genes so....)
Communication between cells (which requires)
signalling molecules secreted from one cell to another (which requires....)
the other cells to have receptors (which require another signalling pathway or at least a intracellular mediator)
or, if these go directly to the nucleus, to activate the proper genes
activation of the proper genes and the suppression of the proper genes (cancer cells are cells that have lost their allegiance to their "host" if you will)
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Re: Humans cause yeast to become multicellular, a threat to

#55

Post by Stu » Sat Jan 28, 2012 2:07 pm

zoegirl wrote:Gotcha, didn't know about the details of that particular journal.

Ultimately what we have here is simply a selection experiment for yeast cells to have stronger binding to each other. Considering that they are known to do this already, it seems that this is taking a character trait that already exists and selection for it. The differentiation claim seems sketchy and a reach, but it is intriguing.

Remember that if these cells can already do this, then selecting for yeast that have more binding proteins or stronger binding proteins does not merit the jubilation that seemed to accompany this experiment. There are plenty of unicellular protists that can exist as colonies and yet not perform like a true multi-cellular organism.

Just seems to be that things like this are welcomed all too easily as solid foundation, the bullwark of evidence needed. What's fascinating is that being critical of an experiment like this seems to immediately warrant the label "anti-evolution". Seems that this is exactly what science always needs, skepticism. Remember, we should always be developing strong experiments that can withstand scrutiny and welcome that scrutiny. Something that seems to be absent in the press of this experiment. Hmm, a little bias, don't you think? :ewink: We *like* this result of this experiment and therefore it is all good. First thing that any good researcher should do in response to the scrutiny should be "you're right, further experiments need to be done". (which seem to be taking place).

Like most articles concerning evolutionary theories, the pop media takes it and runs with it, where hopefully the real story should be more cautious.
Agreed.

I think one of the reasons these types of experiment receive so much hype and (premature) fanfare is that evolutionists don't actually have anything like it to support their theory.
I don't say this in some smug way; it's just the way it is. So anything with a hint of substantiating their claims is given much praise, with scientific skepticism and method taking a back seat.
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Re: Humans cause yeast to become multicellular, a threat to

#56

Post by sandy_mcd » Sat Jan 28, 2012 2:27 pm

As far as the comments "more experiments" should be done; yes that is true. That is true for almost any scientific paper - it will reference earlier papers which the current work is an extension of. It is common in areas of unfamiliarity (auto repair, science, programming, etc) to underestimate the time and effort involved to get something done. If everyone waited until a story were complete, people would only publish a few papers in their careers and not hundreds. Papers report work in progress; books tell the entire story afterwards. [Although I do agree that way too many papers are published.]

I'm not aware that there is that much excitement in the scientific community as has been referred to in several posts here. The original source was wired.com. Anybody who has ever read a press story about something known to them realizes how misleading the stories often are. A major goal of journalism is to get readers.

And this is not the only paper on the topic of uni to multicellularity.
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
Abstract
The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 108 synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.

Functional development of Src tyrosine kinases during evolution from a unicellular ancestor to multicellular animals
Abstract
The Src family of tyrosine kinases play pivotal roles in regulating cellular functions characteristic of multicellular animals, including cell–cell interactions, cell-substrate adhesion, and cell migration. To investigate the functional alteration of Src kinases during evolution from a unicellular ancestor to multicellular animals, we characterized Src orthologs from the unicellular choanoflagellate Monosiga ovata and the primitive multicellular sponge Ephydatia fluviatilis. Here, we show that the src gene family and its C-terminal Src kinase (Csk)-mediated regulatory system already were established in the unicellular M. ovata and that unicellular Src has unique features relative to multicellular Src: It can be phosphorylated by Csk at the negative regulatory site but still exhibits substantial activity even in the phosphorylated form. Analyses of chimera molecules between M. ovata and E. fluviatilis Src orthologs reveal that structural alterations in the kinase domain are responsible for the unstable negative regulation of M. ovata Src. When expressed in vertebrate fibroblasts, M. ovata Src can induce cell transformation irrespective of the presence of Csk. These findings suggest that a structure of Src required for the stable Csk-mediated negative regulation still is immature in the unicellular M. ovata and that the development of stable negative regulation of Src may correlate with the evolution of multicellularity in animals.

And those are just two fairly recent papers in PNAS.

Part of the problem is that people here are looking for documentation of the uni- to multicellular evolution. As you can tell from the abstracts, the authors and the intended audiences have long ago accepted this transformation.



Edited for misspelling.
Last edited by sandy_mcd on Sat Jan 28, 2012 3:10 pm, edited 1 time in total.

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Re: Humans cause yeast to become multicellular, a threat to

#57

Post by zoegirl » Sat Jan 28, 2012 2:56 pm

hmmm, should a scientist already expect a certain outcome??

