Friday, December 23, 2005

Stem Cell research under fire

Although this isn't anything particularly new, as stem cells have been under fire for some time by numerous 'pro-life' groups due to the controversial use of embryonic stem cells it seems that things have just got worse. For those not following the basic disaster, here is a general time-line to help put everything into perspective.

1) Researchers at Seoul National University, led by Woo Suk Hwang successfully used a technique called somatic-cell nuclear transfer to produce a line of patient derived stem cells. This has basically been the holy grail of stem cell cloning, because developing such patient specific stem cells avoids problems like donor incompatibilities and allows for new sources of tissue to be derived easily. The importance of this should be fairly clear from the fact this was published in Science and if you're wondering, that is one of the most prestigious journals around so this was big news.

2) An anonymous writer on the 6th of December leaks word that some of the photographs of the original paper are suspicious. This culminates in a phone call between Hwang and the editors of Science, where it turns out that some of the photographs have been duplicated. Not only that, but closer inspection of the paper revealed that some of the genetic sequence traces also turn out to be suspicious.

3) Things rapidly get worse with Sung II Roh claiming that Hwang had directly falsified results and then the revelation that of 11 stem cell lines, 6 had been contaminated and destroyed (more on this below).

4) Escalation from this point is inevitable with one of the authors, Gerald Schatton who collaborated on the paper, asking for his name to be removed because he no longer trusts the result. For a scientist to declare this on a paper is a massive thing to do and also something you can't do. So instead, the editors of Science after consulting Hwang, actually retracted the paper.

5) Now the full weight of scientific scrutiny has been placed on all of the research from Hwangs lab. This starts with the observation that one of their earlier papers has also been found to be dubious:
And there are now concerns about earlier work. For example, in the paper in which Hwang claimed to have extracted the first stem-cell line from a cloned human embryo (W. S. Hwang et al. Science 303, 1669-1674; 2004), figures supposedly showing cloned cell lines are identical to those in an earlier paper showing normal embryonic stem cells (J. H. Park et al. Molecules and Cells 17, 309-315; 2004).
Additionally, Nature has also decided that they should
launch an investigation into another paper from the same group where they made the first cloned dog "Snuppy".
Lanza says that Snuppy, seen on the right with the dog from which he was supposedly cloned, might have been created by a technique called embryo splitting, in which cells from an early-stage embryo are divided and then implanted separately. The technique creates identical twins. One set of cells could have been used immediately to create a dog while another was frozen and stored. If the frozen cells were later used to create a dog with identical DNA, that could be presented as an SCNT clone.
Such trickery could be caught by examining mitochondrial DNA, which is passed maternally with the egg cell. If Snuppy were really a SCNT clone, he should have the mitochondrial DNA of the dog from which the egg was taken. If he's a fake, he'd share it with the dog from which he was supposedly cloned. Mitochondrial DNA data have not been part of previous cloning papers, and were not presented in Nature. Lanza suggests that it would now be a good idea to do the test. "If the mitochondrial DNA is the same, that's the end of that paper," says Lanza.
Nature is starting an investigation, including a mitochondrial DNA test, that is unlikely to be complete before January 2006.

6) Finally we come to the newest development (23rd of December), where a Seoul National University panel has determined that the research has been intentionally fabricated. This has resulted in Hwang deciding to step down. Now this is not confirmation of any particular fabrication as Hwang has defiantly said that the research will stack up, but at the moment it's sounding like the vultures are circling for him and his research team.

So with the background out of the way it's important to consider three seperate issues:

1) How likely is it that the results are falsified?

2) What does this mean in terms of stem-cell research.

3) How can this fiasco be prevented from happening again?

How likely is it that the results are falsified?