I mean, of course they are going to accept it, so the scrutiny will not be there.

Again, it is intriguing, but considering that they have already accepted it, there is hardly any hard skepticism, is there?
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Re: Humans cause yeast to become multicellular, a threat to

#58

Post by sandy_mcd » Sat Jan 28, 2012 10:30 pm

zoegirl wrote:hmmm, should a scientist already expect a certain outcome??
Well, yes. Most experiments are designed to produce a certain outcome. Experiments are costly (time and money) so there is usually a plan. Failed experiments are hard to publish. [And if your experiment doesn't go as planned, and you produce B instead of A, you often write the paper as "a novel way to get B" and act as though that were your goal all along.]
zoegirl wrote:I mean, of course they are going to accept it, so the scrutiny will not be there.
Again, it is intriguing, but considering that they have already accepted it, there is hardly any hard skepticism, is there?
There was one editor and probably 3 reviewers who approved the paper. Now that it is in the literature, other people can weigh in.
I really don't understand what you are getting at.
It is true the paper probably is getting less scrutiny than if it had reported something completely unexpected. But that is understandable. If you are inside in Chicago in February and someone comes in and says it is snowing, you probably just accept that. However, if you were in Houston in August, you would probably go to the window to verify.

This article isn't even in the top 50 most downloaded http://www.nature.com/nature/most.html? ... ded&page=5

Read the last paragraph in this quote from Nature http://www.nature.com/news/yeast-sugges ... ife-1.9810
Safety in numbers
Many single-celled organisms, including yeast, often form clumps of genetically distinct cells. But Ratcliff’s snowflakes were made up of genetically identical cells that had budded off and stuck together. Many other multicellular organisms may well have evolved through a similar 'divide-and-stick' process.

The snowflakes behaved like true multicellular organisms. They had a simple life cycle with a juvenile stage, when they grew unimpeded, and an adult one, when they reached a certain size and split into a large parent flake and a smaller, daughter flake.

Ratcliff could even tune these stages. If he cultivated only those snowflakes that settled faster, he ended up with larger ones that grew bigger before splitting. This confirmed that natural selection was acting on the entire flake, rather than on the individual cells within it. “They survive as a whole, or they die as a whole. Selection shifts to the multicellular level,” says Ratcliff.

The snowflakes split because some of their component cells sacrifice themselves, allowing pieces to snap off. These individual cells die for the good of the whole, allowing the parent flake to continue growing and produce many offspring. This mirrors the split seen in more complex multicellular organisms, with body cells that die off every generation and germline cells (sperm and eggs) that carry over into the next one.

Other studies have shown that single cells benefit from staying together because they are less susceptible to being eaten by predators2 and better at foraging for nutrients3. But Ratcliff’s study is one of the few to show how clusters of cells could become true multicellular individuals. “They have done a very good job of seeing what happens after multicellularity has evolved,” says Homayoun Bagheri, who studies the evolution of multicellularity at the University of Zurich in Switzerland.

“I think this paper marks the beginning of a really important body of work that may take many years to play out — not only dissecting the genetics of what's happened so far, but asking just how far the yeast can go in terms of a multicellular lifestyle,” says Lenski.

Yeast evolved from multicellular ancestors, so it is possible that they had an easier time of recreating their ancient lifestyle. However, Ratcliff notes that yeast became single-celled organisms billions of generations ago, and would probably have lost the genes for multicellularity. Even so, he now wants to repeat his experiment with single-celled organisms that do not have a multicellular past, such as species of green algae from the genus Chlamydomonas.

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Re: Humans cause yeast to become multicellular, a threat to

#59

Post by zoegirl » Sun Jan 29, 2012 7:35 am

That is cool.

I still hold, though, to the idea that these receive far less scrutiny than they should because the researchers are merely looking for things that are confirming their already made conclusions.
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Re: Humans cause yeast to become multicellular, a threat to

#60

Post by MarcusOfLycia » Sun Jan 29, 2012 8:10 am

zoegirl wrote:That is cool.

I still hold, though, to the idea that these receive far less scrutiny than they should because the researchers are merely looking for things that are confirming their already made conclusions.
It's basic Confirmation Bias... and I wish people would more readily admit to it happening. It's the reason I cringe when people call themselves 'open-minded' or 'skeptical'. Everyone is both of those things for their own beliefs, and neither of those things (usually) for anything else. Naturalist, Christian, etc; doesn't seem to matter for a lot of people, though there are definitely those who get better at avoiding it.

It usually even goes beyond expecting certain conclusions. It includes only taking in information that is supportive of one's own claim. That's why it bothered me that there was a dispute over listening to the claims of a Christian group in regards to this experiment on the basis of 'format'. My natural tendency is just to assume Confirmation Bias, which might be a rush to judgment, but usually ends up being involved in people's decisions anyway.
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