After reading all of the reports on the issue from Nature, Science and other sources, it is looking very definitely to me that the results are falsified. Firstly there is an inherently obvious question that arises from reading all of the reports that just doesn't stack up. From a report in Science I noted this:
....the team had problems with their cell lines. He said that last January, contamination with yeast had destroyed at least six of the lines the team had created. Based on Hwang's statement, it's not clear whether any of these original six lines were alive at the time the Science paper was submitted in March. The group was "lax in our management and committed many mistakes," said Hwang. He said they would thaw the five remaining cell lines to try to demonstrate that they match their donors, a process that Hwang said could take about 10 days.
Now let's be clear on one thing: developing these stem cell lines would have been expensive, highly time consuming and immensely frustrating. To have lost over 50% of the total stem cell lines they had created is highly suspicious. While I acknowledge how difficult it can be to keep a cell culture sterile and preserved, there is just something somewhat fishy about the entire claim. Considering that the security on these things was pretty tight and strictly controlled from what I can gather, for example from Nature we learn this tidbit:
When Nature visited in 2004, he declined to show his first cloned stem-cell line, kept under lock and key. "Many lab members aren't allowed to see it either," he said. Taken together, the concerns about Hwang's work leave biologists with no proof that stem cells can be extracted from cloned human embryos.
So you can see that there was some fairly tight control over this because it was obviously recognised for the important development it was. Yet, months after the paper was published (with unsuccessful attempts at replication by other researchers) we suddenly learn when questions arise that six of the stem cell lines were destroyed? Oddly, only five of the original 11 stem cell lines are supposedly still around and we won't be able to verify anything about them until at least the 26th (they were thawed on the 13th as far as I know). This is all sounding very suspicious indeed as with the importance of these cells wouldn't someone have kept sterile backups? Remember that Hwang was keeping his first cloned cell line under lock and key, refusing to show it to anyone else (which is equally suspicious, but admittingly with the competition in this area of science is understandable). This clearly doesn't add up.

Aside from this issue about this destruction of the stem cell lines, we also see that there appears to be widespread falsification of figures. Now, I'll grant to the reader that this isn't an altogether clear cut thing in science, particularly as to what is making a figure, picture or similar 'clearer' and what is out-right falsification. However, once again I think a clear case can be made for simple 'out-right' falsification. Firstly, it had already been noted that some of the pictures used in the study happened to be duplications during the review process for the paper, and that some of these duplications apparetly survived into the final draft as well. The editors of Science happen to note:
When questions were first raised about duplicated images, editors at Science said that it appeared the duplications occurred after the paper was accepted and when new, higher-resolution images were substituted for publication. But Katrina Kelner, Science's deputy editor for life sciences, says it now appears there were problems in the original submission as well. Although the four duplications that Hwang pointed out to editors were not in the original submission, she says, the original figure had at least one apparent duplication that also appeared in the final version. Figure S1 shows 68 cell photographs, which purport to show evidence of 10 of the 11 cell lines expressing up to 6 different protein markers typical of ES cells. But one image labeled as cell line number 8, expressing a marker called SSEA-4, shows the same colony of cells, though slightly shifted, as an image labeled cell line 7, marker SSEA-3. Kelner says that editors have asked the researchers to explain the images, "but we haven't gotten answers."
And also with a part high-lighted relevant to the above destruction of the stem cell lines.
It also seems that questions raised during the review process may have unwittingly helped undo the paper. In their original submission, Kelner says, the authors provided fingerprints from only some of the cell lines. Reviewers asked for fingerprinting data from the remaining lines. It is not clear if the questionable fingerprints were in the first submission or in the additional data the reviewers requested. Editors declined to specify which lines were missing in the original submission.
It makes me wonder with that particular piece of information, which of the 11 cell lines have been destroyed and what are the 5 surviving ones? It seems awfully convenient that not all of the cell lines had fingerprinting data available, which would be able to verify the exact lineage these stem cells were derived from just happens coincidentally (it turns out) that 6 of the lines are destroyed? Oh now this is really not adding up.

Additionally, Nature reveals that Hwangs team may have falsified figures concerning the original extraction of a stem cell line from a cloned embryo may also contain falsified images.
And there are now concerns about earlier work. For example, in the paper in which Hwang claimed to have extracted the first stem-cell line from a cloned human embryo (W. S. Hwang et al. Science 303, 1669-1674; 2004), figures supposedly showing cloned cell lines are identical to those in an earlier paper showing normal embryonic stem cells (J. H. Park et al. Molecules and Cells 17, 309-315; 2004).
Given an isolated incident that could be a very easily explainable mistake, just got a file name wrong and inserted it into the paper by mistake. In light of the deception given in the pre and post publication science paper that originally came under dispute, that this is deliberate falsification rather than a mistake becomes a much stronger argument. Worse for Hwang, if the investigation into the Nature paper on "Snuppy" the cloned puppy reveals the same mitochondrial DNA as the mother then the paper will have to be retracted, which will be a double blow for the Korean researcher.

So here we have documented and seemingly repeated incidents where results have been falsified by a particular group. Additionally, it appears that the original paper results are difficult to verify and have not been experimentally repeated by other researchers. The destruction of these 'break-through' stem cells is either some amazing incompetence or hiding the fact some of these lines may not have been what they were claimed to be. Although this would be in other cases just be paranoid rambling, the demonstrated falsification in two of their papers and lack of additional experimental verification lends considerable weight to this interpretation.

Frankly, I think things are fairly obvious that the results of the paper have been falsified.

What does this mean in terms of Stem Cell research?

In terms of the future for stem cell research this has probably done a lot of damage not just scientifically but politically as well. Opponents of stem cell research oppose the research based on moral, ethical, religious and political grounds. With a result like this, you can almost expect the knives to come out and opponents to get much more vocal. I think the editor of the American Journal of Bioethics on his weblog wrote a particularly telling point about what the whole affair will mean:
could firmly establish in the public mind the view that stem cell researchers as a group cannot be trusted, not only because they are in a hurry and miss things along the way, but because they may be willing to deceive their own peers and the public about their devotion to ethics.
Bear in mind that to these people, embryonic stem cell research isn't able to "go anywhere" and is simply murder. This kind of mentality is well demonstrated by the likes of prolifeblogs where they write:
But while the reports of faked data and illegitimate results have cast a dark shadow on ESC research, the emphasis of criticism and debate needs to center on the intrinsic value of human life and not on the low probability of ESC success. The latter is a pragmatic argument that places the life of the embryo in a position that is subservient to the potential benefit his or her destruction will provide others. Conversely, the inherent dignity of human life impales any argument supporting pragmatism as a basis for bioethics.
The worst part of all this is with the fine example that Hwang has now set, they will have genuine ammunition to add to empty rhetoric. To most scientists, the incident with Hwang will simply demonstrate irresponsible scientific fraud to 'publish first' in an incredibly competitive field. To the likes of prolifeblogs this will be confirmation of their beliefs that embryonic stem cell research is nothing more than a political tool to advance peoples careers and not legitimate science. However ill-founded this perception is in reality, this incident will not help by any means of the imagination.

This train-wreck (I don't think it can be called anything else at this point) will not prevent the funding or research into stem cells. In fact, in some ways it may even aid the call for increased funding of American stem cell research so that the practice may be more tightly regulated. This is probably an unlikely scenario however, but it will increase the amount of skepticism (ironic really) applied to the claims of researchers in this area. Additionally, the entire thing could potentially give fuel to the establishment or prolonging of laws that ban stem cell research as well. Although I would like to produce a positive note of increased awareness about scientific fraud and being more careful about results that seem 'to good to be true', the most likely result is a religous right led witch hunt that could have disasterous effects on future research.

How can this fiasco be prevented from happening again?

Bearing all of this in mind, it's important to consider how we can avoid this entire debacle happening a second time. From the article written by Science, it is interesting to note that the Hwang paper that made the claim of deriving 11 stem cell lines from patients went through peer review unusually fast. Normal 'review' processes take around 120 days, but in this particular case the review period was only 58 days. Although "hot" science has in the past been given the fast lane to publishing, in this case it was most likely very detrimental as some things such as the duplicated figures were only noticed upon recent close examination.

Further, it's also worth considering that a large amount of data, seemingly critical to many of the papers claims appears to have been omitted such as sequence traces. Additionally, other independant researchers had considerable difficulties in replicating the results from Hwangs group. All of this leads to the unsettling prospect that none of the results are actually real at all and this incident is one of the worst examples of scientific falsification in history.

To avoid such an incident in future requires much more skepticism from even the top journals of the world it would seem, especially when it involves 'hot' science. Papers that appear to have omitted relevant or potentially important information on their results need to be double checked and such information added to the paper. Further, in my opinion there should be an analysis performed on the relevant figures and images that a paper uses, to check for potential duplications and otherwise misleading images. These measures are the sorts of things required to make sure that stem cell research is appropriately conducted so that the field can regain the publics trust.

And as for Woo Suk Hwang? It will indeed be a mighty fall from one of Times people who mattered in 2004 to the first biggest scientific fraud of this century.